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1.  Potential Prognostic Biomarkers of Pancreatic Cancer 
Pancreas  2014;43(1):10.1097/MPA.0b013e3182a6867e.
Objectives
We evaluated whether pancreatic main duct fluid can provide protein biomarkers with prognostic value.
Methods
Mass spectrometry proteomics was applied to as little as 20 microliters of fluid collected at the time of tumor surgical resection. Biomarker proteins identified for 27 patients were correlated with clinical outcomes.
Results
Thirteen patients had pancreatic ductal adenocarcinomas (PDAC), 4 had IPMN with in situ adenocarcinoma, 5 had ampullary adenocarcinomas, 2 had IPMNs and 3 had benign diseases. In pathologic stage II or higher PDAC, moderate or high expression of S100A8 or S100A9 proteins was associated with a median disease recurrence-free survival of 5.8 months compared to 17.3 months in patients with low expression (p=0.002). Median overall survival was 12.6 versus 27 months for patients with moderate to high versus low S100A8 and A9 expression (p=0.02).
Conclusions
This analysis suggests distinct proteomic signatures for pancreatic cancer. Patients in our study with elevated levels of S100A8 or A9 in the ductal fluid, a near absence of pancreatic enzymes, and high levels of mucins, were found to have significantly worse prognosis. Although further validation is needed to corroborate these findings, analysis of pancreatic ductal fluid is a promising tool for identifying biomarkers of interest.
doi:10.1097/MPA.0b013e3182a6867e
PMCID: PMC3859961  PMID: 24326364
PDAC; pancreatic duct fluid; cyst fluid; proteomic biomarkers; mucin; S100
2.  708 common and 2,010 rare DISC1 locus variants identified in 1,542 subjects: analysis for association with psychiatric disorder and cognitive traits 
Molecular psychiatry  2013;19(6):668-675.
A balanced t(1;11) translocation which transects the Disrupted in schizophrenia 1 (DISC1) gene shows genome-wide significant linkage for schizophrenia and recurrent major depressive disorder in a single large Scottish family, but genome-wide and exome sequencing-based association studies have not supported a role for DISC1 in psychiatric illness. To explore DISC1 in more detail, we sequenced 528 kb of the DISC1 locus in 653 cases and 889 controls. We report 2,718 validated single nucleotide polymorphisms of which 2,010 have a minor allele frequency of less than 1%. Only 38% of these variants are reported in the 1000 Genomes Project European subset. This suggests that many DISC1 SNPs remain undiscovered and are essentially private. Rare coding variants identified exclusively in patients were found in likely functional protein domains. Significant region-wide association was observed between rs16856199 and recurrent major depressive disorder (P=0.026, unadjusted P=6.3 × 10−5, OR=3.48). This was not replicated in additional recurrent major depression samples (replication P=0.11). Combined analysis of both the original and replication set supported the original association (P=0.0058, OR=1.46). Evidence for segregation of this variant with disease in families was limited to those of rMDD individuals referred from primary care. Burden analysis for coding and non-coding variants gave nominal associations with diagnosis and measures of mood and cognition. Together, these observations are likely to generalise to other candidate genes for major mental illness and may thus provide guidelines for the design of future studies.
doi:10.1038/mp.2013.68
PMCID: PMC4031635  PMID: 23732877
3.  Long Non-Coding RNA NEAT1 Associates with SRp40 to Temporally Regulate PPARγ2 Splicing during Adipogenesis in 3T3-L1 Cells 
Genes  2014;5(4):1050-1063.
Long non-coding (lnc) RNAs serve a multitude of functions in cells. NEAT1 RNA is a highly abundant 4 kb lncRNA in nuclei, and coincides with paraspeckles, nuclear domains that control sequestration of paraspeckle proteins. We examined NEAT1 RNA levels and its function in 3T3-L1 cells during differentiation to adipocytes. Levels of NEAT1 transcript, measured by RT-PCR, fluctuated in a temporal manner over the course of differentiation that suggested its role in alternative splicing of PPARγ mRNA, the major transcription factor driving adipogenesis. When cells were induced to differentiate by a media cocktail of insulin, dexamethasone, and isobutylmethyxanthine (IBMX) on Day 0, NEAT1 levels dropped on Day 4, when the PPARγ2 variant was spliced and when terminal differentiation occurs The appearance of PPARγ2 coordinates with the PPARγ1 variant to drive differentiation of adipocytes. SiRNA used to deplete NEAT1 resulted in the inability of cells to phosphorylate the serine/arginine-rich splicing protein, SRp40. SiRNA treatment for SRp40 resulted in dysregulation of PPARγ1 and, primarily, PPARγ2 mRNA levels. SRp40 associated with NEAT1, as shown by RNA-IP on days 0 and 8, but decreased on day 4, and concentrations increased over that of IgG control. Overexpression of SRp40 increased PPARγ2, but not γ1. Although lncRNA MALAT1 has been investigated in SR protein function, NEAT1 has not been shown to bind SR proteins for phosphorylation such that alternative splicing results. The ability of cells to increase phosphorylated SR proteins for PPARγ2 splicing suggests that fluxes in NEAT1 levels during adipogenesis regulate alternative splicing events.
doi:10.3390/genes5041050
PMCID: PMC4276926  PMID: 25437750
lncRNA; NEAT1; 3T3-L1 cells; adipogenesis; SR proteins
4.  Achieving Open Access to Conservation Science 
Conservation Biology  2014;28(6):1550-1557.
Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay-per-view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per-article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation-oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees.
Obtención de Acceso Abierto a la Ciencia de la Conservación
Resumen
La ciencia de la conservación es una disciplina de crisis en la que los resultados del cuestionamiento científico deben hacerse disponibles de manera rápida para quienes están implementando el manejo. Evaluamos la extensión a la cual está disponible para el público la investigación científica publicada desde el año 2000 en 20 revistas de ciencia de la conservación. De los 19, 207 artículos publicados, 1, 667 (8.68%) están libres para descargar de un repositorio oficial. Además, sólo 938 artículos (4.88%) cumplen con la definición estándar de acceso abierto en la cual el material puede reutilizarse libremente siempre y cuando se le dé atribución a los autores. Esto se compara pobremente con un conjunto comparable de 20 revistas de biología evolutiva, donde 31.93% de los artículos están libres para descargar y el 7.94% son de acceso abierto. Diecisiete de las 20 revistas de conservación ofrecen una opción de acceso abierto, pero menos del 5% de los artículos están disponibles por medio del acceso abierto. El costo de acceder al cuerpo completo de la ciencia de la conservación llega a estar entre los miles de dólares por año para suscriptores institucionales, y muchos practicantes de la conservación no pueden acceder a la ciencia de paga en sus lugares de trabajo. Sin embargo, iniciativas importantes como Research4Life están poniendo a la ciencia a disponibilidad de organizaciones en países en desarrollo. Urgimos a los autores de la ciencia de la conservación que paguen por acceso abierto en una base por artículo o que escojan publicar en revistas de acceso abierto, tomando en consideración asegurar que la licencia permita reutilizar siempre y cuando se proporcione atribución. Actualmente, costaría $51 millones hacer que toda la ciencia de la conservación publicada desde 2000 esté disponible libremente al pagar las cuotas de acceso abierto que actualmente impuestas a los autores. Los publicadores de revistas de la conservación pueden considerar modelos más rentables para el acceso abierto y las organizaciones orientadas a la conservación que administran revistas podrían considerar un campo más amplio de opciones de acceso abierto para quienes no son miembros, como el patrocinio de acceso abierto por medio de pagos de membrecía
doi:10.1111/cobi.12346
PMCID: PMC4241051  PMID: 25158824
communications; ethics; funding; governance; philanthropy; policy; comunicación; ética; filantropía; financiamiento; gobernanza; política
5.  Biodiversity Conservation in a Changing Climate: A Review of Threats and Implications for Conservation Planning in Myanmar 
Ambio  2013;42(7):789-804.
High levels of species richness and endemism make Myanmar a regional priority for conservation. However, decades of economic and political sanctions have resulted in low conservation investment to effectively tackle threats to biodiversity. Recent sweeping political reforms have placed Myanmar on the fast track to economic development—the expectation is increased economic investments focused on the exploitation of the country’s rich, and relatively intact, natural resources. Within a context of weak regulatory capacity and inadequate environmental safeguards, rapid economic development is likely to have far-reaching negative implications for already threatened biodiversity and natural-resource-dependent human communities. Climate change will further exacerbate prevailing threats given Myanmar’s high exposure and vulnerability. The aim of this review is to examine the implications of increased economic growth and a changing climate within the larger context of biodiversity conservation in Myanmar. We summarize conservation challenges, assess direct climatological impacts on biodiversity and conclude with recommendations for long-term adaptation approaches for biodiversity conservation.
doi:10.1007/s13280-013-0423-5
PMCID: PMC3790132  PMID: 23868440
Myanmar; Climate change; Economic development; Protected areas; Biodiversity; Threats
6.  Tackling antibiotic resistance 
Nature reviews. Microbiology  2011;9(12):894-896.
The development and spread of antibiotic resistance in bacteria is a universal threat to both humans and animals that is generally not preventable, but can nevertheless be controlled and must be tackled in the most effective ways possible. To explore how the problem of antibiotic resistance might best be addressed, a group of thirty scientists from academia and industry gathered at the Banbury Conference Centre in Cold Spring Harbor, New York, May 16-18, 2011. From these discussions emerged a priority list of steps that need to be taken to resolve this global crisis.
doi:10.1038/nrmicro2693
PMCID: PMC4206945  PMID: 22048738
7.  Efficacy of Selective PDE4D Negative Allosteric Modulators in the Object Retrieval Task in Female Cynomolgus Monkeys (Macaca fascicularis) 
PLoS ONE  2014;9(7):e102449.
