Personalized medicine is predicated on the concept of identifying subgroups of a common disease for better treatment. Identifying biomarkers that predict disease subtypes has been a major focus of biomedical science. In the era of genome-wide profiling, there is controversy as to the optimal number of genes as an input of a feature selection algorithm for survival modeling.
Patients and methods
The expression profiles and outcomes of 544 patients were retrieved from The Cancer Genome Atlas. We compared four different survival prediction methods: (1) 1-nearest neighbor (1-NN) survival prediction method; (2) random patient selection method and a Cox-based regression method with nested cross-validation; (3) least absolute shrinkage and selection operator (LASSO) optimization using whole-genome gene expression profiles; or (4) gene expression profiles of cancer pathway genes.
The 1-NN method performed better than the random patient selection method in terms of survival predictions, although it does not include a feature selection step. The Cox-based regression method with LASSO optimization using whole-genome gene expression data demonstrated higher survival prediction power than the 1-NN method, but was outperformed by the same method when using gene expression profiles of cancer pathway genes alone.
The 1-NN survival prediction method may require more patients for better performance, even when omitting censored data. Using preexisting biological knowledge for survival prediction is reasonable as a means to understand the biological system of a cancer, unless the analysis goal is to identify completely unknown genes relevant to cancer biology.
brain; feature selection; glioblastoma; personalized medicine; survival modeling; TCGA
Quality of life (QOL) is increasingly recognized as central to the broad construct of recovery in substance abuse services. QOL measures can supplement more objective symptom measures, identify specific service needs and document changes in functioning that are associated with substance use patterns. To date however, QOL remains an under investigated area in the addictions field, especially in the United States.
This study examines patterns and predictors of QOL at 1 and 6 months post treatment intake among 240 women enrolled in substance abuse treatment in Cleveland, Ohio. The World Health Organization Quality of Life (WHOQOL-BREF) measure was used to assess physical, psychological, social and environmental domains. Hierarchical multiple regressions were conducted to identify correlates of QOL at 6 months post treatment intake.
All QOL domains across the follow up time points improved significantly. However, QOL scores across domains remained below those of healthy population norms. Trauma symptoms significantly predicted Physical and Psychological QOL. Among treatment process variables, alcohol use was the sole significant factor associated with QOL and only for Environmental QOL. Recovery support and friends support for abstinence were consistently associated with QOL across all four domains.
This study suggests the usefulness of the WHOQOL measure as an indicator of functioning in substance abusing populations. Findings underline the importance of helping women deal with trauma symptoms and develop support for recovery. Further research is needed on the longitudinal relationship between QOL and substance use patterns
Substance use; quality of life; women; recovery; social networks
Hepatocellular carcinoma (HCC) is one of the most common and aggressive cancers and is associated with a poor survival rate. Clinically, the level of alpha-fetoprotein (AFP) has been used as a biomarker for the diagnosis of HCC. The discovery of useful biomarkers for HCC, focused solely on the proteome, has been difficult; thus, wide-ranging global data mining of genomic and proteomic databases from previous reports would be valuable in screening biomarker candidates. Further, multiple reaction monitoring (MRM), based on triple quadrupole mass spectrometry, has been effective with regard to high-throughput verification, complementing antibody-based verification pipelines. In this study, global data mining was performed using 5 types of HCC data to screen for candidate biomarker proteins: cDNA microarray, copy number variation, somatic mutation, epigenetic, and quantitative proteomics data. Next, we applied MRM to verify HCC candidate biomarkers in individual serum samples from 3 groups: a healthy control group, patients who have been diagnosed with HCC (Before HCC treatment group), and HCC patients who underwent locoregional therapy (After HCC treatment group). After determining the relative quantities of the candidate proteins by MRM, we compared their expression levels between the 3 groups, identifying 4 potential biomarkers: the actin-binding protein anillin (ANLN), filamin-B (FLNB), complementary C4-A (C4A), and AFP. The combination of 2 markers (ANLN, FLNB) improved the discrimination of the before HCC treatment group from the healthy control group compared with AFP. We conclude that the combination of global data mining and MRM verification enhances the screening and verification of potential HCC biomarkers. This efficacious integrative strategy is applicable to the development of markers for cancer and other diseases.
Mesenchymal stem cells (MSCs) are multi-potent non-hematopoietic progenitor cells possessing an immune-regulatory function, with suppression of proliferation of activated lymphocytes. In this study, adult living donor kidney transplantation (LDKT) recipients were given MSCs derived from the donor bone marrow to evaluate the safety and the feasibility of immunological changes related to the intra-osseous injection of MSC into the bone marrow.
