Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathway-Based Association Analyses Identified TRAIL Pathway for Osteoporotic Fractures

Introduction Hip OF carries the highest morbidity and mortality. Previous studies revealed that individual genes/loci in the Tumor Necrosis Factor (TNF) -Related Apoptosis-Inducing Ligand (TRAIL) pathway were associated with bone metabolism. This study aims to verify the potential association between hip OF and TRAIL pathway. Methods Using genome-wide genotype data from Affymetrix 500 K SNP arrays, we performed novel pathway-based association analyses for hip OF in 700 elderly Chinese Han subjects (350 with hip OF and 350 healthy matched controls). Results The TRAIL pathway achieved a significant p value (p = 0.01) for association with hip OF. Among the 38 genes in the TRAIL pathway, seven genes achieved nominally significant association with hip OF (p<0.05); the TNFSF10 (TRAIL) gene obtained the most significant p value (p = 1.70×10−4). SNPs (rs719126, rs6533015, rs9594738, rs1805034, rs11160706) from five genes (CFLAR, NFKB1, TNFSF11, TNFRSF11A, TRAF3) of the pathway had minor alleles that appear to be protective to hip OF. SNPs (rs6445063 and rs4259415) from two genes (TNFSF10 and TNFRSF10B) of the pathway had minor alleles (A) that are associated with an increased risk of hip OF, with the ORs (odds ratios) of 16.51 (95%CI:3.83–71.24) and 1.37 (95%CI:1.08–1.74), respectively. Conclusions Our study supports the potential role of the TRAIL pathway in the pathogenesis of hip OF in Chinese Han population. Further functional study of this pathway will be pursued to determine the mechanism by which it confers risk to hip OF.
Analysis of clinical characteristics and outcome of patients with previously untreated diffuse large B-cell lymphoma and renal involvement in the rituximab era

Abstract Renal involvement in patients with lymphoma is rare but associated with poor prognosis. We analyzed characteristics and outcome of 22 patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL) and renal involvement treated with a rituximab-containing regimen in curative intent. The majority of patients presented in advanced disease, 86% were Ann Arbor stage ≥ III and had an IPI score ≥ 3. Renal impairment was present in 32%. Outcome was poor with three-year progression-free survival (PFS) 44% and three-year overall survival (OS) 52% and significantly worse compared to DLBCL without renal involvement (p < 0.01). Patients with high-risk IPI had a significantly inferior prognosis compared to intermediate-risk IPI (three-year OS 0% vs. 75%, p = 0.01) as did those with renal impairment. A high rate of central nervous system (CNS) relapse (8/22) was observed. Intravenous high-dose methotrexate and intrathecal therapy showed a trend toward prolonged time to CNS relapse. Implementation of CNS prophylaxis might therefore be considered in these high-risk patients.
Hypomethylation of let-7a-3 is associated with poor prognosis in myelodysplastic syndrome

Abstract Abnormal methylation of let-7a-3 has been found in various cancers and may consequently affect their survival. In this study, real-time quantitative methylation specific PCR (RQ-MSP) was used to determine the unmethylation level of let-7a-3 in 95 patients with myelodysplastic syndrome (MDS). The hypomethylation of let-7a-3 promoter was detected in 22 of 95 (23.2%) patients with MDS compared to 4.2% (1/24) of controls (p= 0.0419). Moreover, the frequency of let-7a-3 hypomethylation was higher in older patients (≥70 years) than in younger patients (<70 years). No significant difference was observed in distribution of WHO, IPSS, and cytogenetic classification. However, hypomethylated patients had significantly shorter overall survival than those without hypomethylation (p= 0.007). Moreover both Kaplan–Meier and Multivariate Cox analyses confirmed that let-7a-3 hypomethylation was an independent prognostic risk factor in cohorts of MDS patients with lower-risk disease. Our study suggested that let-7a-3 hypomethylation may predict poor outcome in MDS.
Evolution of Sexual Dimorphism in the Digit Ratio 2D:4D - Relationships with Body Size and Microhabitat Use in Iguanian Lizards

