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1.  On-the-fly machine-learning for high-throughput experiments: search for rare-earth-free permanent magnets 
Scientific Reports  2014;4:6367.
Advanced materials characterization techniques with ever-growing data acquisition speed and storage capabilities represent a challenge in modern materials science, and new procedures to quickly assess and analyze the data are needed. Machine learning approaches are effective in reducing the complexity of data and rapidly homing in on the underlying trend in multi-dimensional data. Here, we show that by employing an algorithm called the mean shift theory to a large amount of diffraction data in high-throughput experimentation, one can streamline the process of delineating the structural evolution across compositional variations mapped on combinatorial libraries with minimal computational cost. Data collected at a synchrotron beamline are analyzed on the fly, and by integrating experimental data with the inorganic crystal structure database (ICSD), we can substantially enhance the accuracy in classifying the structural phases across ternary phase spaces. We have used this approach to identify a novel magnetic phase with enhanced magnetic anisotropy which is a candidate for rare-earth free permanent magnet.
doi:10.1038/srep06367
PMCID: PMC4163667  PMID: 25220062
2.  Redetermination of LaZn5 based on single crystal X-ray diffraction data 
The crystal structure of the already known binary title compound LaZn5 (lanthanum penta­zinc) (space group P6/mmm, Pearson symbol hP6, CaCu5 structure type) has been redetermined from single-crystal X-ray diffraction data. In contrast to previous determinations based on X-ray powder data [Nowotny (1942). Z. Metallkd. 34, 247–253; de Negri et al. (2008). Inter­metallics, 16, 168–178], where unit-cell parameters and assignment of the structure type were reported, the present study reveals anisotropic displacement parameters for all atoms. The crystal structure consists of three crytallographically distinct atoms. The La atom (Wyckoff site 1a, site symmetry 6/mmm) is surrounded by 18 Zn atoms and two La atoms. The coordination polyhedron around one of the Zn atoms (Wyckoff site 2c, site symmetry -6m2) is an icosa­hedron made up from three La and nine Zn atoms. The other Zn atom (Wyckoff site 3g, site symmetry mmm) is surrounded by four La and eight Zn atoms. Bonding between atoms is explored by means of the TB–LMTO–ASA (tight-binding linear muffin-tin orbital atomic spheres approximation) program package. The positive charge density is localized around La atoms, and the negative charge density is around Zn atoms, with weak covalent bonding between the latter.
doi:10.1107/S1600536811050987
PMCID: PMC3254268  PMID: 22259311
3.  Daytime symptom patterns in insomnia sufferers: is there evidence for subtyping insomnia? 
Journal of sleep research  2011;20(3):425-433.
SUMMARY
The type and severity of daytime symptoms reported by insomnia sufferers may vary markedly. Whether distinctive daytime symptom profiles are related to different insomnia diagnoses has not been studied previously. Using profile analysis via multidimensional scaling, we investigated the concurrent validity of ICSD-2 insomnia diagnoses by analysing the relationship of prototypical profiles of daytime symptoms with a subset of ICSD-2 diagnoses, including insomnia associated to a mental disorder, psychophisiological insomnia, paradoxical insomnia, inadequate sleep hygiene, idiopathic insomnia, obstructive sleep apnea and restless legs syndrome. In a sample of 332 individuals meeting research diagnostic criteria for insomnia (221 women, Mage=46 yrs.), the profile analysis identified four prototypical patterns of daytime features. Pearson correlation coefficients indicated that the diagnoses of insomnia associated to a mental disorder and idiopathic insomnia were associated with a daytime profile characterized by mood disturbance and low sleepiness; whereas the diagnoses of psychophysiological insomnia and inadequate sleep hygiene were related to a profile marked by poor sleep hygiene, daytime tension and low fatigue. Furthermore, whereas paradoxical insomnia was consistently associated to lower daytime impairment, insomnia associated to a mental disorder was related to the most severe daytime impairment. This classification of insomnia sufferers along multiple defining dimensions provides initial validation for two basic insomnia subtypes, with a presumably distinct aetiology: insomnia characterized mainly by an “internal” component, and a “learned” insomnia. Research to determine which dimensions are critical for inclusion or differential weighting for defining a general typological system for insomnia sufferers is warranted.
doi:10.1111/j.1365-2869.2010.00905.x
PMCID: PMC3135706  PMID: 21205038
Insomnia; ICSD-2; Daytime symptoms; Concurrent validity
4.  Inverse Current Source Density Method in Two Dimensions: Inferring Neural Activation from Multielectrode Recordings 
Neuroinformatics  2011;9(4):401-425.
The recent development of large multielectrode recording arrays has made it affordable for an increasing number of laboratories to record from multiple brain regions simultaneously. The development of analytical tools for array data, however, lags behind these technological advances in hardware. In this paper, we present a method based on forward modeling for estimating current source density from electrophysiological signals recorded on a two-dimensional grid using multi-electrode rectangular arrays. This new method, which we call two-dimensional inverse Current Source Density (iCSD 2D), is based upon and extends our previous one- and three-dimensional techniques. We test several variants of our method, both on surrogate data generated from a collection of Gaussian sources, and on model data from a population of layer 5 neocortical pyramidal neurons. We also apply the method to experimental data from the rat subiculum. The main advantages of the proposed method are the explicit specification of its assumptions, the possibility to include system-specific information as it becomes available, the ability to estimate CSD at the grid boundaries, and lower reconstruction errors when compared to the traditional approach. These features make iCSD 2D a substantial improvement over the approaches used so far and a powerful new tool for the analysis of multielectrode array data. We also provide a free GUI-based MATLAB toolbox to analyze and visualize our test data as well as user datasets.
Electronic supplementary material
The online version of this article (doi:10.1007/s12021-011-9111-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s12021-011-9111-4
PMCID: PMC3214268  PMID: 21409556
Current source density; Local field potentials; Evoked potentials; Inverse problems; Rat; Hippocampus; Subiculum; Cortical model
5.  Epidemiological and clinical relevance of insomnia diagnosis algorithms according to the DSM-IV and the International Classification of Sleep Disorders (ICSD) 
Sleep medicine  2009;10(9):952-960.
Background
Although the epidemiology of insomnia in the general population has received considerable attention in the past 20 years, few studies have investigated the prevalence of insomnia using operational definitions such as those set forth in the ICSD and DSM-IV, specifying what proportion of respondents satisfied the criteria to reach a diagnosis of insomnia disorder.
Methods
This is a cross-sectional study involving 25,579 individuals aged 15 years and over representative of the general population of France, the United Kingdom, Germany, Italy, Portugal, Spain and Finland. The participants were interviewed on sleep habits and disorders managed by the Sleep-EVAL expert system using DSM-IV and ICSD classifications.