Cyclic adenosine monophosphate (cAMP) signalling plays an important role in synaptic plasticity and information processing in the hippocampal and basal ganglia systems. The augmentation of cAMP signalling through the selective inhibition of phosphodiesterases represents a viable strategy to treat disorders associated with dysfunction of these circuits. The phosphodiesterase (PDE) type 4 inhibitor rolipram has shown significant pro-cognitive effects in neurological disease models, both in rodents and primates. However, competitive non-isoform selective PDE4 inhibitors have a low therapeutic index which has stalled their clinical development. Here, we demonstrate the pro-cognitive effects of selective negative allosteric modulators (NAMs) of PDE4D, D159687 and D159797 in female Cynomolgous macaques, in the object retrieval detour task. The efficacy displayed by these NAMs in a primate cognitive task which engages the corticostriatal circuitry, together with their suitable pharmacokinetic properties and safety profiles, suggests that clinical development of these allosteric modulators should be considered for the treatment of a variety of brain disorders associated with cognitive decline.
doi:10.1371/journal.pone.0102449
PMCID: PMC4106781  PMID: 25050979
8.  Targeting Global Protected Area Expansion for Imperiled Biodiversity 
PLoS Biology  2014;12(6):e1001891.
Meeting international targets for expanding protected areas could simultaneously contribute to species conservation, but only if the distribution of threatened species informs the future establishment of protected areas.
Governments have agreed to expand the global protected area network from 13% to 17% of the world's land surface by 2020 (Aichi target 11) and to prevent the further loss of known threatened species (Aichi target 12). These targets are interdependent, as protected areas can stem biodiversity loss when strategically located and effectively managed. However, the global protected area estate is currently biased toward locations that are cheap to protect and away from important areas for biodiversity. Here we use data on the distribution of protected areas and threatened terrestrial birds, mammals, and amphibians to assess current and possible future coverage of these species under the convention. We discover that 17% of the 4,118 threatened vertebrates are not found in a single protected area and that fully 85% are not adequately covered (i.e., to a level consistent with their likely persistence). Using systematic conservation planning, we show that expanding protected areas to reach 17% coverage by protecting the cheapest land, even if ecoregionally representative, would increase the number of threatened vertebrates covered by only 6%. However, the nonlinear relationship between the cost of acquiring land and species coverage means that fivefold more threatened vertebrates could be adequately covered for only 1.5 times the cost of the cheapest solution, if cost efficiency and threatened vertebrates are both incorporated into protected area decision making. These results are robust to known errors in the vertebrate range maps. The Convention on Biological Diversity targets may stimulate major expansion of the global protected area estate. If this expansion is to secure a future for imperiled species, new protected areas must be sited more strategically than is presently the case.
Author Summary
Under the Convention on Biological Diversity (CBD), governments have agreed to ambitious targets for expanding the global protected area network that could drive the greatest surge in new protected areas in history. They have also agreed to arrest the decline of known threatened species. However, existing protected areas perform poorly for coverage of threatened species, with only 15% of threatened vertebrates being adequately represented. Moreover, we find that if future protected area expansion continues in a business-as-usual fashion, threatened species coverage will increase only marginally. This is because low-cost priorities for meeting the CBD targets have little overlap with priorities for threatened species coverage. Here we propose a method for averting this outcome, by linking threatened species coverage to protected area expansion. Our analyses clearly demonstrate that considerable increases in protected area coverage of species could be achieved at minimal additional cost. Exploiting this opportunity will require directly linking the CBD targets on protected areas and threatened species, thereby formalizing the interdependence of these key commitments.
doi:10.1371/journal.pbio.1001891
PMCID: PMC4068989  PMID: 24960185
9.  First Identification of Resident and Circulating Fibrocytes in Dupuytren’s Disease Shown to Be Inhibited by Serum Amyloid P and Xiapex 
PLoS ONE  2014;9(6):e99967.
Dupuytren’s disease (DD) is a common progressive fibroproliferative disorder causing permanent digital contracture. Proliferative myofibroblasts are thought to be the cells responsible for DD initiation and recurrence, although their source remains unknown. DD tissue has also been shown to harbor mesenchymal and hematopoietic stem cells. Fibrocytes are circulating cells that show characteristics of fibroblasts and they express surface markers for both hematopoietic and mesenchymal stromal cells. Fibrocytes differentiate from peripheral CD14+ mononuclear cells, which can be inhibited by serum amyloid P (SAP). In this study we have demonstrated the presence of fibrocytes in DD blood and tissue, moreover we have evaluated the effects of SAP and Xiapex (Collagenase Clostridium histolyticum) on fibrocytes derived from DD. H&E staining showed typical Spindle shaped morphology of fibrocytes. FACS analysis based on a unique combination of 3 markers, revealed the increased presence of fibrocytes in blood and tissue of DD patients. Additionally, immunohistology of DD nodule and cord tissue showed the presence of collagen 1+/CD34+ cells. No difference in plasma SAP levels was observed between DD and control. Higher concentrations of SAP significantly inhibited fibrocytes differentiated from DD derived monocytes compared to control. DD fascia derived fibrocytes showed resistance to growth inhibition by SAP, particularly nodule derived fibrocytes showed robust growth even at higher SAP concentrations compared to control. DD derived fibrocytes were positive for typical fibrocyte dual markers, i.e. Collagen 1/LSP-1 and collagen 1/CD34. Xiapex was more effective in inhibiting the growth of nodule derived cells compared to commercially available collagenase A. Our results show for the first time the increased presence of fibrocytes in DD patient’s blood and disease tissue compared to control tissue. Additionally, we evaluate the response of these fibrocytes to SAP and Xiapex therapy.