MSCs were derived from negative HLA cross-match donors. Donor bone marrow was harvested 5 weeks prior to KT. At the time of transplantation, 1 x 106 cell/kg of donor MSC was directly injected into the bone marrow of the recipient’s right iliac bone. Patients’ clinical outcomes, presence of mixed chimerism by short tandem repeat polymerase chain reaction, analysis of plasma FoxP3 mRNA and cytokine level, and mixed lymphocyte reaction (MLR) were performed.
Seven patients enrolled in this study and received donor MSC injections simultaneously with LDKT. The median age of recipients was 36 years (32 ~ 48). The number of HLA mismatches was 3 or less in 5 and more than 3 in 2. No local complications or adverse events such as hypersensitivity occurred during or after the injection of donor MSC. There was no graft failure, but the biopsy-proven acute rejections were observed in 3 recipients during the follow-up period controlled well with steroid pulse therapy (SPT). The last serum creatinine was a median of 1.23 mg/dL (0.83 ~ 2.07). Mixed chimerism was not detected in the peripheral blood of the recipients at 1 and 8 week of post-transplantation. Donor-specific lymphocyte or T cell proliferation and Treg priming responses were observed in some patients. Plasma level of IL-10, a known mediator of MSC-induced immune suppression, increased in the patients with Treg induction.
Donor MSC injection into the iliac bone at the time of KT was feasible and safe. A possible correlation was observed between the induction of inhibitory immune responses and the clinical outcome in the MSC-kidney transplanted patients. Further research will be performed to evaluate the efficacy of MSC injection for the induction of mixed chimerism and subsequent immune tolerance in KT.
Donor MSC; Intra-osseous injection; Living Donor Kidney Transplantation (LDKT); Immune response
The aim of this study was to compare the efficacy, rebleeding rates, survival, and complications of endoscopic variceal ligation (EVL) with those of endoscopic variceal obliteration (EVO) in patients with acute type 1 gastroesophageal variceal (GOV1) bleeding. Data were collected retrospectively at a single center. A total of 84 patients were selected (20 patients underwent EVL; 64 patients underwent EVO) from February 2004 to September 2011. Their clinical characteristics, laboratory results, vital signs, Child-Pugh score, Model for End-stage Liver Disease (MELD) score, and overall mortality were evaluated. There were no significant differences in baseline characteristics between the two groups. The success rate in initial control of active bleeding was not significantly different between the EVL and EVO groups (18/20 EVL, or 90.0%, compared with 62/64 EVO, or 96.9%; p=0.239). The early rebleeding rate was also not significantly different between the groups (3/18 EVL, or 16.7% compared with 17/62 EVO, or 27.4%; p=0.422). The late rebleeding rate of the EVL group was lower than that of the EVO group (3/18 EVL, or 16.7%, compared with 26/59 EVO, or 44.1%; p=0.042). The time-to-rebleeding was 594 days for the EVL group and 326 days for the EVO group (p=0.054). In the multivariate analysis, portal vein thrombosis (PVT) was a significant risk factor for early rebleeding. Hepatocellular carcinoma (HCC) and previous history of bleeding were significant risk factors for very late rebleeding. In conclusion, EVL is better than EVO in reducing late rebleeding in acute GOV1 bleeding. HCC, PVT, and previous bleeding history were significant risk factors for rebleeding.
Esophageal and gastric varices; Hemostasis; Endoscopy; Risk factors
Structural equation modeling was used to simultaneously examine maternal psychological distress and social support as mediators linking maternal childhood trauma (MCT) to both maternal and child-reported behavior at 9 years of age in 231 birth mother-child dyads, who were primarily poor, urban, and African American. One half of the mothers (n = 116) reported a history of childhood abuse and neglect. Although MCT was associated with both increased maternal psychological distress and limited social support at 6 years, the pathway to child behavior ratings at 9 years was informant dependent. MCT influenced maternal ratings of her child’s behavior, with some effects mediated through psychological distress. MCT indirectly influenced children’s self-perception of behavior through maternal experience of social support. Maternal ratings and child self-ratings of child behavior problems were moderately correlated. No significant gender interaction was found. Findings suggest a need for understanding trauma histories in the lives of mothers who seek assistance for parenting and child behavior problems, especially in urban low income communities. Interventions targeting both increasing maternal social support and reducing psychological distress may promote competency and resiliency among children for whom MCT poses a risk to optimal development.