Results
At the complaint level, too short sleep (15.8%), light sleep (16.6%), and global sleep dissatisfaction (8.5%) were reported by 37% of the subjects. At the symptom level (difficulty initiating or maintaining sleep and non-restorative sleep at least 3 nights per week), 34.5% of the sample reported at least one of them. At the criterion level, (symptoms + daytime consequences), 9.8% of the total sample reported having them. At the diagnostic level, 6.6% satisfied the DSM-IV requirement for positive and differential diagnosis. However, many respondents failed to meet diagnostic criteria for duration, frequency and severity in the two classifications, suggesting that multidimensional measures are needed.
Conclusions
A significant proportion of the population with sleep complaints do not fit into DSM-IV and ICSD classifications. Further efforts are needed to identify diagnostic criteria and dimensional measures that will lead to insomnia diagnoses and thus provide a more reliable, valid and clinically relevant classification.
doi:10.1016/j.sleep.2009.07.008
PMCID: PMC3715324  PMID: 19748312
Insomnia; Epidemiology; classifications; mental disorders
6.  Prevalence of restless leg syndrome in subjects with depressive disorder 
Indian Journal of Psychiatry  2013;55(1):70-73.
Background:
Restless legs syndrome (RLS) is known to be associated with depression. We hypothesized that RLS in depression is linked to the severity, duration, and frequency of depressive episodes.
Materials and Methods:
Subjects fulfilling DSM-IV-TR criteria of depressive disorders were included in this study after seeking informed consent. Using structured interview of MINI-Plus their demographic data and history were recorded. Severity of depression was assessed with the help of HAM-D. Insomnia was diagnosed following ICSD-2 criteria. RLS was diagnosed according to IRLSSG criteria. Descriptive statistics, Chi-square test, independent sample t test and MANOVA were computed with the help of SPSS v 17.0.
Results:
RLS was reported by 31.48% of sample. There was no gender difference in prevalence of RLS (X2 =0.46; P=0.33). There was no difference in the age , total duration of depressive illness and number of depressive episodes between RLS and non-RLS groups (F=0.44; P=0.77; Wilk's Lambda=0.96). The HAM-D score was higher in the non-RLS group (P=0.03). Onset of RLS symptoms was not related to onset of depressive symptoms.
Conclusion:
RLS is prevalent in depressive disorder. However, onset of RLS is unrelated to age and number or duration of depressive disorders.
doi:10.4103/0019-5545.105515
PMCID: PMC3574459  PMID: 23439849
Adults; depression; prevalance; restless leg syndrome
7.  Actigraphy as a diagnostic aid for REM sleep behavior disorder in Parkinson’s disease 
BMC Neurology  2014;14:76.
Background
Rapid eye movement (REM) sleep behavior disorder (RBD) is a common parasomnia in Parkinson’s disease (PD) patients. The current International Classification of Sleep Disorders (ICSD-II) requires a clinical interview combined with video polysomnography (video-PSG) to diagnose. The latter is time consuming and expensive and not always feasible in clinical practice. Here we studied the use of actigraphy as a diagnostic tool for RBD in PD patients.
Methods
We studied 45 consecutive PD patients (66.7% men) with and without complaints of RBD. All patients underwent one night of video-PSG and eight consecutive nights of actigraphy. Based on previous studies, the main outcome measure was the total number of bouts classified as “wake”, compared between patients with (PD + RBD) and without RBD (PD- RBD).
Results
23 (51.1%) patients had RBD according to the ICSD-II criteria. The total number of wake bouts was significantly higher in RBD patients (PD + RBD 73.2 ± 40.2 vs. PD-RBD 48.4 ± 23.3, p = .016). A cut off of 95 wake bouts per night resulted in a specificity of 95.5%, a sensitivity of 20.1% and a positive predictive value of 85.7%. Seven patients were suspected of RBD based on the interview alone, but not confirmed on PSG; six of whom scored below 95 wake bouts per night on actigraphy.
Conclusion
PD patients with RBD showed a significantly higher number of bouts scored as “wake” using actigraphy, compared to patients without RBD. In clinical practice, actigraphy has a high specificity, but low sensitivity in the diagnosis of RBD. The combination of actigraphy and previously reported RBD questionnaires may be a promising method to diagnose RBD in patients with PD.
doi:10.1186/1471-2377-14-76
PMCID: PMC3986453  PMID: 24708629
Parkinson’s disease; Actigraphy; REM sleep behavior disorder; Polysomnography
8.  Delayed sleep phase syndrome in adolescents: prevalence and correlates in a large population based study 
BMC Public Health  2013;13:1163.
Background
The aims of this study were to estimate the prevalence of Delayed Sleep Phase Syndrome (DSPS) in adolescence, and to examine the association to insomnia and school non-attendance.
Methods
Data stem from a large population based study in Hordaland County in Norway conducted in 2012, the ung@hordaland study. In all, 10,220 adolescents aged 16–18 years (54% girls) provided self-reported data on a range of sleep parameters: DSPS was defined according to the International Classification of Sleep Disorders, Revised (ICSD-R) criteria, while insomnia was defined according to the Quantitative Criteria for Insomnia. Other sleep parameters included time in bed, sleep duration, sleep efficiency, oversleeping, sleep onset latency, wake after sleep onset, subjective sleep need, sleep deficiency, sleepiness and tiredness. Sleep data were calculated separately for weekdays and weekends. Data on school non-attendance were provided by official registers.
Results
The prevalence of DSPS was 3.3%, and significantly higher among girls (3.7%) than boys (2.7%). There was a strong overlap between DSPS and insomnia, with more than half of the adolescents with DSPS also meeting the criteria for insomnia (53.8% for boys and 57.1% for girls). Adolescents with DSPS had significantly higher odds ratios (OR) of non-attendance at school. After adjusting for sociodeographical factors, insomnia and depression, the adjusted ORs for days of non-attendance were OR = 3.22 (95% CI: 1.94-5.34) for boys and OR = 1.87 (95% CI: 1.25-2.80) for girls. A similar effect was found for hours of non-attendance for boys, with an adjusted OR = 3.05 (95% CI: 1.89-4.92). The effect for girls was no longer significant after full adjustment (OR =1.48 [95% CI: 0.94-2.32]).