The ratio between lengths of digit II and IV (digit ratio 2D:4D) is a morphological feature that likely affects tetrapod locomotor performances in different microhabitats. Modifications of this trait may be triggered by changes in steroids concentrations during embryo development, which might reflect direct selection acting on digit ratio or be solely a consequence of hormonal differences related for example to body size. Here we apply both conventional and phylogenetic analyses on morphological data from 25 lizard species of 3 families of Iguania (Iguanidae, Polychrotidae, and Tropiduridae), in order to verify whether selective pressures related to locomotion in different microhabitats could override the prenatal developmental cues imposed on the digit ratio 2D:4D by differences in body size between males and females. Data suggest that this trait evolved in association with ecological divergence in the species studied, despite the clear effect of body size on the digit ratio 2D:4D. The ecological associations of size-corrected digit ratios were restricted to one sex, and females of species that often use perches exhibited small digit ratios in the front limbs, which translated into larger sexual dimorphism indexes of arboreal species. The results, together with the subsequent discussion, provide outlines for further investigation about possible developmental mechanisms related to the evolution of adaptive changes in digit lengths that may have occurred during the evolution of ecological divergence in squamates.
DEVELOPMENT AND VALIDATION OF A COLLAGEN-BASED SCAFFOLD FOR VASCULAR TISSUE ENGINEERING

Tissue engineering provides insight into solving the organ shortage. This is especially the case for small diameter vascular substitutes, with which a shortage is due in part to the prevalence of cardiovascular disease in the industrialized world. For this, in our opinion, one of the most appropriate approaches involves using a structure to guide the cells during the regeneration phase. Collagen has many characteristics that make it suitable as a scaffold material for vascular tissue engineering. Two slightly different methods for extracting and processing collagen type I from rat tail were compared with respect to the molecular structure of the collagen molecule, the mechanical properties of thin films obtained from solvent evaporation and preliminary cellular viability with fibroblasts seeded on these same collagen films. One of the above methods was chosen and this collagen was then characterized with respect to cellular viability with smooth muscle cells and endothelial cells and also with blood contact assays. A method for producing three-dimensional gels seeded with vascular cells was developed. Cell distribution and viability, preliminary compliance testing and blood contact assays were performed on these gels. This project has provided the basis for further studies in order to maximize cell functionality and the structural properties required for implantation of collagen-gel-based vascular grafts.
A case for multiple and parallel RRAMs as synaptic model for training SNNs

To enable a dense integration of model synapses in a spiking neural networks (SNN) hardware, various nano- scale devices are being considered. Such devices, besides exhibiting spike-timing dependent plasticity (STDP), need to be highly scalable, have a large endurance and require low energy for transitioning between states. In this work, first, we introduce and empirically determine two new specifications for a resistive random-access memory (RRAM) based synapse: number of conductance levels per synapse and learning-rate. To the best of our knowledge, there are no RRAMs that meet the latter specification. As a solution, we propose the use of multiple RRAMs in parallel within a synapse. While synaptic reading, all RRAMs are simultaneously read and for each synaptic conductance-change event, the mechanism for conductance STDP is initiated on only one RRAM, randomly picked from the set. Second, to validate our solution, we experimentally demonstrate STDP of conductance of a $\mathrm {P}\mathrm {r}_{0}. {}_{7}\mathrm {C}\mathrm {a}_{0.3}\mathrm {M}\mathrm {n}\mathrm {O}_{3}$ (PCMO)-RRAM and then show that due to a large learning-rate, a single PCMO-RRAM fails to model a synapse in the training of an SNN. As anticipated, network training improved as more PCMO-RRAMs were added to the synapse. Fourth, we discuss circuit-requirements for implementing such a scheme, to conclude that the requirements are within bounds. Thus, our work presents specifications for synaptic devices in trainable SNNs, indicates the shortcomings of state-of-art synaptic contenders, and provides a solution to extrinsically meet the specifications and discusses the peripheral circuitry that implements the solution.
A Cell-Free Assembly System for Generating Infectious Human Papillomavirus 16 Capsids Implicates a Size Discrimination Mechanism for Preferential Viral Genome Packaging