Maternal childhood abuse & neglect; child behavioral problems; maternal psychological distress; maternal social support; cross-informant
Anaphylactic transfusion reactions are rare complications of blood transfusions. Anhaptoglobinemia, a condition that has high incidence in Asia, can cause allergic transfusion reactions or anaphylaxis in severe cases. A 50-yr-old Korean woman was diagnosed with relapsed acute promyelocytic leukemia. She developed thrombocytopenia during chemotherapy and an anaphylactic transfusion reaction on the 4th and 5th platelet transfusions immediately after the transfusion of the platelet concentrates was initiated. Blood analysis showed no detectable serum haptoglobin. We examined her genetic phenotype and detected anhaptoglobinemia, which occurs because of an allelic deletion in the Hp gene cluster. The presence of an antibody against haptoglobin was detected by performing ELISA. To prevent anaphylactic reactions, apheresis platelets were transfused after washing. Consequently, anaphylactic transfusion reactions did not develop. Here, we report the first case of anhaptoglobinemia causing anaphylactic transfusion reaction in Korea.
Platelet transfusion; Anaphylaxis; Haptoglobin
This study examines the relationship among 4 treatment stages (i.e., engagement, persuasion, active treatment, relapse prevention) and the composition, social support, and structural characteristics of personal networks. The study sample includes 242 women diagnosed with substance dependence who were interviewed within their first month of intensive outpatient treatment. Using EgoNet software, the women reported on their 25 alter personal networks and the characteristics of each alter. With one exception, few differences were found in the network compositions at different stages of substance abuse treatment. The exception was the network composition of women in the active treatment stage, which included more network members from treatment programs or 12-Step meetings. Although neither the type nor amount of social support differed across treatment stages, reciprocity differed between women in active treatment and those in the engagement stage. Networks of women in active treatment were less connected, as indicated by a higher number of components, whereas networks of women in the persuasion stage had a higher degree of centralization, as indicated by networks dominated by people with the most ties. Overall, we find social network structural variables to relate to the stage of treatment, whereas network composition, type of social support, and sociodemographic variables (with a few exceptions) do not relate to treatment stage. Results suggest that social context, particularly how social contacts are arranged around clients, should be incorporated into treatment programs, regardless of demographic background.
women; substance dependence; social networks; treatment stage
Pegylated-interferon plus ribavirin is the standard treatment for chronic hepatitis C. Sustained virological response (SVR) rates of up to 80% are reported in genotype 2 and 3 chronic hepatitis C cases. Obesity, a modifiable risk factor, may have a deleterious effect on antiviral treatment. We performed this study to examine the efficacy and safety of pegylated-interferon and ribavirin therapy in Korean patients with genotype 2 and 3 chronic hepatitis C and to investigate the risk factors for nonresponse to antiviral treatment. A total of 121 patients were treated with peginterferon alpha-2a 180 mcg/week plus ribavirin 800 mg/day for 24 weeks. The end-of-treatment virologic response (ETVR), the SVR, the end-of-treatment biochemical response (ETBR), the sustained biochemical response (SBR), and the adverse events were analyzed. The ETVR and SVR were 94.1% and 89.1%, respectively. The ETBR was 80.2% and the SBR was 96%. Multivariate analysis showed that a body mass index of 25 and over was the only independent factor that affected the SVR (odds ratio=10.5, 95% confidence interval: 2.006-54.948, p=0.005). Twenty patients (16.5%) dropped out at the end of treatment, and 7 (5.8%) patients discontinued treatment because of treatment-related adverse events. Our study showed that combination therapy with pegylated-interferon and ribavirin as an initial treatment for genotype 2 and 3 chronic hepatitis C is very effective and safe, and that body mass index is an independent risk factor for nonresponse to antiviral treatment in patients with genotype 2 and 3 chronic hepatitis C.
Hepatitis C, chronic; Peginterferon alfa-2a; Ribavirin; Body mass Index
To better understand how sex differences in anterior knee joint laxity (AKL) impact knee joint biomechanics, we examined the consequence of greater absolute baseline (males and females) and cyclic increases in AKL during the menstrual cycle (females) on anterior tibial translation (ATT) as the knee transitioned from non-weight bearing (NWB) to weight bearing (WB) conditions, while also controlling for genu recurvatum (GR).
