Deduced probable HLA-B*40:01:35-associated HLA haplotype (A*24-B*40:01:35-DRB1*11) found in a Taiwanese unrelated hematopoietic bone marrow stem cell donor

AbstractObjectiveHuman leukocyte antigen (HLA)-B*40:01:35 is a low incidence allele in the HLA-B locus. The objective of this study is to report the ethnicity of B*40:01:35 and its deduced probable HLA associated haplotype in a Taiwanese unrelated bone marrow hematopoietic stem cell donor.Materials and methodsA sequence-based typing method was employed to confirm the low incidence allele B*40:01:35. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced using the BigDye Terminator Cycle Sequencing Ready Reaction kit in both directions according to the manufacturer's protocols.ResultsThe DNA sequence of B*40:01:35 is identical to B*40:01:01 in exons 2 and 3, except for residue 324 where C is changed to T (codon 84, TAC→TAT). The nucleotide exchange does not cause amino acid alteration to the protein sequence of B*40:01:01 due to the silent mutation. We deduced the probable HLA haplotype in association with B*40:01:35 in Taiwanese to be A*24-B*40:01:35-DRB1*11.ConclusionInformation on the deduced probable HLA haplotype in association with the low incidence B*40:01:35 allele that we report here is of value for HLA testing laboratories for reference purposes. In addition, it can be used by stem cell transplantation donor search coordinators to determine a strategy for finding compatible donors in unrelated bone marrow donor registries when a patient has this uncommon HLA allele

Diagnostic assessment of glaucoma and non-glaucomatous optic neuropathies via optical texture analysis of the retinal nerve fibre layer

The clinical diagnostic evaluation of optic neuropathies relies on the analysis of the thickness of the retinal nerve fibre layer (RNFL) by optical coherence tomography (OCT). However, false positives and false negatives in the detection of RNFL abnormalities are common. Here we show that an algorithm integrating measurements of RNFL thickness and reflectance from standard wide-field OCT scans can be used to uncover the trajectories and optical texture of individual axonal fibre bundles in the retina and to discern distinctive patterns of loss of axonal fibre bundles in glaucoma, compressive optic neuropathy, optic neuritis and non-arteritic anterior ischaemic optic neuropathy. Such optical texture analysis can detect focal RNFL defects in early optic neuropathy, as well as residual axonal fibre bundles in end-stage optic neuropathy that were indiscernible by conventional OCT analysis and by red-free RNFL photography. In a diagnostic-performance study, optical texture analysis of the RNFL outperformed conventional OCT in the detection of glaucoma, as defined by visual-field testing or red-free photography. Our findings show that optical texture analysis of the RNFL for the detection of optic neuropathies is highly sensitive and specific

ALMaQUEST. IV. The ALMA-MaNGA QUEnching and STar Formation (ALMaQUEST) Survey

The ALMaQUEST (ALMA-MaNGA QUEnching and STar formation) survey is a program with spatially-resolved $^{12}$CO(1-0) measurements obtained with the Atacama Large Millimeter Array (ALMA) for 46 galaxies selected from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) DR15 optical integral-field spectroscopic survey. The aim of the ALMaQUEST survey is to investigate the dependence of star formation activity on the cold molecular gas content at kpc scales in nearby galaxies. The sample consists of galaxies spanning a wide range in specific star formation rate (sSFR), including starburst (SB), main-sequence (MS), and green valley (GV) galaxies. In this paper, we present the sample selection and characteristics of the ALMA observations, and showcase some of the key results enabled by the combination of spatially-matched stellar populations and gas measurements. Considering the global (aperture-matched) stellar mass, molecular gas mass, and star formation rate of the sample, we find that the sSFR depends on both the star formation efficiency (SFE) and the molecular gas fraction ($f_{\rm H_{2}}$), although the correlation with the latter is slightly weaker. Furthermore, the dependence of sSFR on the molecular gas content (SFE or $f_{\rm H_{2}}$) is stronger than that on either the atomic gas fraction or the molecular-to-atomic gas fraction, albeit with the small HI sample size. On kpc scales, the variations in both SFE and $f_{\rm H_{2}}$ within individual galaxies can be as large as 1-2 dex thereby demonstrating that the availability of spatially-resolved observations is essential to understand the details of both star formation and quenching processes.STFC ER