Conclusions
This is one of the first studies to estimate the prevalence of DSPS in adolescents. The high prevalence of DSPS, and overlap with insomnia, in combination with the odds of school non-attendance, suggest that a broad and thorough clinical approach is warranted when adolescents present with symptoms of DSPS.
doi:10.1186/1471-2458-13-1163
PMCID: PMC3878844  PMID: 24330358
Delayes sleep phase syndrome; Sleep; Prevalence; Correlates; Epidemiology
9.  FR3D: finding local and composite recurrent structural motifs in RNA 3D structures 
Journal of mathematical biology  2007;56(1-2):215-252.
New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose geometric discrepancy with respect to the query motif falls below a user-specified cutoff discrepancy. This technique can be applied to RMSD searches. Candidate motifs identified geometrically may be further screened symbolically to identify those that contain particular basepair types or base-stacking arrangements or that conform to sequence continuity or nucleotide identity constraints. Purely symbolic searches for motifs containing user-defined sequence, continuity and interaction constraints have also been implemented. We demonstrate that FR3D finds all occurrences, both local and composite and with nucleotide substitutions, of sarcin/ricin and kink-turn motifs in the 23S and 5S ribosomal RNA 3D structures of the H. marismortui 50S ribosomal subunit and assigns the lowest discrepancy scores to bona fide examples of these motifs. The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes.
doi:10.1007/s00285-007-0110-x
PMCID: PMC2837920  PMID: 17694311
10.  Pirquitasite, Ag2ZnSnS4  
Pirquitasite, ideally Ag2ZnSnS4 (disilver zinc tin tetra­sulfide), exhibits tetra­gonal symmetry and is a member of the stannite group that has the general formula A2BCX 4, with A = Ag, Cu; B = Zn, Cd, Fe, Cu, Hg; C = Sn, Ge, Sb, As; and X = S, Se. In this study, single-crystal X-ray diffraction data are used to determine the structure of pirquitasite from a twinned crystal from the type locality, the Pirquitas deposit, Jujuy Province, Argentina, with anisotropic displacement parameters for all atoms, and a measured composition of (Ag1.87Cu0.13)(Zn0.61Fe0.36Cd0.03)SnS4. One Ag atom is located on Wyckoff site Wyckoff 2a (symmetry -4..), the other Ag atom is statistically disordered with minor amounts of Cu and is located on 2c (-4..), the (Zn, Fe, Cd) site on 2d (-4..), Sn on 2b (-4..), and S on general site 8g. This is the first determination of the crystal structure of pirquitasite, and our data indicate that the space group of pirquitasite is I-4, rather than I-42m as previously suggested. The structure was refined under consideration of twinning by inversion [twin ratio of the components 0.91 (6):0.09 (6)].
doi:10.1107/S1600536813001013
PMCID: PMC3569172  PMID: 23424398
11.  Penta­lanthanum zinc diplumbide, La5Zn1−xPb2+x (x ≃ 0.6) 
The title non-stoichiometric penta­lanthanum zinc diplumbide, La5Zn1−xPb2+x (x ≃ 0.6), was prepared from the elements in an evacuated silica ampoule. It adopts the Nb5Sn2Si-type structure (space group I4/mcm, Pearson symbol tI32), a ternary ordered superstructure of the W5Si3 type. Among the four independent crystallographic positions, three are fully occupied by La (Wyckoff 16k), La (4b), and Pb (8h) and one is occupied by a statistical mixture [occupancy ratio 0.394 (12):0.606 (12)] of Zn and Pb (4a). The structure is constructed by face-sharing 10-vertex polyhedra around the unmixed Pb sites. These fragments enclose channels of trans-face-sharing tetra­gonal anti­prisms occupied by the disordered Zn and Pb sites.
doi:10.1107/S1600536813033618
PMCID: PMC3914033  PMID: 24526938
12.  HIERARCHY OF INSOMNIA CRITERIA BASED ON DAYTIME CONSEQUENCES 
Sleep medicine  2011;13(1):52-57.
Objectives
To explore how insomnia symptoms are hierarchically organized in individuals reporting daytime consequences of their sleep disturbances.
Methods
This is a cross-sectional study conducted in the general population of the states of California, New York and Texas. The sample included 8,937 individuals aged 18 years or older representative of the general population. Telephone interviews on sleep habits and disorders were managed with the Sleep-EVAL expert system and using DSM-IV and ICSD classifications. Insomnia symptoms and Global Sleep Dissatisfaction (GSD) had to occur at least three times per week for at least three months.
Results
A total of 26.2% of the sample had a GSD. Individuals with GSD reported at least one insomnia symptom in 73.1% of the cases. The presence of GSD in addition to insomnia symptoms considerably increased the proportion of individuals with daytime consequences related to insomnia. In the classification trees performed, GSD arrived as the first predictor for daytime consequences related to insomnia. The second predictor was nonrestorative sleep followed by difficulty resuming sleep and difficulty initiating sleep.
Conclusions
Classification trees are a useful way to hierarchically organize symptoms and to help diagnostic classifications. In this study, GSD was found to be the foremost symptom in identifying individuals with daytime consequences related to insomnia.
doi:10.1016/j.sleep.2011.06.010
PMCID: PMC3249005  PMID: 22036602
13.  Insomnia in Older Veterans: Prevalence, Self-Rated Health, and Talking to a Doctor About Sleep Problems 
Objectives
To determine insomnia prevalence and variations in prevalence with age among older Veterans and examine the relationships among insomnia, self-rated health, and talking to a doctor about sleep problems.
Design
A cross-sectional postal survey. Setting: VA Greater Los Angeles Healthcare System - Sepulveda Ambulatory Care Center (SACC) Participants: Veterans over age 60, who received outpatient care at SACC in the prior 12 months and resided within 25 miles of SACC (n=9080) Interventions: None
Measures
Data were collected from a postal survey, which included items addressing the diagnostic criteria for insomnia (difficultly falling or staying asleep, early awakening, insufficient/non-restorative sleep, daytime symptoms, duration of sleep problems) plus demographics, self-rated health, and whether the Veteran had previously talked to a doctor about sleep problems.
Results
Of 9080 surveys 4758 were returned. Of responders 51.5% met International Classification of Sleep Disorders (ICSD) insomnia diagnostic criteria. An unadjusted logistic regression model showed that individuals in the 60–65 year age bin were at the highest risk for insomnia, with the odds of having insomnia decreasing with each successively older age group (all P<.05). Veterans with poor self-rated health had higher insomnia prevalence, more daytime symptoms of insomnia, and reported fewer hours of sleep compared to Veterans with good self-rated health. In a regression model, poorer self-rated health, meeting insomnia criteria, younger age, and more daytime symptoms were significant independent predictors of discussing sleep problems with a doctor.