Males and females (71F,48M;18-30 years) were measured for AKL and GR, and underwent measurement of ATT. Females were tested on the days of their cycle when AKL was at its minimum (T1) and maximum (T2); males were matched in time to a female with similar AKL. Linear regressions examined relationships between absolute baseline (AKLT1, GRT1) and cyclic changes (Δ=T2-T1; AKLΔ, GRΔ)(females only) in knee laxity with ATT as measured at T1 and T2, and Δ (T2-T1) (females only).
AKL and GR increased in females, but not males, from T1 to T2. Greater AKLT1 and GRT1 predicted greater ATTT1 and ATTT2 in males (R2=21.0, P<.007). The combination of greater AKLT1, AKLΔ and less GRΔ predicted greater ATTT1 and ATTT2 in females (R2=12.5-13.1, P<.05), with AKLΔ being a stronger predictor (coefficient, P-value) of ATTT2 (0.864, P=.027) compared to ATTT1 (0.333, P=.370). AKLΔ was the sole predictor of ATTΔ (R2=.104; 0.740, P=.042).
Greater absolute baseline and cyclic increases in AKL were consistently associated with greater ATT produced by transition of the knee from NWB to WB. As the ACL is the primary restraint to ATT, these findings provide insight into possible mechanisms by which greater AKL may be associated with at risk knee biomechanics during the weight acceptance phase of dynamic tasks.
Injury Mechanism; anterior knee laxity; genu recurvatum; knee biomechanics; hormone response; menstrual cycle
We have investigated the effect of pentacene-doped poly(3,4-ethylenedioxythiophene:poly(4-styrenesulfonate) [PEDOT:PSS] films as a hole-conducting layer on the performance of polymer photovoltaic cells. By increasing the amount of pentacene and the annealing temperature of pentacene-doped PEDOT:PSS layer, the changes of performance characteristics were evaluated. Pentacene-doped PEDOT:PSS thin films were prepared by dissolving pentacene in 1-methyl-2-pyrrolidinone solvent and mixing with PEDOT:PSS. As the amount of pentacene in the PEDOT:PSS solution was increased, UV-visible transmittance also increased dramatically. By increasing the amount of pentacene in PEDOT:PSS films, dramatic decreases in both the work function and surface resistance were observed. However, the work function and surface resistance began to sharply increase above the doping amount of pentacene at 7.7 and 9.9 mg, respectively. As the annealing temperature was increased, the surface roughness of pentacene-doped PEDOT:PSS films also increased, leading to the formation of PEDOT:PSS aggregates. The films of pentacene-doped PEDOT:PSS were characterized by AFM, SEM, UV-visible transmittance, surface analyzer, surface resistance, and photovoltaic response analysis.
electronic materials; polymers; vapor deposition; electrochemical measurement; electrochemical properties
Changes in anterior knee laxity (AKL), genu recurvatum (GR) and general joint laxity (GJL) were quantified across days of the early follicular and early luteal phases of the menstrual cycle in 66 females, and the similarity in their pattern of cyclic variations examined. Laxity was measured on each of the first 6 days of menses (M1–M6) and the first 8 days following ovulation (L1–L8) over two cycles. The largest mean differences were observed between L5 and L8 for AKL (0.32mm), and between L5 and M1 for GR (0.56°) and GJL (0.26)(P<.013). At the individual level, mean absolute cyclic changes in AKL (1.8±0.7mm, 1.6±0.7mm), GR (2.8±1.0°, 2.4±1.0°) and GJL (1.1±1.1, 0.7±1.0) were more apparent, with minimum, maximum and delta values being quite consistent from month to month (ICC2,3=.51–.98). Although the average daily pattern of change in laxity was quite similar between variables (Spearman correlation range 0.61 and 0.90), correlations between laxity measures at the individual level were much lower (range −0.07 to 0.43). Substantial, similar, and reproducible cyclic changes in AKL, GR and GJL were observed across the menstrual cycle, with the magnitude and pattern of cyclic changes varying considerably among females.
joint laxity; menstrual cycle; anterior cruciate ligament; knee
Ten cancer patients (Six renal cell carcinoma and four breast cancer patients) were treated in a phase I/II study with a vaccine composed of autologous dendritic cells (DCs) and IL-2 to evaluate the DC vaccine-related toxicity and antigen-specific immune alteration.