Dengue Virus Targets the Adaptor Protein MITA to Subvert Host Innate Immunity

Dengue is one of the most important arboviral diseases caused by infection of four serotypes of dengue virus (DEN). We found that activation of interferon regulatory factor 3 (IRF3) triggered by viral infection and by foreign DNA and RNA stimulation was blocked by DEN-encoded NS2B3 through a protease-dependent mechanism. The key adaptor protein in type I interferon pathway, human mediator of IRF3 activation (MITA) but not the murine homologue MPYS, was cleaved in cells infected with DEN-1 or DEN-2 and with expression of the enzymatically active protease NS2B3. The cleavage site of MITA was mapped to LRR↓96G and the function of MITA was suppressed by dengue protease. DEN replication was reduced with overexpression of MPYS but not with MITA, while DEN replication was enhanced by MPYS knockdown, indicating an antiviral role of MITA/MPYS against DEN infection. The involvement of MITA in DEN-triggered innate immune response was evidenced by reduction of IRF3 activation and IFN induction in cells with MITA knockdown upon DEN-2 infection. NS2B3 physically interacted with MITA, and the interaction and cleavage of MITA could be further enhanced by poly(dA:dT) stimulation. Thus, we identified MITA as a novel host target of DEN protease and provide the molecular mechanism of how DEN subverts the host innate immunity

Health-related quality of life in glioma patients in China

<p>Abstract</p> <p>Background</p> <p>Health-related quality of life (HRQOL) has been increasingly emphasized in cancer patients. There are no reports comparing baseline HRQOL of different subgroups of glioma patients prior to surgery.</p> <p>Methods</p> <p>HRQOL assessments by the standard Chinese version of the European Organization for Research and Treatment of Cancer Quality of Life Core Questionnaire 30 (EORTC QLQ-C30, version 3.0), the Mini-Mental State Examination and Karnofsky Performance Status were obtained from glioma patients prior to surgery.</p> <p>Results</p> <p>Ninety-two pathologically confirmed glioma patients were recruited. There were 84.8% patients with emotional impairment, 75% with social and cognitive impairment, 70.7% with physical impairment, and 50% with role impairment. Eighty-two percent of patients reported fatigue symptoms, 72.8% reported pain, 50% reported appetite loss, 39.1% reported insomnia, and 36.9% reported nausea/vomiting, whereas other symptoms (dyspnea, diarrhea, constipation) in the QLQ-C30 were reported by fewer than 30% of patients. Fatigue and pain symptoms and all "functioning" scales were strongly correlated with global health status/quality of life (QoL). Fatigue was strongly related to all functioning scales, pain, appetite loss, and global health status/QoL. No difference in baseline HRQOL prior to surgery was reported between females and males, among different lesion locations, or between normal- and abnormal-cognition subgroups of glioma patients. Age, KPS, WHO grade, and tumor recurrence significantly affected HRQOL in glioma patients.</p> <p>Conclusions</p> <p>These data provided the baseline HRQOL in glioma patients prior to surgery in China. Most pre-surgery glioma patients indicated emotional, social, cognitive, physical, and role impairment. Fatigue, pain, appetite loss, insomnia, and nausea/vomiting were common in these patients. The fatigue and pain symptoms and all types of functioning strongly affected global health status/QoL. Old age, worse performance status, WHO grade IV and tumor recurrence had deleterious effects on HRQOL.</p

Associations of Amylin with Inflammatory Markers and Metabolic Syndrome in Apparently Healthy Chinese

BACKGROUND: Cellular and animal studies implicate multiple roles of amylin in regulating insulin action, glucose and lipid metabolisms. However, the role of amylin in obesity related metabolic disorders has not been thoroughly investigated in humans. Therefore, we aimed to evaluate the distribution of circulating amylin and its association with metabolic syndrome (MetS) and explore if this association is influenced by obesity, inflammatory markers or insulin resistance in apparently healthy Chinese. METHODS: A population-based sample of 1,011 Chinese men and women aged 35-54 years was employed to measure plasma amylin, inflammatory markers (C-reactive protein [CRP] and interleukin-6 [IL-6]), insulin, glucose and lipid profiles. MetS was defined according to the updated National Cholesterol Education Program Adult Treatment Panel III criteria for Asian-Americans. RESULTS: Plasma amylin concentrations were higher in overweight/obese participants than normal-weight counterparts (P<0.001) without sex difference. Circulating amylin was positively associated with CRP, IL-6, BMI, waist circumference, blood pressure, fasting glucose, insulin, amylin/insulin ratio, HOMA-IR, LDL cholesterol and triglycerides, while negatively associated with HDL cholesterol (all P<0.001). After multiple adjustments, the risk of MetS was significantly higher (odds ratio 3.71; 95% confidence interval: 2.53 to 5.46) comparing the highest with the lowest amylin quartile. The association remained significant even further controlling for BMI, inflammatory markers, insulin or HOMA-IR. CONCLUSIONS: Our study suggests that amylin is strongly associated with inflammatory markers and MetS. The amylin-MetS association is independent of established risk factors of MetS, including obesity, inflammatory markers and insulin resistance. The causal role of hyperamylinemia in the development of MetS needs to be confirmed prospectively

BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs

<p>Abstract</p> <p>Background</p> <p>The identification of drug characteristics is a clinically important task, but it requires much expert knowledge and consumes substantial resources. We have developed a statistical text-mining approach (BInary Characteristics Extractor and biomedical Properties Predictor: BICEPP) to help experts screen drugs that may have important clinical characteristics of interest.</p> <p>Results</p> <p>BICEPP first retrieves MEDLINE abstracts containing drug names, then selects tokens that best predict the list of drugs which represents the characteristic of interest. Machine learning is then used to classify drugs using a document frequency-based measure. Evaluation experiments were performed to validate BICEPP's performance on 484 characteristics of 857 drugs, identified from the Australian Medicines Handbook (AMH) and the PharmacoKinetic Interaction Screening (PKIS) database. Stratified cross-validations revealed that BICEPP was able to classify drugs into all 20 major therapeutic classes (100%) and 157 (of 197) minor drug classes (80%) with areas under the receiver operating characteristic curve (AUC) > 0.80. Similarly, AUC > 0.80 could be obtained in the classification of 173 (of 238) adverse events (73%), up to 12 (of 15) groups of clinically significant cytochrome P450 enzyme (CYP) inducers or inhibitors (80%), and up to 11 (of 14) groups of narrow therapeutic index drugs (79%). Interestingly, it was observed that the keywords used to describe a drug characteristic were not necessarily the most predictive ones for the classification task.</p> <p>Conclusions</p> <p>BICEPP has sufficient classification power to automatically distinguish a wide range of clinical properties of drugs. This may be used in pharmacovigilance applications to assist with rapid screening of large drug databases to identify important characteristics for further evaluation.</p

Promoter methylation-associated loss of ID4 expression is a marker of tumour recurrence in human breast cancer

<p>Abstract</p> <p>Background</p> <p>Inhibitor of DNA binding/Inhibitor of differentiation 4 (<it>ID4</it>) is a critical factor for cell proliferation and differentiation in normal vertebrate development. <it>ID4</it> has regulative functions for differentiation and growth of the developing brain. The role of <it>ID1</it>, <it>ID2</it> and <it>ID3</it> are expected to be oncogenic due to their overexpression in pancreatic cancer and colorectal adenocarcinomas, respectively. Aside from these findings, loss of <it>ID3</it> expression was demonstrated in ovarian cancer. The aim of the present study was to reveal the factual role of <it>ID4</it> in carcinogenesis in more detail, since its role for the pathogenesis of human breast cancer has been discussed controversially, assigning both oncogenic and tumour suppressive functions. </p> <p>Methods</p> <p><it>ID4</it> promoter methylation, <it>ID4</it> mRNA expression and <it>ID4</it> protein expression were analysed in primary human breast cancer specimens using methylation-specific PCR (MSP) (n=170), semiquantitative realtime RT-PCR (n=46) and immunhistochemistry (n=3), respectively. In order to demonstrate a functional association of <it>ID4</it> promoter methylation with its gene silencing, we performed DNA demethylation analysis with four human breast cell lines using MSP and semiquantitative realtime RT-PCR. In addition, we performed correlations of <it>ID4</it> promoter methylation with <it>ID4</it> mRNA and <it>ID4</it> protein expression in matched samples of breast tumour and corresponding normal tissue. We carried out statistical analyses in order to find correlations between <it>ID4</it> promoter methylation and clinicopathological parameters. </p> <p>Results</p> <p>Frequent <it>ID4</it> promoter methylation was observed in primary breast cancer samples (69%, 117/170). We found a tight correlation (P<0.0001) between <it>ID4</it> promoter methylation and loss of <it>ID4</it> expression in primary breast cancer 3 specimens. Demethylating treatment with breast cancer cell lines was associated with clear ID4 mRNA re-expression. Tumours with <it>ID4</it> promoter methylation showed distinct loss of <it>ID4</it> expression on both transcription and protein level. Interestingly, <it>ID4</it> promoter methylation was a factor for unfavourable recurrence-free survival (P=0.036) and increased risk for lymph node metastasis (P=0.030). </p> <p>Conclusion</p> <p>ID4 is indeed a novel tumour suppressor gene in normal human breast tissue and is epigenetically silenced during cancer development, indicating increased risk for tumour relapse. Thus, <it>ID4</it> methylation status could serve as a prognostic biomarker in human breast cancer.</p