Conclusion
Older Veterans had high rates of insomnia, but contrary to most prior work, insomnia became less prevalent as age increased. Greater efforts are needed to help older Veterans recognize and disclose sleep problems, and doctors should routinely screen for insomnia and account for comorbidities when treating insomnia patients.
PMCID: PMC3764564
14.  Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry 
BMC Bioinformatics  2007;8:105.
Background
Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas.
Results
An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries.
Conclusion
The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65–81%. Corresponding software and supplemental data are available for downloads from the authors' website.
doi:10.1186/1471-2105-8-105
PMCID: PMC1851972  PMID: 17389044
15.  STRUCTURAL UNITS OF STARCH DETERMINED BY X-RAY CRYSTAL STRUCTURE METHOD 
A few brief statements summarizing the foregoing conclusions may make a picture of the structure of the starch grain somewhat clearer. 1. The presence of lines on the negatives indicates a regular arrangement of the planes of atoms. 2. The lines are in close agreement with lines which would be produced by a lattice of the tetragonal system, the elementary cell of which is a square prism with the dimensions 5.94 x 5.94 x 5.05 Å.u. 3. The unit of the lattice occupies a space equal to the volume of the starch group, C6H10O5. 4. The large number of atoms in the unit makes it highly probable that principal planes and secondary planes of atoms occur for every reflecting position. 5. The effect of the secondary upon the principal planes may readily account for the differences in the density of the lines produced on the negatives. 6. From theoretical considerations, reflections, such as those obtained, would occur if starch grains were built up of concentric layers of units. 7. Two other factors which might affect the density of the lines are thermal agitation and the curvature of the concentric layers. 8. A model of the starch group was constructed to scale based on the accepted sizes of the atoms involved and upon rather meager chemical evidence. The model apparently fulfills the requirements necessary to produce reflections such as were obtained. 9. The model fits the elementary cell loosely enough to suggest a low density and to allow for considerable thermal movement. At the same time, parts of it approach the faces of the cell closely enough to make cohesion seem possible. 10. The model makes clearer the basis for the assumption that reflection from certain positions would be stronger than from others. If the interpretation of the data is correct and if the assumptions made are sound, then the starch grain is built up of units arranged in concentric layers, and the units are groups of atoms, each containing 6 carbon, 10 hydrogen, and 5 oxygen atoms. Such a structure is certainly not an amorphous structure, and on the other hand it is not crystalline in the common sense of the term. Parts of the grain, it is true, act as crystals in that for certain distances the layers of units are in planes, but taken as a whole the layers are curved. As to the validity of the conclusions, those pertaining to the type of lattice and to the size of the unit may be accepted as sound in our present knowledge of x-rays and crystal structure; those, however, pertaining to the nature and the spherical arrangement of the units, while they seem convincing, need the support of further investigation into the various structures deposited by living protoplasm. In conclusion, the assumption that the units form a sort of spherical space lattice, gives a picture of the starch grain which leads us to ponder over the nature of the activity in protoplasm when it is depositing solid substances. Starch, cellulose, and pectic bodies are about the only solid deposits made directly by the living substance of plants, and all three have the same proportional formula, C6H10O5. Investigations, as yet incomplete, indicate that cellulose also consists of a regular arrangement of C6H10O5 groups, each acting as a unit, but the spacing (6.14 x 6.14 x 5.55) is slightly different from that of starch. Pectin has not been studied. Protoplasm may be thought of as being composed of molecules of many different sizes, polypeptides, or even proteins forming the larger, and amino-acids the smaller, if water and electrolytes are ignored. The smaller molecules, such as those of the amino-acid, leucine, are approximately equal in size to the C6H10O5 group of starch. That being the case, what can be the state of affairs at the interface when the starch particles are being deposited? Is it probable that protoplasm is homogeneous to the extent of being able to deposit these particles at 6 Å.u. intervals? From quite another view-point a clear picture of the units of structure and their arrangement in cellulose should give a new point of attack on the many problems connected with osmosis. And from still a different view-point, it might lead perhaps, to a solution of problems connected with swelling. Another line of thought is suggested by the uniformity of the groups in the starch grain. Since the C6H10O5 group occurs as an individual unit, one is inclined to suspect that it is really the molecule. Generally the starch molecule is considered to be very large, to be composed of several dozens of such groups, and to have a molecular weight of 7,000 or much more. No one figure, however, seems satisfactory to the different authorities. There is already at hand considerable evidence which will be assembled in a later paper favoring the single group, C6H10O5, as the molecule. Finally, problems in polarized light may receive more satisfactory explanations through a clearer notion of the molecular structure of the carbohydrates.
PMCID: PMC2140597  PMID: 19872035
16.  Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses 
Nucleic Acids Research  2008;36(11):3552-3569.
For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans: proteins with no detectable similarity to each other and to any other protein in the database, despite common cellular and biochemical function. Crystallographic analyses published until January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences available in the Restriction Enzyme database (REBASE). Among these structures, all but two possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a new fold termed ‘half-pipe’. Thus far, bioinformatic studies supported by site-directed mutagenesis have extended the number of tentatively assigned REase folds to five (now including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided structural predictions for dozens of REase sequences without experimentally solved structures. Here, we present a comprehensive study of all Type II REase sequences available in REBASE together with their homologs detectable in the nonredundant and environmental samples databases at the NCBI. We present the summary and critical evaluation of structural assignments and predictions reported earlier, new classification of all REase sequences into families, domain architecture analysis and new predictions of three-dimensional folds. Among 289 experimentally characterized (not putative) Type II REases, whose apparently full-length sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The HNH domain is the second most common, with 24 (8%) members. When putative REases are taken into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively. Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase folds identified so far, and may exhibit new architectures. These enzymes are proposed as the most interesting targets for structure determination by high-resolution experimental methods. Our analysis provides the first comprehensive map of sequence-structure relationships among Type II REases and will help to focus the efforts of structural and functional genomics of this large and biotechnologically important class of enzymes.
doi:10.1093/nar/gkn175
PMCID: PMC2441816  PMID: 18456708
17.  Self-reported sleep disturbances in renal transplant recipients 
BMC Nephrology  2013;14:220.
Background
Poor sleep quality (SQ) and daytime sleepiness (DS) are common in renal transplant (RTx) recipients; however, related data are rare. This study describes the prevalence and frequency of self-reported sleep disturbances in RTx recipients.
Methods
This cross-sectional study included 249 RTx recipients transplanted at three Swiss transplant centers. All had reported poor SQ and / or DS in a previous study. With the Survey of Sleep (SOS) self-report questionnaire, we screened for sleep and health habits, sleep history, main sleep problems and sleep-related disturbances. To determine a basis for preliminary sleep diagnoses according to the International Classification of Sleep Disorders (ICSD), 164 subjects were interviewed (48 in person, 116 via telephone and 85 refused). Descriptive statistics were used to analyze the data and to determine the frequencies and prevalences of specific sleep disorders.