Cancer patients were treated twice with autologous CD34+ hematopoietic stem cell-derived, GM-CSF/IFN-γ-differentiated DCs pulsed with autologous tumor lysate and KLH, by 4-week interval. Following each subcutaneous injection of therapeutic DCs, low-dose (200 MIU) IL-2 was introduced for 14 consecutive days as an immune adjuvant. To determine the DC vaccine-induced immunological alterations, the KLH-specific lymphocyte proliferation, number of IFN-γ secreting T cells (ELISPOT assay), NK activity and the cytokine modulation were measured.
Cultured-DCs expressing HLA-DR, CD11c, CD83, and B7.1/B7.2 produced IL-12p70. After vaccination, the patients tolerated it. Clinical response was observed in one RCC patient as stable disease. However DC-vaccine related antigen-specific immune responses including peripheral blood lymphocyte proliferation and the number of IFN-r secreting cells were induced in six patients without clear correlation with clinical responses. Also NK activity was induced significantly in six patients after vaccination. DC vaccine-related decrease of TGF-β level or increase of IL-12p70 level and decline of CD4+CD25+ T cells were observed in three patients. However only in the RCC patient whose disease stabilized, combination of stimulatory as well as inhibitory immune alterations including induction of IFN-γ secreting T cell with reduction of CD4+ CD25+ T cell were correlated with clinical responses.
Data indicated that DC vaccine combined with IL-2 is well tolerated without major side effects. DC vaccine induced the specific immunity against introduced antigen. Combinatorial alterations of immunological parameters indicating antigen-specific immune induction along with reduction of inhibitory immunity were correlated with clinical responses in DC vaccine treated patients.
Dendritic cell vaccine; Renal cell carcinoma; Breast cancer; Phase I/II trial; Immune response
Most of the position weight matrix (PWM) based bioinformatics methods developed to predict transcription factor binding sites (TFBS) assume each nucleotide in the sequence motif contributes independently to the interaction between protein and DNA sequence, usually producing high false positive predictions. The increasing availability of TF enrichment profiles from recent ChIP-Seq methodology facilitates the investigation of dependent structure and accurate prediction of TFBSs. We develop a novel Tree-based PWM (TPWM) approach to accurately model the interaction between TF and its binding site. The whole tree-structured PWM could be considered as a mixture of different conditional-PWMs. We propose a discriminative approach, called TPD (TPWM based Discriminative Approach), to construct the TPWM from the ChIP-Seq data with a pre-existing PWM. To achieve the maximum discriminative power between the positive and negative datasets, the cutoff value is determined based on the Matthew Correlation Coefficient (MCC). The resulting TPWMs are evaluated with respect to accuracy on extensive synthetic datasets. We then apply our TPWM discriminative approach on several real ChIP-Seq datasets to refine the current TFBS models stored in the TRANSFAC database. Experiments on both the simulated and real ChIP-Seq data show that the proposed method starting from existing PWM has consistently better performance than existing tools in detecting the TFBSs. The improved accuracy is the result of modelling the complete dependent structure of the motifs and better prediction of true positive rate. The findings could lead to better understanding of the mechanisms of TF-DNA interactions.
mRNA-Seq technology has revolutionized the field of transcriptomics for identification and quantification of gene transcripts not only at gene level but also at isoform level. Estimating the expression levels of transcript isoforms from mRNA-Seq data is a challenging problem due to the presence of constitutive exons.
We propose a novel algorithm (IsoformEx) that employs weighted non-negative least squares estimation method to estimate the expression levels of transcript isoforms. Validations based on in silico simulation of mRNA-Seq and qRT-PCR experiments with real mRNA-Seq data showed that IsoformEx could accurately estimate transcript expression levels. In comparisons with published methods, the transcript expression levels estimated by IsoformEx showed higher correlation with known transcript expression levels from simulated mRNA-Seq data, and higher agreement with qRT-PCR measurements of specific transcripts for real mRNA-Seq data.
IsoformEx is a fast and accurate algorithm to estimate transcript expression levels and gene expression levels, which takes into account short exons and alternative exons with a weighting scheme. The software is available at http://bioinformatics.wistar.upenn.edu/isoformex.