ABSTRACT We have established a cell-free in vitro system to study human papillomavirus type 16 (HPV16) assembly, a poorly understood process. L1/L2 capsomers, obtained from the disassembly of virus-like particles (VLPs), were incubated with nuclear extracts to provide access to the range of cellular proteins that would be available during assembly within the host cell. Incorporation of a reporter plasmid “pseudogenome” was dependent on the presence of both nuclear extract and ATP. Unexpectedly, L1/L2 VLPs that were not disassembled prior to incubation with a reassembly mixture containing nuclear extract also encapsidated a reporter plasmid. As with HPV pseudoviruses (PsV) generated intracellularly, infection by cell-free particles assembled in vitro required the presence of L2 and was susceptible to the same biochemical inhibitors, implying the cell-free assembled particles use the infectious pathway previously described for HPV16 produced in cell culture. Using biochemical and electron microscopy analyses, we observed that, in the presence of nuclear extract, intact VLPs partially disassemble, providing a mechanistic explanation to how the exogenous plasmid was packaged by these particles. Further, we provide evidence that capsids containing an <8-kb pseudogenome are resistant to the disassembly/reassembly reaction. Our results suggest a novel size discrimination mechanism for papillomavirus genome packaging in which particles undergo iterative rounds of disassembly/reassembly, seemingly sampling DNA until a suitably sized DNA is encountered, resulting in the formation of a stable virion structure. IMPORTANCE Little is known about papillomavirus assembly biology due to the difficulties in propagating virus in vitro. The cell-free assembly method established in this paper reveals a new mechanism for viral genome packaging and will provide a tractable system for further dissecting papillomavirus assembly. The knowledge gained will increase our understanding of virus-host interactions, help to identify new targets for antiviral therapy, and allow for the development of new gene delivery systems based on in vitro-generated papillomavirus vectors.
Exploratory pooled analysis evaluating the effect of sequence of biological therapies on overall survival in patients with RAS wild-type metastatic colorectal carcinoma

Background The aim of this study was to evaluate the optimal sequence of targeted therapies (epidermal growth factor receptor inhibitors (EGFRi) and vascular endothelial growth factor inhibitors (VEGFi)), combined with chemotherapy, in patients with RAS wild-type (WT) metastatic colorectal carcinoma (mCRC). Exploratory analyses of overall survival (OS) for patients treated with either first-line panitumumab (EGFRi) and second-line VEGFi therapy, or first-line bevacizumab (VEGFi) and second-line EGFRi, were conducted. Methods Patients from PEAK (NCT00819780), PRIME (NCT00364013) and Study 181 (NCT00339183), with RAS WT or RAS WT/BRAF WT tumours, were included in the analyses. OS data were pooled for patients receiving first-line panitumumab (PEAK and PRIME) or first-line bevacizumab (PEAK and 181), followed by second-line VEGFi or EGFRi, respectively. Results Overall, 104 RAS WT patients were included (n=66 panitumumab→VEGFi, n=38 bevacizumab→EGFRi). At the time of final data analysis, 63.6% versus 92.1% of patients in the panitumumab→VEGFi versus bevacizumab→EGFRi arms had died; median OS was 36.8 versus 27.8 months, respectively (HR 0.65; 95% CI 0.42 to 1.03). The OS HR for patients with RAS WT/BRAF WT mCRC overall was 0.58 (95% CI 0.36 to 0.95) and was 0.56 (95% CI 0.30 to 1.04) in those with left-sided tumours. Conclusion Although numbers are small, these exploratory analyses suggest a trend towards improved OS for first-line panitumumab plus chemotherapy followed by second-line VEGFi, compared with first-line bevacizumab followed by second-line EGFRi in patients with RAS WT and RAS WT/BRAF WT mCRC. Large prospective randomised trials are needed to further evaluate the optimum sequence of EGFRi/VEGFi in mCRC.
Transcriptional Alterations Related to Neuropathology and Clinical Manifestation of Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common cause of dementia in the human population, characterized by a spectrum of neuropathological abnormalities that results in memory impairment and loss of other cognitive processes as well as the presence of non-cognitive symptoms. Transcriptomic analyses provide an important approach to elucidating the pathogenesis of complex diseases like AD, helping to figure out both pre-clinical markers to identify susceptible patients and the early pathogenic mechanisms to serve as therapeutic targets. This study provides the gene expression profile of postmortem brain tissue from subjects with clinic-pathological AD (Braak IV, V, or V and CERAD B or C; and CDR ≥1), preclinical AD (Braak IV, V, or VI and CERAD B or C; and CDR = 0), and healthy older individuals (Braak ≤ II and CERAD 0 or A; and CDR = 0) in order to establish genes related to both AD neuropathology and clinical emergence of dementia. Based on differential gene expression, hierarchical clustering and network analysis, genes involved in energy metabolism, oxidative stress, DNA damage/repair, senescence, and transcriptional regulation were implicated with the neuropathology of AD; a transcriptional profile related to clinical manifestation of AD could not be detected with reliability using differential gene expression analysis, although genes involved in synaptic plasticity, and cell cycle seems to have a role revealed by gene classifier. In conclusion, the present data suggest gene expression profile changes secondary to the development of AD-related pathology and some genes that appear to be related to the clinical manifestation of dementia in subjects with significant AD pathology, making necessary further investigations to better understand these transcriptional findings on the pathogenesis and clinical emergence of AD.
Comparison of APRI, FIB-4 and fibro test in prediction of fibrosis and cirrhosis in patients with hepatitis C