Results
The sample had a mean age of 59.1 ± 11.6 years (60.2% male); mean time since Tx was 11.1 ± 7.0 years. The most frequent sleep problem was difficulty staying asleep (49.4%), followed by problems falling asleep (32.1%). The most prevalent sleep disturbance was the need to urinate (62.9%), and 27% reported reduced daytime functionality. Interview data showed that most suffered from the first ICSD category: insomnias.
Conclusion
Though often disregarded in RTx recipients, sleep is an essential factor of wellbeing. Our findings show high prevalences and incidences of insomnias, with negative impacts on daytime functionality. This indicates a need for further research on the clinical consequences of sleep disturbances and the benefits of insomnia treatment in RTx recipients.
doi:10.1186/1471-2369-14-220
PMCID: PMC3852502  PMID: 24112372
Renal transplantation; Sleep disturbances; Sleep quality; Daytime sleepiness
18.  A PDB-wide, evolution-based assessment of protein–protein interfaces 
Background
Thanks to the growth in sequence and structure databases, more than 50 million sequences are now available in UniProt and 100,000 structures in the PDB. Rich information about protein–protein interfaces can be obtained by a comprehensive study of protein contacts in the PDB, their sequence conservation and geometric features.
Results
An automated computational pipeline was developed to run our Evolutionary Protein–Protein Interface Classifier (EPPIC) software on the entire PDB and store the results in a relational database, currently containing > 800,000 interfaces. This allows the analysis of interface data on a PDB-wide scale. Two large benchmark datasets of biological interfaces and crystal contacts, each containing about 3000 entries, were automatically generated based on criteria thought to be strong indicators of interface type. The BioMany set of biological interfaces includes NMR dimers solved as crystal structures and interfaces that are preserved across diverse crystal forms, as catalogued by the Protein Common Interface Database (ProtCID) from Xu and Dunbrack. The second dataset, XtalMany, is derived from interfaces that would lead to infinite assemblies and are therefore crystal contacts. BioMany and XtalMany were used to benchmark the EPPIC approach. The performance of EPPIC was also compared to classifications from the Protein Interfaces, Surfaces, and Assemblies (PISA) program on a PDB-wide scale, finding that the two approaches give the same call in about 88% of PDB interfaces. By comparing our safest predictions to the PDB author annotations, we provide a lower-bound estimate of the error rate of biological unit annotations in the PDB. Additionally, we developed a PyMOL plugin for direct download and easy visualization of EPPIC interfaces for any PDB entry. Both the datasets and the PyMOL plugin are available at http://www.eppic-web.org/ewui/#downloads.
Conclusions
Our computational pipeline allows us to analyze protein–protein contacts and their sequence conservation across the entire PDB. Two new benchmark datasets are provided, which are over an order of magnitude larger than existing manually curated ones. These tools enable the comprehensive study of several aspects of protein–protein contacts in the PDB and represent a basis for future, even larger scale studies of protein–protein interactions.
doi:10.1186/s12900-014-0022-0
PMCID: PMC4274722  PMID: 25326082
Protein–protein interfaces; Biological interfaces; Crystal contacts; EPPIC; PISA; PDB
19.  Gene expression signature based approach identifies a pro-resolving mechanism of action for histone deacetylase inhibitors 
Cell death and differentiation  2012;20(4):567-575.
Despite several therapies are currently available to treat inflammatory diseases, new drugs to treat chronic conditions with less side effects and lower production costs are still needed. An innovative approach to drug discovery, the Connectivity Map (CMap), shows how integrating genome-wide gene expression data of drugs and diseases can accelerate this process. Comparison of genome-wide gene expression data generated with Annexin A1 (AnxA1) with the CMap revealed significant alignment with gene profiles elicited by histone deacetylase inhibitors (HDACIs), what made us to hypothesize that AnxA1 might mediate the anti-inflammatory actions of HDACIs. Addition of HDACIs (valproic acid, sodium butyrate and thricostatin A) to mouse macrophages caused externalization of AnxA1 with concomitant inhibition of cytokine gene expression and release, events that occurred independently since this inhibition was retained in AnxA1 null macrophages. However, novel AnxA1-mediated functions for HDACIs could be unveiled, including promotion of neutrophil apoptosis and macrophage phagocytosis, both steps crucial for effective resolution of inflammation. In a model of acute resolving inflammation, administration of valproic acid and sodium butyrate to mice at the peak of disease accelerated resolution processes in wild type, but much more modestly in AnxA1 null mice. Deeper analyses revealed a role for endogenous AnxA1 in the induction of neutrophil death in vivo by HDACIs. In summary, interrogation of the CMap revealed an unexpected association between HDACIs and AnxA1 that translated in mechanistic findings with particular impact on the processes that regulate the resolution of inflammation. We propose non-genomic modulation of AnxA1 in immune cells as a novel mechanism of action for HDACIs, which may underlie their reported efficacy in models of chronic inflammatory pathologies.
doi:10.1038/cdd.2012.154
PMCID: PMC3595482  PMID: 23222458
Annexin A1; Efferocytosis; Genomics; Inflammation; Resolution
20.  Gene expression signature-based approach identifies a pro-resolving mechanism of action for histone deacetylase inhibitors 
Cell Death and Differentiation  2012;20(4):567-575.
Despite several therapies being currently available to treat inflammatory diseases, new drugs to treat chronic conditions with less side effects and lower production costs are still needed. An innovative approach to drug discovery, the Connectivity Map (CMap), shows how integrating genome-wide gene expression data of drugs and diseases can accelerate this process. Comparison of genome-wide gene expression data generated with annexin A1 (AnxA1) with the CMap revealed significant alignment with gene profiles elicited by histone deacetylase inhibitors (HDACIs), what made us to hypothesize that AnxA1 might mediate the anti-inflammatory actions of HDACIs. Addition of HDACIs (valproic acid, sodium butyrate and thricostatin A) to mouse macrophages caused externalization of AnxA1 with concomitant inhibition of cytokine gene expression and release, events that occurred independently as this inhibition was retained in AnxA1 null macrophages. In contrast, novel AnxA1-mediated functions for HDACIs could be unveiled, including promotion of neutrophil apoptosis and macrophage phagocytosis, both steps crucial for effective resolution of inflammation. In a model of acute resolving inflammation, administration of valproic acid and sodium butyrate to mice at the peak of disease accelerated resolution processes in wild type, but much more modestly in AnxA1 null mice. Deeper analyses revealed a role for endogenous AnxA1 in the induction of neutrophil death in vivo by HDACIs. In summary, interrogation of the CMap revealed an unexpected association between HDACIs and AnxA1 that translated in mechanistic findings with particular impact on the processes that regulate the resolution of inflammation. We propose non-genomic modulation of AnxA1 in immune cells as a novel mechanism of action for HDACIs, which may underlie their reported efficacy in models of chronic inflammatory pathologies.
doi:10.1038/cdd.2012.154
PMCID: PMC3595482  PMID: 23222458
annexin A1; efferocytosis; genomics; inflammation; resolution
21.  Nanohydroxyapatite Application to Osteoporosis Management 
Journal of Osteoporosis  2013;2013:679025.