doi:10.1371/journal.pone.0099967
PMCID: PMC4059720  PMID: 24933153
10.  Conserved features of cancer cells define their sensitivity of HAMLET-induced death; c-Myc and glycolysis 
Oncogene  2011;30(48):4765-4779.
HAMLET is the first member of a new family of tumoricidal protein-lipid complexes that kill cancer cells broadly, while sparing healthy, differentiated cells. Many and diverse tumor cell types are sensitive to the lethal effect, suggesting that HAMLET identifies and activates conserved death pathways in cancer cells. Here we investigated the molecular basis for the difference in sensitivity between cancer cells and healthy cells. Using a combination of small hairpin RNA inhibition, proteomic and metabolomic technology we identified the c-Myc oncogene as one essential determinant of HAMLET sensitivity. Increased c-Myc expression levels promoted the sensitivity to HAMLET and shRNA knockdown of c-Myc suppressed the lethal response, suggesting that oncogenic transformation with c-Myc creates a HAMLET-sensitive phenotype. Furthermore, the HAMLET sensitivity was modified by the glycolytic state of the tumor cells. Glucose deprivation sensitized tumor cells to HAMLET-induced cell death and in the shRNA screen Hexokinase 1, PFKFB1 and HIF1α modified HAMLET sensitivity. Hexokinase 1 was shown to bind HAMLET in a protein array containing approximately 8000 targets and Hexokinase activity decreased within 15 minutes of HAMLET treatment, prior to morphological signs of tumor cell death. In parallel, HAMLET triggered rapid metabolic paralysis in carcinoma cells. The glycolytic machinery was modified and glycolysis was shifted towards the pentose phosphate pathway. Tumor cells were also shown to contain large amounts of oleic acid and its derivatives already after 15 minutes. The results identify HAMLET as a novel anti-cancer agent that kills tumor cells by exploiting unifying features of cancer cells such as oncogene-addiction or the Warburg effect.
doi:10.1038/onc.2011.196
PMCID: PMC4041205  PMID: 21643007
HAMLET; metabolism; c-Myc; glycolysis
11.  Pulse oximetry-derived respiratory rate in general care floor patients 
Respiratory rate is recognized as a clinically important parameter for monitoring respiratory status on the general care floor (GCF). Currently, intermittent manual assessment of respiratory rate is the standard of care on the GCF. This technique has several clinically-relevant shortcomings, including the following: (1) it is not a continuous measurement, (2) it is prone to observer error, and (3) it is inefficient for the clinical staff. We report here on an algorithm designed to meet clinical needs by providing respiratory rate through a standard pulse oximeter. Finger photoplethysmograms were collected from a cohort of 63 GCF patients monitored during free breathing over a 25-min period. These were processed using a novel in-house algorithm based on continuous wavelet-transform technology within an infrastructure incorporating confidence-based averaging and logical decision-making processes. The computed oximeter respiratory rates (RRoxi) were compared to an end-tidal CO2 reference rate (RRETCO2). RRETCO2 ranged from a lowest recorded value of 4.7 breaths per minute (brpm) to a highest value of 32.0 brpm. The mean respiratory rate was 16.3 brpm with standard deviation of 4.7 brpm. Excellent agreement was found between RRoxi and RRETCO2, with a mean difference of −0.48 brpm and standard deviation of 1.77 brpm. These data demonstrate that our novel respiratory rate algorithm is a potentially viable method of monitoring respiratory rate in GCF patients. This technology provides the means to facilitate continuous monitoring of respiratory rate, coupled with arterial oxygen saturation and pulse rate, using a single non-invasive sensor in low acuity settings.
doi:10.1007/s10877-014-9575-5
PMCID: PMC4309914  PMID: 24796734
Respiratory rate; Pulse oximeter; Continuous monitoring; Low acuity monitoring
12.  Comparison of Markers and Functional Attributes of Human Adipose-Derived Stem Cells and Dedifferentiated Adipocyte Cells from Subcutaneous Fat of an Obese Diabetic Donor 
Advances in Wound Care  2014;3(3):219-228.
Objective: Adipose tissue is a robust source of adipose-derived stem cells (ADSCs) that may be able to provide secreted factors that promote the ability of wounded tissue to heal. However, adipocytes also have the potential to dedifferentiate in culture to cells with stem cell-like properties that may improve their behavior and functionality for certain applications.