Aspartate aminotransferase platelet ratio index (APRI), Fibrosis-4 (FIB-4) and Fibro test are noninvasive methods to assess liver fibrosis. The objective of this study is to analyze the diagnostic performance of these tests for assessment of hepatic fibrosis and cirrhosis during hepatitis C infection. Data for comparison of significant fibrosis and cirrhosis was obtained through earlier studies where the degree of fibrosis and cirrhosis was measured in accordance with METAVIR and Ishak scoring system. 52 studies analyzing APRI, FIB-4 and Fibro test for various stages of fibrosis in hepatitis C patients were assessed. The area under the SROC curves of the APRI, FIB-4 and Fibro test to estimate fibrosis were 0.7736, 0.7163, and 0.8921 respectively while the areas under SROC curves of the APRI, FIB-4 and Fibro test to predict cirrhosis were 0.8244, 0.8167, and 0.9422, respectively. Fibro test is better than others in estimating both presence and absence of fibrosis and cirrhosis.
Solution of Parabolic Equations by Backward Euler-Mixed Finite Element Methods on a Dynamically Changing Mesh

We develop and analyze methods based on combining the lowest-order mixed finite element method with backward Euler time discretization for the solution of diffusion problems on dynamically changing meshes. The methods developed are shown to preserve the optimal rate error estimates that are well known for static meshes. The novel aspect of the scheme is the construction of a linear approximation to the solution, which is used in projecting the solution from one mesh to another. Extensions to advection-diffusion equations are discussed, where the advection is handled by upwinding. Numerical results validating the theory are also presented.
Bivalirudin in percutaneous coronary intervention for chronic total occlusion: A single‐center pilot study

Bivalirudin has been reported to be an alternative to unfractionated heparin (UFH) for anticoagulation during percutaneous coronary intervention (PCI) and associated with less bleeding risk. However, the feasibility of bivalirudin during PCI of chronic total occlusion lesions (CTO) remains unknown.
None of the Six SNPs of IL28B Could Predict Treatment Responses in Genotype 2 Chronic HCV Infected Patients by Propensity Score Matching Analysis