Hydroxyapatite is chemically related to the inorganic component of bone matrix as a complex structure with the formula of Ca10(OH)2(PO4)6. Previous studies have reported the application of microsized hydroxyapatite to bone regeneration, but the result is not satisfied. The limitation comes from the size of hydroxyapatite. In addition, the duration of treatment is very long. The advantages of hydroxyapatite nanocrystal are the osteoconduction, bioresorption, and contact in close distance. Crystal in osteoporotic bone is calcium phosphate hydroxide with the chemical formula of Ca10(OH)2(PO4)6. Crystal of normal bone is sodium calcium hydrogen carbonate phosphate hydrate with the chemical formula of Ca8H2(PO4)6·H2O–NaHCO3–H2O. The recent development is applying nanobiology approach to hydroxyapatite. This is based on the concept that the mineral atoms arranged in a crystal structure of hydroxyapatite can be substituted or incorporated by the other mineral atoms. In conclusion, the basic elements of hydroxyapatite crystals, composed of atomic minerals in a certain geometric pattern, and their relationship to the bone cell biological activity have opened opportunities for hydroxyapatite crystals supplement application on osteoporosis. Understanding of the characteristics of bone hydroxyapatite crystals as well as the behavior of mineral atom in the substitution will have a better impact on the management of osteoporosis.
doi:10.1155/2013/679025
PMCID: PMC3830883  PMID: 24288653
22.  Osteogenic Protein-1 for Long Bone Nonunion 
Executive Summary
Objective
To assess the efficacy of osteogenic protein-1 (OP-1) for long bone nonunion.
Clinical Need
Although most fractures heal within a normal period, about 5% to 10% do not heal and are classified as delayed or nonunion fractures. Nonunion and segmental bone loss after fracture, reconstructive surgery, or lesion excision can present complex orthopedic problems, and the multiple surgical procedures often needed are associated with patient morbidity and reduced quality of life.
Many factors contribute to the pathogenesis of a delayed union or nonunion fractures, including deficiencies of calcium, vitamin D, or vitamin C, and side effects of medications such as anticoagulants, steroids, some anti-inflammatory drugs, and radiation. It has been shown that smoking interferes with bone repair in several ways.
Incidence of Nonunion and Delayed Union Cases
An estimated 5% to 10% of fractures do not heal properly and go on to delayed union or nonunion. If this overall estimate of incidence were applied to the Ontario population1, the estimated number of delayed union or nonunion in the province would be between 3,863 and 7,725.
Treatment of Nonunion Cases
The treatment of nonunion cases is a challenge to orthopedic surgeons. However, the basic principle behind treatment is to provide both mechanical and biological support to the nonunion site.
Fracture stabilization and immobilization is frequently used with the other treatment modalities that provide biological support to the fractured bone. Biological support includes materials that could be served as a source of osteogenic cells (osteogenesis), a stimulator of mesenchymal cells (osteoinduction), or a scaffold-like structure (osteoconduction).
The capacity to heal a fracture is a latent potential of the stromal stem cells, which synthesize new bone. This process has been defined as osteogenesis. Activation of the stem cells to initiate osteogenic response and to differentiate into bone-forming osteoblasts is called osteoinduction. These 2 properties accelerate the rate of fracture healing or reactivate the ineffective healing process. Osteoconduction occurs when passive structures facilitate the migration of osteoprogenitor cells, the perivascular tissue, and capillaries into these structures.
Bone Grafts and Bone Graft Substitutes
Bone graft and bone graft substitutes have one or more of the following components:
Undifferentiated stem cells
Growth factors
Structural lattice
Undifferentiated stem cells are unspecialized, multipotential cells that can differentiate into a variety of specialized cells. They can also replicate themselves. The role of stem cells is to maintain and repair the tissue in which they are residing. A single stem cell can generate all cell types of that tissue. Bone marrow is a source of at least 2 kinds of stem cells. Hematopoietic stem cells that form all types of blood cells, and bone marrow stromal stem cells that have osteogenic properties and can generate bone, cartilage, and fibrous tissue.
Bone marrow has been used to stimulate bone formation in bone defects and cases of nonunion fractures. Bone marrow can be aspirated from the iliac crest and injected percutaneously with fluoroscopic guidance into the site of the nonunion fracture. The effectiveness of this technique depends on the number and activity of stem cells in the aspirated bone marrow. It may be possible to increase the proliferation and speed differentiation of stem cells by exposing them to growth factor or by combining them with collagen.
Many growth factors and cytokines induced in response to injury are believed to have a considerable role in the process of repair. Of the many bone growth factors studied, bone morphogenetics (BMPs) have generated the greatest attention because of their osteoinductive potential. The BMPs that have been most widely studied for their ability to induce bone regeneration in humans include BMP-2 and BMP-7 (osteogenic protein). Human osteogenic protein-1 (OP-1) has been cloned and produced with recombinant technology and is free from the risk of infection or allergic reaction.
The structural lattice is osteoconductive; it supports the ingrowth of developing capillaries and perivascular tissues. Three distinct groups of structural lattice have been identified: collagen, calcium sulphate, and calcium phosphate. These materials can be used to replace a lost segment of bone.
Grafts Used for Nonunion
Autologous bone graft is generally considered the gold standard and the best material for grafting because it contains several elements that are critical in promoting bone formation, including osteoprogenitor cells, the matrix, and bone morphogenetic proteins. The osteoconductive property of cancellous autograft is related to the porosity of bone. The highly porous, scaffold-like structure of the graft allows host osteoblasts and host osteoprogenitor cells to migrate easily into the area of the defect and to begin regeneration of bone. Sources of cancellous bone are the iliac crest, the distal femur, the greater trochanter, and the proximal tibia. However, harvesting the autologous bone graft is associated with postoperative pain at the donor site, potential injury to the surrounding arteries, nerves, and tissues, and the risk of infection. Thus the development of synthetic materials with osteoconductive and osteoinductive properties that can eliminate the need for harvesting has become a major goal of orthopedic research.