Single nucleotide polymorphisms (SNPs) associated with polygenetic disorders, such as breast cancer (BC), can create, destroy or modify microRNA (miRNA) binding sites; however, the extent to which SNPs interfere with miRNA gene regulation and affect cancer susceptibility remains largely unknown. We hypothesize that disruption of miRNA target binding by SNPsis a widespread mechanism relevant to cancer susceptibility. In order to test this, we analyzed SNPs known to be associated with BC risk, in silico and in vitro, for their ability to modify miRNA binding sites and miRNA gene regulation and referred to these as target SNPs. We identified rs1982073-TGFB1 and rs1799782-XRCC1 as target SNPs, whose alleles could modulate gene expression by differential interaction with miR-187 and miR-138, respectively. Genome-wide bioinformatics analysis predicted approximately 64% of transcribed SNPs as target SNPs that can modify (increase/decrease) the binding energy of putative miRNA::mRNA duplexes by over 90%. To assess whether target SNPs are implicated in BC susceptibility, we conducted a case-control population study and observed that germline occurrence of rs799917-BRCA1 and rs334348-TGFR1, significantly varies among populations with different risks of developing BC. Luciferase activity of target SNPs allelic variants and protein levels in cancer cell lines with different genotypes showed differential regulation of target genes following over-expression of the two interacting miRNAs (miR-638 and miR-628-5p). Therefore, we propose that transcribed target SNPs alter miRNA gene regulation and consequently protein expression, contributing to the likelihood of cancer susceptibility, by a novel mechanism of subtle gene regulation.
Single nucleotide polymorphism; microRNAs; mRNA; BC; tumor susceptibility
While the application of compressive joint loads and thigh muscle activity are associated with anterior tibial translation in vitro, less is known during early load acceptance in-vivo. We investigated the effects of increasing axial loads on anterior tibial translation and thigh muscle activity in healthy knees during transition from non-weight bearing to early weight bearing.
Participants (11 Male, 11 Female) underwent 20%, 40%, and 60% body weight acceptance trials at 20° knee flexion while electromagnetic sensors measured anterior tibial translation (mm), and surface electromyography recorded quadriceps and hamstring muscle onset times (ms) and amplitudes (% maximal voluntary isometric contraction). Repeated measures ANOVA compared values across loads. Pearson correlations examined relationships between anterior tibial translation and muscle onset times and amplitudes within each load.
As load increased, anterior tibial translation (Mean (standard deviation)) (20%=4.7(1.7)mm < 40%=7.1(1.9)mm < 60%=8.8(2.1)mm), and quadriceps (20%=23.6(14.9)% maximal voluntary isometric contraction < 40%=32.7(11.8)% maximal voluntary isometric contraction < 60%=41.1(13.5)% maximal voluntary isometric contraction) and hamstring (20%=15.5(15.7)% maximal voluntary isometric contraction < 40%=23.0(16.4)% maximal voluntary isometric contraction < 60%=27.6(19.1)% maximal voluntary isometric contraction) activation increased, while quadriceps (20% = 96.7(28.4)ms > 60% 80.2(21.8)ms) and hamstring (20% = 141.5(65.0)ms & 40% = 126.3(68.8)> 60% 107.6(28.4)ms) onset times decreased (P≤0.05). There were no relationships between anterior tibial translation and muscle activation amplitudes (R = .033–.294) or onset times (R = −.031–.374)(P>.09).
Greater axial loads near full knee extension during early weight acceptance result in greater anterior tibial translation, regardless of faster and stronger activation amplitudes. These findings support injury prevention programs aimed to reduce impact forces as they may in turn reduce anterior tibial translation and corresponding ligamentous strain during dynamic activity.
Knee; ACL; Loading Rate
The removal of high-abundance proteins from plasma is an efficient approach to investigating flow-through proteins for biomarker discovery studies. Most depletion methods are based on multiple immunoaffinity methods available commercially including LC columns and spin columns. Despite its usefulness, high-abundance depletion has an intrinsic problem, the sponge effect, which should be assessed during depletion experiments. Concurrently, the yield of depletion of high-abundance proteins must be monitored during the use of the depletion column. To date, there is no reasonable technique for measuring the recovery of flow-through proteins after depletion and assessing the capacity for capture of high-abundance proteins.
In this study, we developed a method of measuring recovery yields of a multiple affinity removal system column easily and rapidly using enhanced green fluorescence protein as an indicator of flow-through proteins. Also, we monitored the capture efficiency through depletion of a high-abundance protein, albumin labeled with fluorescein isothiocyanate.
This simple method can be applied easily to common high-abundance protein depletion methods, effectively reducing experimental variations in biomarker discovery studies.