Approach: ADSCs are adult mesenchymal stem cells that are cultured from the stromal vascular fraction of adipose tissue. However, adipocytes are capable of dedifferentiating into cells with stem cell properties. In this case study, we compare ADSC and dedifferentiated fat (DFAT) cells from the same patient and fat depot for mesenchymal cell markers, embryonic stem cell markers, ability to differentiate to adipocytes and osteoblasts, senescence and telomerase levels, and ability of conditioned media (CM) to stimulate migration of human dermal fibroblasts (HDFs).
Innovation and Conclusions: ADSCs and DFAT cells displayed identical levels of CD90, CD44, CD105, and were CD34- and CD45-negative. They also expressed similar levels of Oct4, BMI1, KLF4, and SALL4. DFAT cells, however, showed higher efficiency in adipogenic and osteogenic capacity. Telomerase levels of DFAT cells were double those of ADSCs, and senescence declined in DFAT cells. CM from both cell types altered the migration of fibroblasts. Despite reports of ADSCs from a number of human depots, there have been no comparisons of the ability of dedifferentiated DFAT cells from the same donor and depot to differentiate or modulate migration of HDFs. Since ADSCs were from an obese diabetic donor, reprogramming of DFAT cells may help improve a patient's cells for regenerative medicine applications.
doi:10.1089/wound.2013.0452
PMCID: PMC3955970  PMID: 24669358
13.  Phase II Trial of Neoadjuvant/adjuvant Imatinib Mesylate for Advanced Primary and Metastatic/recurrent Operable Gastrointestinal Stromal Tumors: Long-term Follow-up Results of Radiation Therapy Oncology Group 0132 
Annals of surgical oncology  2011;19(4):1074-1080.
Background
Imatinib inhibits the KIT and PDGFR tyrosine kinases, resulting in its notable antitumor activity in gastrointestinal stromal tumor (GIST). We previously reported the early results of a multi-institutional prospective trial (RTOG 0132) using neoadjuvant/adjuvant imatinib either in primary resectable GIST or as a planned preoperative cytoreduction agent for metastatic/recurrent GIST.
Methods
Patients with primary GIST (≥5 cm, group A) or resectable metastatic/recurrent GIST (≥2 cm, group B) received neoadjuvant imatinib (600 mg/day) for approximately 2 months and maintenance postoperative imatinib for 2 years. We have now updated the clinical outcomes including progression-free survival, disease-specific survival, and overall survival at a median follow-up of 5.1 years, and we correlate these end points with duration of imatinib therapy.
Results
Sixty-three patients were originally entered (53 analyzable: 31 in group A and 22 in group B). Estimated 5-year progression-free survival and overall survival were 57% in group A, 30% in group B; and 77% in group A, 68% in group B, respectively. Median time to progression has not been reached for group A and was 4.4 years for group B. In group A, in 7 of 11 patients, disease progressed >2 years from registration; 6 of 7 patients with progression had stopped imatinib before progression. In group B, disease progressed in 10 of 13 patients >2 years from registration; 6 of 10 patients with progressing disease had stopped imatinib before progression. There was no significant increase in toxicity compared with our previous shortterm analysis.
Conclusions
This long-term analysis suggests a high percentage of patients experienced disease progression after discontinuation of 2-year maintenance imatinib therapy after surgery. Consideration should be given to studying longer treatment durations in intermediate- to high-risk GIST patients.
doi:10.1245/s10434-011-2190-5
PMCID: PMC3800166  PMID: 22203182
14.  Identification of the Plasmodium berghei resistance locus 9 linked to survival on chromosome 9 
Malaria Journal  2013;12:316.
Background
One of the main causes of mortality from severe malaria in Plasmodium falciparum infections is cerebral malaria (CM). An important host genetic component determines the susceptibility of an individual to develop CM or to clear the infection and become semi-immune. As such, the identification of genetic loci associated with susceptibility or resistance may serve to modulate disease severity.
Methodology
The Plasmodium berghei mouse model for experimental cerebral malaria (ECM) reproduces several disease symptoms seen in human CM, and two different phenotypes, a susceptible (FVB/NJ) and a resistant mouse strain (DBA/2J), were examined.
Results
FVB/NJ mice died from infection within ten days, whereas DBA/2J mice showed a gender bias: males survived on average nineteen days and females either died early with signs of ECM or survived for up to three weeks. A comparison of brain pathology between FVB/NJ and DBA/2J showed no major differences with regard to brain haemorrhages or the number of parasites and CD3+ cells in the microvasculature. However, significant differences were found in the peripheral blood of infected mice: For example resistant DBA/2J mice had significantly higher numbers of circulating basophils than did FVB/NJ mice on day seven. Analysis of the F2 offspring from a cross of DBA/2J and FVB/NJ mice mapped the genetic locus of the underlying survival trait to chromosome 9 with a Lod score of 4.9. This locus overlaps with two previously identified resistance loci (char1 and pymr) from a blood stage malaria model.