Allograft is the graft of tissue between individuals who are of the same species but are of a disparate genotype. Allograft has osteoconductive and limited osteoinductive properties. Demineralized bone matrix (DBM) is human cortical and cancellous allograft. These products are prepared by acid extraction of allograft bone, resulting in the loss of most of the mineralized component while collagen and noncollagenous proteins, including growth factors, are retained. Figures 1 to 5 demonstrate the osteogenic, osteoinduction, and osteoconduction properties of autologous bone graft, allograft, OP-1, bone graft substitutes, and bone marrow.
Autologous Bone Graft
Osteogenic Protein-1
Allograft bone and Demineralized Bone Matrix
Bone Graft Substitutes
Autologous Bone Marrow Graft
New Technology Being Reviewed: Osteogenic Protein-1
Health Canada issued a Class IV licence for OP-1 in June 2004 (licence number 36320). The manufacturer of OP-1 is Stryker Biotech (Hapkinton, MA).
The United States Food and Drug Administration (FDA) issued a humanitarian device exemption for the application of the OP-1 implant as an “alternative to autograft in recalcitrant long bone nonunions where use of autograft is unfeasible and alternative treatments have failed.” Regulatory agencies in Europe, Australia, and New Zealand have permitted the use of this implant in specific cases, such as in tibial nonunions, or in more general cases, such as in long bone nonunions.
According to the manufacturer, OP-1 is indicated for the treatment of long bone nonunions. It is contraindicated in the patient has a hypersensitivity to the active substance or collagen, and it should not be applied at the site of a resected tumour that is at or near the defect or fracture. Finally, it should not be used in patients who are skeletally immature (< 18 years of age), or if there is no radiological evidence of closure of epiphysis.
Review Strategy
Objective
To summarize the safety profile and effectiveness of OP-1 in the treatment of cases of long bone nonunion and bone defects
To compare the effectiveness and cost effectiveness of OP-1 in the treatment of long bone nonunions and bone defects with the alternative technologies, particularly the gold standard autologous bone graft.
Literature Search
International Network of Agencies for Health Technology Assessments (INAHTA), the Cochrane Database of Systematic Reviews and the CCTR (formerly Cochrane Controlled Trials Register) were searched for health technology assessments. MEDLINE, EMBASE, Medline In Process and Other Non-Indexed Citations were searched from January 1, 1996 to January 27, 2004 for studies on OP-1. The search was limited to English-language articles and human studies. The search yielded 47 citations. Three studies met inclusion criteria (2 RCTs and 1 Ontario-based study presented at an international conference.
Summary of Findings
Friedlaender et al. conducted a prospective, randomized, partially blinded clinical trial on the treatment tibial nonunions with OP-1. Tibial nonunions were chosen for this study because of their high frequency, challenging treatment requirements, and substantial morbidity. All of the nonunions were at least 9 months old and had shown no progress toward healing over the previous 3 months. The patients were randomized to receive either treatment with autologous bone grafting or treatment with OP-1 in a type-1 collagen carrier. Both groups received reduction and fixation with an intramedullary rod. Table 1 summarizes the clinical outcomes of this study.
Outcomes in a Randomized Clinical Trial on Tibial Nonunions: Osteogenic Protein-1 versus Autologous Bone Grafting
Clinical success was defined as full weight-bearing, loss of severe pain at the fracture site on weight-bearing, and no further surgical treatment to enhance fracture repair.
The results of this study demonstrated that recombinant OP-1 is associated with substantial clinical and radiographic success for the treatment of tibial nonunions when used with intramedullary rod fixation. No adverse event related to sensitization was reported. Five per cent of the patients in the OP-1 group had circulating antibodies against type 1 collagen. Only 10% of the patients had a low level of anti-OP-1 antibodies, and all effects were transient. Furthermore, the success rate with the OP-1 implant was comparable with those achieved with autograft at 9 and 24 months follow-up. Eighty-two per cent of patients were successful at 24 months follow-up in both groups.
Statistically significant increased blood loss in the group treated with the autograft was observed (P = .049). Patients treated with autograft had longer operation and hospitalization times. All patients in the autograft group had pain at the donor site after surgery, and more than 80% judged their postoperative pain as moderate or severe. At their 6-month visit, 20% of the patients in the autograft group had persistent pain, mild or moderate in nature, at the donor site. This number fell to 13% at 12 months.
All patients in each of the groups had at least 1 adverse event that wasn’t serious, such as fever, nausea and vomiting, leg edema, discomfort, and bruising at the operative site. The incidence of these events was similar in both groups. Serious adverse events were observed in 44% of both groups, none of which were considered related to the OP-1 implant or autograft.
On the basis of this data, the FDA issued a humanitarian device exemption for the application of OP-1 implant as an alternative to autograft in recalcitrant long bone nonunions when the use of autograft is unfeasible and alternative treatments have failed.
Study on Fibular Defects
Geesink et al. investigated the osteogenic activity of OP-1 by assessing its value in bridging fibular defects made at the time of tibial osteotomy for varus or valgus deformity of the knee. This study had 2 phases and included 12 patients in each phase. Each phase included 12 patients (6 in each group). Patients in the first phase received either DBM or were left untreated. Patients in the second phase received either OP-1 on collagen type-1 or collagen type-1 alone.
Radiological and Dual Energy X-ray Absorptiometry (DEXA) evaluation showed that in patients in whom the defect was left untreated, no formation of bone occurred. At 12 months follow-up, new bone formation with bridging occurred in 4 of the 6 patients in DMB group, and 5 of the 6 patients in OP-1 group. One patient in OP-1 group did not show any evidence of new bone formation at any point during the study.
Ontario Pilot Study
A prospective pilot study was conducted in Ontario, Canada to investigate the safety and efficacy of OP-1 for the treatment of recalcitrant long bone nonunions. The study looked at 15 patients with complex, recalcitrant, long bone nonunions whose previous treatment had failed. The investigators concluded that this bone graft substitute appears to be safe and effective in providing sufficient biological stimulation in difficult to treat nonunions. Results of a more complete study on 70 patients are ready for publication. According to the principal investigator, OP-1 was 90% effective in inducing bone formation and bone healing in this sample.
Alternative Technologies
The Medical Advisory Secretariat conducted a literature search from January 1, 2000 to February 28, 2005 to identify studies on nonunions/bone defects that had been treated with alternative technologies. A review of these studies showed that, in addition to the gold standard autologous bone marrow grafting, bone allografts, demineralized bone matrices, bone graft substitutes, and autologous bone marrow have been used for treatment of nonunions and bone defects. These studies were categorized according to the osteoinductive, osteoconductive, and osteogenesis properties of the technologies studied.