Regulation of the formation and function of bone-resorbing osteoclasts (OCs) is a key to understanding the pathogenesis of skeletal disorders. Gene-targeting studies have shown that the RANK signaling pathway plays a critical role in OC differentiation and function. Although pharmaceutical blockade of RANK may be a viable strategy for preventing bone destruction, RANK is implicated in multiple biological processes. Recently, a cytoplasmic motif of RANK was identified that may be specifically involved in OC differentiation. Here, we developed a cell-permeable inhibitor termed the RANK receptor inhibitor (RRI), which targets this motif. The RRI peptide blocked RANKL-induced OC formation from murine bone marrow–derived macrophages. Furthermore, RRI inhibited the resorptive function of OCs and induced OC apoptosis. Treatment with the peptide impaired downstream signaling of RANK linked to Vav3, Rac1, and Cdc42 and resulted in disruptions of the actin cytoskeleton in differentiated OCs. In addition, RRI blocked inflammation-induced bone destruction and protected against ovariectomy-induced bone loss in mice. These data may be useful in the development of selective therapeutic agents for the treatment of osteoporosis and other bone diseases.
This study was undertaken to identify cellular proteins that bind an orally active natural product insulin mimic. Phage display cloning was used with a biotinylated derivative of this molecule as bait. Among the proteins identified was glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which has recently been shown to affect insulin receptor signaling. Binding data support a role for human GAPDH as another target of the insulin mimic, which could explain its action as a selective insulin receptor modulator.
The construction of literature-based networks of gene-gene interactions is one of the most important applications of text mining in bioinformatics. Extracting potential gene relationships from the biomedical literature may be helpful in building biological hypotheses that can be explored further experimentally. Recently, latent semantic indexing based on the singular value decomposition (LSI/SVD) has been applied to gene retrieval. However, the determination of the number of factors k used in the reduced rank matrix is still an open problem.
In this paper, we introduce a way to incorporate a priori knowledge of gene relationships into LSI/SVD to determine the number of factors. We also explore the utility of the non-negative matrix factorization (NMF) to extract unrecognized gene relationships from the biomedical literature by taking advantage of known gene relationships. A gene retrieval method based on NMF (GR/NMF) showed comparable performance with LSI/SVD.
Using known gene relationships of a given gene, we can determine the number of factors used in the reduced rank matrix and retrieve unrecognized genes related with the given gene by LSI/SVD or GR/NMF.
Gene expression and transcription factor (TF) binding data have been used to reveal gene transcriptional regulatory networks. Existing knowledge of gene regulation can be presented using gene connectivity networks. However, these composite connectivity networks do not specify the range of biological conditions of the activity of each link in the network.
We present a novel method that utilizes the expression and binding patterns of the neighboring nodes of each link in existing experimentally-based, literature-derived gene transcriptional regulatory networks and extend them in silico using TF-gene binding motifs and a compendium of large expression data from Saccharomyces cerevisiae. Using this method, we predict several hundreds of new transcriptional regulatory TF-gene links, along with experimental conditions in which known and predicted links become active. This approach unravels new links in the yeast gene transcriptional regulatory network by utilizing the known transcriptional regulatory interactions, and is particularly useful for breaking down the composite transcriptional regulatory network to condition specific networks.
Our methods can facilitate future binding experiments, as they can considerably help focus on the TFs that must be surveyed to understand gene regulation.
(Supplemental material and the latest version of the MATLAB implementation of the United Signature Algorithm is available online at  or [see Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
The status of intestinal parasite infections was investigated in two rural villages (Chitrasar, Jerona) in Chitwan District, Nepal in 1999. Stool examination was performed with a total of 300 specimens from schoolchildren by formalin-ether sedimentation technique. The prevalence rate of intestinal parasite infections in the surveyed areas was 44.0%. The prevalence rate in Jerona was slightly higher than that in Chitrasar. The prevalence rate of intestinal parasite infections in female was slighly higher than that in male without statistically significant difference. Entamoeba coli was the most commonly found protozoan parasite (21.0%) followed by Giardia lamblia (13.7%) and others (5.3%). Hookworm was the most prevalent intestinal helminth (13.0%) followed by Trichuris trichiura (3.0%) and others (5.0%). Forty-three specimens (14.3%) showed mixed infections. It is necessary to implement large-scale treatment with anthelminthics, health education and sanitary improvement for intestinal parasite control in the surveyed areas.
Nepal; intestinal parasites; formalin-ether sedimentation technique