Conclusions
Survival best distinguishes malaria infections between FVB/NJ and DBA/2J mice. The importance of char1 and pymr on chromosome 9 in malaria resistance to P. berghei was confirmed. In addition there was an association of basophil numbers with survival.
doi:10.1186/1475-2875-12-316
PMCID: PMC3848760  PMID: 24025732
Plasmodium berghei; Experimental cerebral malaria; Quantitative trait locus; Malaria; Basophil; Chromosome mapping; Mouse
15.  The Nucleus Accumbens as a Potential Target for Central Poststroke Pain 
Mayo Clinic Proceedings  2012;87(10):1025-1031.
Although deep brain stimulation (DBS) has been found to be efficacious for some chronic pain syndromes, its usefulness in patients with central poststroke pain (CPSP) has been disappointing. The most common DBS targets for pain are the periventricular gray region (PVG) and the ventralis caudalis of the thalamus. Despite the limited success of DBS for CPSP, few alternative targets have been explored. The nucleus accumbens (NAC), a limbic structure within the ventral striatum that is involved in reward and pain processing, has emerged as an effective target for psychiatric disease. There is also evidence that it may be an effective target for pain. We describe a 72-year-old woman with a large right hemisphere infarct who subsequently experienced refractory left hemibody pain. She underwent placement of 3 electrodes in the right PVG, ventralis caudalis of the thalamus, and NAC. Individual stimulation of the NAC and PVG provided substantial improvement in pain rating. The patient underwent implantation of permanent electrodes in both targets, and combined stimulation has provided sustained pain relief at nearly 1 year after the procedure. These results suggest that the NAC may be an effective DBS target for CPSP.
doi:10.1016/j.mayocp.2012.02.029
PMCID: PMC3498057  PMID: 22980165
CPSP, central poststroke pain; DBS, deep brain stimulation; ECT, electroconvulive therapy; ICL, intercommissural line; MCS, motor cortex stimulation; NAC, nucleus accumbens; PFC, prefrontal cortex; PVG, periventricular gray region; VC, ventralis caudalis of the thalamus
16.  RTOG 0247: A Randomized Phase II Study of Neoadjuvant Capecitabine and Irinotecan or Capecitabine and Oxaliplatin with Concurrent Radiation Therapy for Patients with Locally Advanced Rectal Cancer 
Purpose
To evaluate rate of pathologic complete response (pCR) and toxicity of two neoadjuvant chemoradiation (chemoRT) regimens for T3/T4 rectal cancer in a randomized phase II study.
Methods and Materials
Patients with T3 or T4 rectal cancer < 12 cm from the anal verge were randomized to preoperative RT (50.4 Gy in 1.8 Gy fractions) with (1) concurrent capecitabine (1200 mg/m2/d M-F) and irinotecan (50 mg/m2 weekly × 4 doses) (arm 1), or (2) concurrent capecitabine (1650 mg/m2/d M-F) and oxaliplatin (50 mg/m2 weekly × 5 doses) (arm 2). Surgery was performed 4–8 weeks after chemoRT, and adjuvant chemotherapy 4–6 weeks after surgery. The primary endpoint was pCR rate, requiring 48 evaluable patients per arm.
Results
146 patients were enrolled. Protocol chemotherapy was modified due to excessive GI toxicity after treatment of 35 patients; 96 were assessed for the primary endpoint—final regimen described above. Patient characteristics were similar for both arms. Following chemoRT, tumor downstaging was 52% and 60%, and nodal downstaging (excluding N0 patients) was 46% and 40%, for arms 1 and 2, respectively. The pCR rate for arm 1 was 10% and for arm 2 was 21%. For arms 1 and 2, respectively, preop chemoRT grade 3/4 hematologic toxicity was 9% and 4%, and grade 3/4 non-hematologic toxicity was 26% and 27%.
Conclusions
Preoperative chemoRT with capecitabine plus oxaliplatin for distal rectal cancer has significant clinical activity (10/48 pCRs) and acceptable toxicity. This regimen is currently being evaluated in a phase III randomized trial (NSABP R04).
doi:10.1016/j.ijrobp.2011.05.027
PMCID: PMC3208721  PMID: 21775070
Neoadjuvant; chemotherapy; radiation; rectal; cancer
17.  Clk/STY (cdc2-Like Kinase 1) and Akt Regulate Alternative Splicing and Adipogenesis in 3T3-L1 Pre-Adipocytes 
PLoS ONE  2013;8(1):e53268.