Background & Aims A combination of pegylated interferon-alpha and ribavirin (PR) is the standard therapy for patients with chronic hepatitis C. The impact of polymorphism of interleukin-28B (IL28B) on sustained virological response (SVR) to PR has been well documented in patients with CHC genotype-1 (GT1), but it is controversial in genotype-2 (GT2) CHC patients. This study investigated the predictability of six single nucleotide polymorphisms (SNP) of IL28B on the treatment responses of PR in patients with CHC GT2. Method 197 CHC GT2 consecutive patients who received PR treatment in our prospective cohort were enrolled. Hepatitis C virus (HCV) genotyping, quantification of HCV-RNA and genotyping of the ten SNPs of IL28B were performed. Six SNPs of IL28B were chosen for analysis. The propensity score matching (PSM) analysis was applied using patients with CHC GT1 in another prospective cohort as a positive comparison to avoid covariate bias. Results The distribution of the six SNPs was similar in GT1 and GT2 patients. Five of these SNPs had strong association with treatment responses in GT1 but not in GT2 patients. After PSM analysis, these five SNPs still showed strong association with rapid virological response (RVR), cEVR and SVR in GT1 and had no influence in GT2 patients. Furthermore, rs12979860 and baseline viral load were the predictors for both RVR and SVR in GT1 patients. However, only baseline viral load could predict RVR and SVR in GT2 patients. In addition, in patients without RVR, rs12979860 was the only predictor for SVR in GT1 but no predictor for SVR was found in GT2. Conclusions The genetic polymorphisms of IL28B had no impact on treatment responses in GT2 patients.
Active shape models with optimised texture features for radiotherapy

There is now considerable interest in radiation oncology on the use of shape models of anatomy to improve target delineation and assess anatomical disparity at time of radiotherapy. In this paper a texture based active shape model (ASM) is presented for automatic delineation of the gross tumor volume (GTV), containing the prostate, on computed tomography (CT) images of prostate cancer patients. The model was trained on two-dimensional (2D) contours identified by a radiation oncologist on sequential CT image slices. A three-dimensional (3D) GTV shape was constructed from these and iteratively aligned using Procrustes analysis. To train the model the shape deformation variance was learnt using the Active Shape Model (ASM) approach. In a novel development to this approach a profile feature was selected from pre-computed texture features by minimizing the Mahalanobis distance to obtain the most distinct feature for each landmark. The interior of the GTV was modelled using quantile histograms to initialize the shape model on new cases. From the archive of 42 cases of contoured CT scans, 32 cases were randomly selected for training the model and 10 cases for evaluating performance. The gold standard was defined by the radiation oncologist. The shape model achieved an overall Dice coefficient of 0.81 for all test cases. Performance was found to increase, mean Dice coefficient of 0.87, when the volume size of the new case was similar to the mean shape of the model. With further work the approach has the potential to be used in real-time delineation of target volumes and improve segmentation accuracy.
Evidence of Weak Habitat Specialisation in Microscopic Animals

Macroecology and biogeography of microscopic organisms (any living organism smaller than 2 mm) are quickly developing into fruitful research areas. Microscopic organisms also offer the potential for testing predictions and models derived from observations on larger organisms due to the feasibility of performing lab and mesocosm experiments. However, more empirical knowledge on the similarities and differences between micro- and macro-organisms is needed to ascertain how much of the results obtained from the former can be generalised to the latter. One potential misconception, based mostly on anedoctal evidence rather than explicit tests, is that microscopic organisms may have wider ecological tolerance and a lower degree of habitat specialisation than large organisms. Here we explicitly test this hypothesis within the framework of metacommunity theory, by studying host specificify in the assemblages of bdelloid rotifers (animals about 350 µm in body length) living in different species of lichens in Sweden. Using several regression-based and ANOVA analyses and controlling for both spatial structure and the kind of substrate the lichen grow over (bark vs rock), we found evidence of significant but weak species-specific associations between bdelloids and lichens, a wide overlap in species composition between lichens, and wide ecological tolerance for most bdelloid species. This confirms that microscopic organisms such as bdelloids have a lower degree of habitat specialisation than larger organisms, although this happens in a complex scenario of ecological processes, where source-sink dynamics and geographic distances seem to have no effect on species composition at the analysed scale.