A review of these studies showed that bone allografts have been used mostly in various reconstruction procedures to restore the defect after excavating a bone lesion. Two studies investigated the effectiveness of DBM in healing fracture nonunions. Calcium phosphate and calcium sulphate have been used mostly for repair of bone defects.
Several investigators have looked at the use of autologous bone marrow for treatment of long bone nonunions. The results of these studies show that method of percutaneous bone marrow grafting is highly effective in the treatment of long bone nonunions. In a total of 301 fractures across all studies, 268 (89%) healed with a mean healing time of 2.5 to 8 months. This healing time as derived from these case series is less than the timing of the primary end point in Friedlaender’s study (9 months). Table 2 summarizes the results of these studies. Table 2 summarizes the results of these studies.
Studies that used Percutaneous Bone Marrow Grafting for Treatment of Nonunions
Economic Analysis
Based on annual estimated incidence of long-bone nonunion of 3,863 - 7,725, the annual hospitalization costs associated with this condition is between $21.2 and $42.3 million based on a unit cost of $5,477 per hospital separation. When utilized, the device, a single vial of OP-1, is approximately $5,000 and if adopted universally in Ontario, the total device costs would be in the range of $19.3 - $38.6 million annually. The physician fee for harvest, insertion of bone, or OP-1 is $193 and is $193 for autologous bone marrow transplantation. Total annual physician costs are expected to be in the range of from $0.7 million to $1.3 million per year. Expenditures associated with long-bone nonunion are unlikely to increase since incidence of long-bone nonunion is unlikely to change in the future. However, the rate of uptake of OP-1 could have a significant impact on costs if the uptake were large.
The use of OP-1 and autologous bone marrow transplantation may offset pain medication costs compared with those associated with autologous bone harvest given that the former procedures do not involve the pain associated with the bone harvest site. However, given that this pain is normally not permanent, the overall offset is likely to be small. There are likely to be smaller OHIP costs associated with OP-1 than bone-harvest procedures given that only 1, rather than 2, incisions are needed when comparing the former with the latter procedure. This offset could amount to between $0.3 million to $0.7 million annually.
No data on the cost-effectiveness of OP-1 is available.
PMCID: PMC3382627  PMID: 23074475
23.  Complementary ab initio and X-ray nanodiffraction studies of Ta2O5 
Acta Materialia  2015;83:276-284.
The complex structure of Ta2O5 led to the development of various structural models. Among them, superstructures represent the most stable configurations. However, their formation requires kinetic activity and long-range ordering processes, which are hardly present during physical vapor deposition. Based on nano-beam X-ray diffraction and concomitant ab initio studies, a new metastable orthorhombic basic structure is introduced for Ta2O5 with lattice parameters a = 6.425 Å, b = 3.769 Å and c = 7.706 Å. The unit cell containing only 14 atoms, i.e. two formula unit blocks in the c direction, is characterized by periodically alternating the occupied oxygen site between two possible positions in succeeding 002-planes. This structure can be described by the space group 53 (Pncm) with four Wyckoff positions, and exhibits an energy of formation of −3.209 eV atom−1. Among all the reported basic structures, its energy of formation is closest to those of superstructures. Furthermore, this model exhibits a 2.5 eV band gap, which is closer to experimental data than the band gap of any other basic-structure model. The sputtered Ta2O5 films develop only a superstructure if annealed at temperatures >800 °C in air or vacuum. Based on these results and the conveniently small unit cell size, it is proposed that the basic-structure model described here is an ideal candidate for both structure and electronic state descriptions of orthorhombic Ta2O5 materials.
doi:10.1016/j.actamat.2014.10.006
PMCID: PMC4308001  PMID: 25642136
Ta2O5; Structure; Nanobeam diffraction; Ab initio; DOS
24.  Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures 
Proteins  2013;81(6):1051-1057.
The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations.
doi:10.1002/prot.24262
PMCID: PMC3659166  PMID: 23401043
configurational isomer; conformational isomer; crystal structure; NMR structure
25.  Annexin A5 Binds to Lipopolysaccharide and Reduces Its Endotoxin Activity 
mBio  2012;3(2):e00292-11.
ABSTRACT
Annexin A5 (AnxA5) has a high affinity for phosphatidylserine. The protein is widely used to detect apoptotic cells because phosphatidylserine, a phospholipid that is normally present in the inner leaflets of cytoplasmic membranes, becomes translocated to the outer leaflets during programmed cell death. Here we report the novel observation that AnxA5 binds to Gram-negative bacteria via the lipid A domain of lipopolysaccharide (LPS). Binding of AnxA5 to bacteria was measured quantitatively, confirmed by fluorescence microscopy, and found to be inhibited by antibodies against lipid A. AnxA5 also bound to purified dot-blotted LPS and lipid A. Through ellipsometry, we found that the binding of AnxA5 to purified LPS was calcium dependent and rapid and showed a high affinity—characteristics similar to those of AnxA5 binding to phosphatidylserine. Initial functional studies indicated that AnxA5 can affect LPS activities. AnxA5 inhibited LPS-mediated gelation in the Limulus amebocyte lysate assay. Incubation of LPS with the protein reduced the quantity of tumor necrosis factor alpha (TNF-α) released by cultured monocytes compared to that released upon incubation with LPS alone. Initial in vivo experiments indicated that injection of mice with LPS preincubated with AnxA5 produced serum TNF-α levels lower than those seen after injection of LPS alone. These data demonstrate that AnxA5 binds to LPS and open paths to investigation of the potential biological and therapeutic implications of this interaction.
IMPORTANCE
AnxA5 is highly expressed in cells that have a barrier function—including, among others, vascular endothelium, placental trophoblasts, and epithelial cells lining bile ducts, renal tubules, mammary ducts, and nasal epithelium. The protein has been well characterized for its binding to phospholipid bilayers that contain phosphatidylserine. This report of a previously unrecognized activity of AnxA5 opens the door to investigation of the possibility that this binding may have biological and therapeutic ramifications. In view of the tissue expression of the protein, the present results suggest the possibility that AnxA5 plays a role in modulating the host defense against lipopolysaccharide at these anatomic sites, where cells may interface with microorganisms. These results also raise the intriguing possibility that AnxA5 or analogous proteins or peptides could provide novel approaches to addressing the difficult clinical problem of Gram-negative sepsis.
doi:10.1128/mBio.00292-11
PMCID: PMC3312215  PMID: 22415004

Results 1-25 (1088012)