The development of adipocytes from their progenitor cells requires the action of growth factors signaling to transcription factors to induce the expression of adipogenic proteins leading to the accumulation of lipid droplets, induction of glucose transport, and secretion of adipokines signaling metabolic events throughout the body. Murine 3T3-L1 pre-adipocytes sequentially express all the proteins necessary to become mature adipocytes throughout an 8–10 day process initiated by a cocktail of hormones. We examined the role of Clk/STY or Clk1, a cdc2-like kinase, in adipogenesis since it is known to be regulated by Akt, a pivotal kinase in development. Inhibition of Clk1 by a specific inhibitor, TG003, blocked alternative splicing of PKCβII and expression of PPARγ1 and PPARγ2. SiRNA depletion of Clk1 resulted in early expression of PKCβII and sustained PKCβI expression. Since Clk1 is a preferred Akt substrate, required for phosphorylation of splicing factors, mutation of Clk1 Akt phosphorylation sites was undertaken. Akt sites on Clk1 are in the serine/arginine-rich domain and not the kinase domain. Mutation of single and multiple sites resulted in dysregulation of PKCβII, PKCβI, and PPARγ1&2 expression. Additionally, adipogenesis was blocked as assessed by Oil Red O staining, adiponectin, and Glut1 and 4 expression. Immunofluorescence microscopy revealed that Clk1 triple mutant cDNA, transfected into pre-adipocytes, resulted in excluding SRp40 (SFSR6) from co-localizing to the nucleus with PFS, a perispeckle specific protein. This study demonstrates the role of Akt and Clk1 kinases in the early differentiation of 3T3-L1 cells to adipocytes.
doi:10.1371/journal.pone.0053268
PMCID: PMC3537621  PMID: 23308182
18.  Housing Characteristics and their Influence on Health-Related Quality of Life in Persons Living with HIV in Ontario, Canada: Results from the Positive Spaces, Healthy Places Study 
AIDS and Behavior  2012;16(8):2361-2373.
Although lack of housing is linked with adverse health outcomes, little is known about the impacts of the qualitative aspects of housing on health. This study examined the association between structural elements of housing, housing affordability, housing satisfaction and health-related quality of life over a 1-year period. Participants were 509 individuals living with HIV in Ontario, Canada. Regression analyses were conducted to examine relationships between housing variables and physical and mental health-related quality of life. We found significant cross-sectional associations between housing and neighborhood variables—including place of residence, housing affordability, housing stability, and satisfaction with material, meaningful and spatial dimensions of housing—and both physical and mental health-related quality of life. Our analyses also revealed longitudinal associations between housing and neighborhood variables and health-related quality of life. Interventions that enhance housing affordability and housing satisfaction may help improve health-related quality of life of people living with HIV.
doi:10.1007/s10461-012-0284-0
PMCID: PMC3481053  PMID: 22903401
Housing; Housing affordability; Housing satisfaction; Health-related quality of life; HIV
19.  Target Selection and Determination of Function in Structural Genomics 
Iubmb Life  2003;55(4-5):249-255.
Summary
The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.
doi:10.1080/1521654031000123385
PMCID: PMC3366504  PMID: 12880206
Structural genomics; target selection; function from structure; functional annotation
20.  CXCR4 Expression in Prostate Cancer Progenitor Cells 
PLoS ONE  2012;7(2):e31226.
Tumor progenitor cells represent a population of drug-resistant cells that can survive conventional chemotherapy and lead to tumor relapse. However, little is known of the role of tumor progenitors in prostate cancer metastasis. The studies reported herein show that the CXCR4/CXCL12 axis, a key regulator of tumor dissemination, plays a role in the maintenance of prostate cancer stem-like cells. The CXCL4/CXCR12 pathway is activated in the CD44+/CD133+ prostate progenitor population and affects differentiation potential, cell adhesion, clonal growth and tumorigenicity. Furthermore, prostate tumor xenograft studies in mice showed that a combination of the CXCR4 receptor antagonist AMD3100, which targets prostate cancer stem-like cells, and the conventional chemotherapeutic drug Taxotere, which targets the bulk tumor, is significantly more effective in eradicating tumors as compared to monotherapy.
doi:10.1371/journal.pone.0031226
PMCID: PMC3281066  PMID: 22359577
21.  Phase II and Coagulation Cascade Biomarker Study of Bevacizumab with or without Docetaxel in Patients with Previously Treated Metastatic Pancreatic Adenocarcinoma 
Purpose
Treatment options are limited for advanced pancreatic cancer progressive after gemcitabine therapy. The vascular endothelial growth factor (VEGF) pathway is biologically important in pancreatic cancer, and docetaxel has modest anti-tumor activity. We evaluated the role of the anti-VEGF antibody bevacizumab as second-line treatment for patients with metastatic pancreatic cancer.
Design
Patients with metastatic adenocarcinoma of the pancreas who had progressive disease on a gemcitabine-containing regimen were randomized to receive bevacizumab alone or bevacizumab in combination with docetaxel.
Results
Thirty-two patients were enrolled; 16 to bevacizumab alone (Arm A) and 16 to bevacizumab plus docetaxel (Arm B). Toxicities were greater in Arm B with the most common grade 3/4 nonhematologic toxicities including fatigue, diarrhea, dehydration and anorexia. No confirmed objective responses were observed. At 4 months, 2/16 patients in Arm A and 3/16 in Arm B were free from progression. The study was stopped according to the early stopping rule for futility. Median PFS and OS were 43 days and 165 days in Arm A and 48 days and 125 days in Arm B. Elevated D-dimer levels and thrombin-antithrombin complexes were associated with decreased survival and increased toxicity.
Conclusion
Bevacizumab with or without docetaxel does not have antitumor activity in gemcitabine-refractory metastatic pancreatic cancer. Baseline and on-treatment D-dimer and thrombin-antithrombin complex levels are associated with increased toxicity and decreased survival.
doi:10.1097/COC.0b013e3181d2734a
PMCID: PMC3030655  PMID: 20458210
22.  Developing an algorithm for pulse oximetry derived respiratory rate (RRoxi): a healthy volunteer study 
Objective The presence of respiratory information within the pulse oximeter signal (PPG) is a well-documented phenomenon. However, extracting this information for the purpose of continuously monitoring respiratory rate requires: (1) the recognition of the multi-faceted manifestations of respiratory modulation components within the PPG and the complex interactions among them; (2) the implementation of appropriate advanced signal processing techniques to take full advantage of this information; and (3) the post-processing infrastructure to deliver a clinically useful reported respiratory rate to the end user. A holistic algorithmic approach to the problem is therefore required. We have developed the RROXI algorithm based on this principle and its performance on healthy subject trial data is described herein.
Methods Finger PPGs were collected from a cohort of 139 healthy adult volunteers monitored during free breathing over an 8-min period. These were subsequently processed using a novel in-house algorithm based on continuous wavelet transform technology within an infrastructure incorporating weighted averaging and logical decision making processes. The computed oximeter respiratory rates (RRoxi) were then compared to an end-tidal CO2 reference rate (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {\text{RR}}_{{{\text{ETCO}}_{ 2} }} $$\end{document}).
Results\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {\text{RR}}_{{{\text{ETCO}}_{ 2} }} $$\end{document} ranged from a lowest recorded value of 2.97 breaths per min (br/min) to a highest value of 28.02 br/min. The mean rate was 14.49 br/min with standard deviation of 4.36 br/min. Excellent agreement was found between RRoxi and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {\text{RR}}_{{{\text{ETCO}}_{ 2} }} $$\end{document}, with a mean difference of −0.23 br/min and standard deviation of 1.14 br/min. The two measures are tightly spread around the line of agreement with a strong correlation observable between them (R2 = 0.93).
Conclusions These data indicate that RRoxi represents a viable technology for the measurement of respiratory rate of healthy individuals.
doi:10.1007/s10877-011-9332-y
PMCID: PMC3268017  PMID: 22231359
Respiratory rate; Pulse oximeter; Continuous monitoring
23.  Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers 
Briefings in Bioinformatics  2011;13(3):383-389.
Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.
doi:10.1093/bib/bbr064
PMCID: PMC3357490  PMID: 22110242
Bioinformatics; training; end users; bioinformatics courses; learning bioinformatics
24.  Efficient Use and Recycling of the Micronutrient Iodide in Mammals 
Biochimie  2010;92(9):1227-1235.
Daily ingestion of iodide alone is not adequate to sustain production of the thyroid hormones, tri- and tetraiodothyronine. Proper maintenance of iodide in vivo also requires its active transport into the thyroid and its salvage from mono- and diiodotyrosine that are formed in excess during hormone biosynthesis. The enzyme iodotyrosine deiodinase responsible for this salvage is unusual in its ability to catalyze a reductive dehalogenation reaction dependent on a flavin cofactor, FMN. Initial characterization of this enzyme was limited by its membrane association, difficult purification and poor stability. The deiodinase became amenable to detailed analysis only after identification and heterologous expression of its gene. Site-directed mutagenesis recently demonstrated that cysteine residues are not necessary for enzymatic activity in contrast to precedence set by other reductive dehalogenases. Truncation of the N-terminal membrane anchor of the deiodinase has provided a soluble and stable source of enzyme sufficient for crystallographic studies. The structure of an enzyme•substrate co-crystal has become invaluable for understanding the origins of substrate selectivity and the mutations causing thyroid disease in humans.
doi:10.1016/j.biochi.2010.02.013
PMCID: PMC2888766  PMID: 20167242
Deiodinase; Flavoprotein; Reductive Dehalogenation; Iodide Metabolism; Thyroid
25.  Investing in Threatened Species Conservation: Does Corruption Outweigh Purchasing Power? 
PLoS ONE  2011;6(7):e22749.
In many sectors, freedom in capital flow has allowed optimization of investment returns through choosing sites that provide the best value for money. These returns, however, can be compromised in countries where corruption is prevalent. We assessed where the best value for money might be obtained for investment in threatened species that occur at a single site, when taking into account corruption. We found that the influence of corruption on potential investment decisions was outweighed by the likely value for money in terms of pricing parity. Nevertheless global conservation is likely to get best returns in terms of threatened species security by investing in “honest” countries than in corrupt ones, particularly those with a high cost of living.
doi:10.1371/journal.pone.0022749
PMCID: PMC3144939  PMID: 21818383

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