Miracle-dz/UniFAR-FTUs huggingface dataset:
Neutrophil Gelatinase-Associated Lipocalin: A Novel Early Urinary Biomarker for Cisplatin Nephrotoxicity

Background: Cisplatin is one of the most widely used chemotherapeutic agents, but the risk of nephrotoxicity frequently hinders the use of higher doses to maximize its antineoplastic effects. The lack of early biomarkers has impaired our ability to initiate potential therapeutic or preventive interventions in cisplatin nephrotoxicity in a timely manner. In this study, we have explored the expression and urinary excretion of neutrophil gelatinase-associated lipocalin (NGAL) in a mouse model of cisplatin-induced nephrotoxic injury. Methods: Mice were subjected to intraperitoneal injections of 20 mg/kg (high dose) or 5 mg/kg (low dose) cisplatin. The expression of NGAL was measured in the kidney and urine by Western analysis and immunofluorescence, and compared to changes in serum creatinine and urinary N-acetyl-β-D-glucosaminidase (NAG). Results: Cisplatin resulted in tubule cell necrosis and apoptosis following the high dose, but not the low dose. By Western analysis, NGAL protein was rapidly induced in the kidney within 3 h of high-dose cisplatin. By immunofluorescence, NGAL was induced predominantly in proximal tubule cells in a punctate cytoplasmic distribution, reminiscent of a secreted protein. NGAL was easily detected in the urine by Western analysis within 3 h of cisplatin administration in a dose- and duration-dependent manner. By comparison, changes in urinary NAG or serum creatinine were not evident until 96 h after cisplatin. Using defined concentrations of purified recombinant NGAL, urinary NGAL excretion following cisplatin administration was quantified to be in the 20–80 ng/ml range. Conclusion: The results indicate that NGAL represents an early and quantitative urinary biomarker for cisplatin nephrotoxicity.
A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence

Merkel cell polyomavirus (MCPyV) is considered the etiological agent of Merkel cell carcinoma and persists asymptomatically in the majority of its healthy hosts. Largely due to the lack of appropriate model systems, the mechanisms of viral replication and MCPyV persistence remain poorly understood. Using a semi-permissive replication system, we here report a comprehensive analysis of the role of the MCPyV-encoded microRNA (miRNA) mcv-miR-M1 during short and long-term replication of authentic MCPyV episomes. We demonstrate that cells harboring intact episomes express high levels of the viral miRNA, and that expression of mcv-miR-M1 limits DNA replication. Furthermore, we present RACE, RNA-seq and ChIP-seq studies which allow insight in the viral transcription program and mechanisms of miRNA expression. While our data suggest that mcv-miR-M1 can be expressed from canonical late strand transcripts, we also present evidence for the existence of an independent miRNA promoter that is embedded within early strand coding sequences. We also report that MCPyV genomes can establish episomal persistence in a small number of cells for several months, a time period during which viral DNA as well as LT-Ag and viral miRNA expression can be detected via western blotting, FISH, qPCR and southern blot analyses. Strikingly, despite enhanced replication in short term DNA replication assays, a mutant unable to express the viral miRNA was severely limited in its ability to establish long-term persistence. Our data suggest that MCPyV may have evolved strategies to enter a non- or low level vegetative stage of infection which could aid the virus in establishing and maintaining a lifelong persistence.
Respiratory sinus arrhythmia on the ESA-short-arm human centrifuge

In this article, we investigated the hypothesis that the effects of hypergravity on respiratory sinus arrhythmia (RSA) can mimic the effects observed after spaceflight cardiovascular deconditioning. Artificial gravity along the head-to-feet axis on a short-arm centrifuge induces gravity gradients. This physiological condition of significantly higher g at the feet than at the heart level is specific and likely induces blood sequestration in the lower limbs. After spaceflight, astronauts are in a condition of cardiovascular deconditioning, where blood pooling in the lower part of the body and autonomic adaptation are factors contributing to orthostatic intolerance and changes in heart-rate variability (HRV). ECG and respiration were recorded during imposed and controlled breathing (ICB) protocols, which were repeated at different levels of artificial gravity as well as during supine and standing control conditions, and the changes were analyzed.
Dietary Fiber, Carbohydrate Quality and Quantity, and Mortality Risk of Individuals with Diabetes Mellitus

Background Dietary fiber, carbohydrate quality and quantity are associated with mortality risk in the general population. Whether this is also the case among diabetes patients is unknown. Objective To assess the associations of dietary fiber, glycemic load, glycemic index, carbohydrate, sugar, and starch intake with mortality risk in individuals with diabetes. Methods This study was a prospective cohort study among 6,192 individuals with confirmed diabetes mellitus (mean age of 57.4 years, and median diabetes duration of 4.4 years at baseline) from the European Prospective Investigation into Cancer and Nutrition (EPIC). Dietary intake was assessed at baseline (1992–2000) with validated dietary questionnaires. Cox proportional hazards analysis was performed to estimate hazard ratios (HRs) for all-cause and cardiovascular mortality, while adjusting for CVD-related, diabetes-related, and nutritional factors. Results During a median follow-up of 9.2 y, 791 deaths were recorded, 306 due to CVD. Dietary fiber was inversely associated with all-cause mortality risk (adjusted HR per SD increase, 0.83 [95% CI, 0.75–0.91]) and CVD mortality risk (0.76[0.64–0.89]). No significant associations were observed for glycemic load, glycemic index, carbohydrate, sugar, or starch. Glycemic load (1.42[1.07–1.88]), carbohydrate (1.67[1.18–2.37]) and sugar intake (1.53[1.12–2.09]) were associated with an increased total mortality risk among normal weight individuals (BMI≤25 kg/m2; 22% of study population) but not among overweight individuals (P interaction≤0.04). These associations became stronger after exclusion of energy misreporters. Conclusions High fiber intake was associated with a decreased mortality risk. High glycemic load, carbohydrate and sugar intake were associated with an increased mortality risk in normal weight individuals with diabetes.
Key issues in e-procurement: Procurement implementation and operation in the public sector

This paper presents the analysis from a study into the key lessons learned from e-procurement implementation across a range of UK public sector organisations. The literature relating to e-procurement implementation and operation is reviewed, identifying five main themes addressed by the current literature: impact on cost efficiency; the impact on the form and nature of supplier transaction; e-procurement system implementation; broader IT infrastructure issues; and the behavioural and relational impact of eprocurement. The research carried out was intended to explore the perceptions and reflections of both 'early' and 'late' adopters of e-procurement. Seven key lessons are drawn from the study and presented here. We conclude by proposing areas for further research, including the need for research into failed eprocurement projects.
TCP New Vegas: Improving the Performance of TCP Vegas Over High Latency Links

TCP Vegas provides significant performance gains over most TCP variants, especially when used over networks that utilise error prone links. However, whilst examining the impact of latency on TCP we noticed that the performance of TCP Vegas decreases significantly when the network round trip time exceeds 50ms. This paper details research undertaken to identify the cause of this performance decreasing behaviour in TCP Vegas. Three sender-side modifications are proposed and implemented as TCP New Vegas, before being validated via simulation
An Empirical Research of Factors Affecting Collaborative Decision Making System

This paper studies empirically business intelligence and social network service used to leverage the performance of collaborative decision making. A model is developed and tested empirically to find out meaningful relationships among those variables. This paper examines the current trend of social media within business intelligence, the importance of integrating these types of features within a BI solution, and why organizations should consider this type of functionality within their current decision making infrastructures. The result also shows that social media will increase in relation to use and expand within business related BI use, developing solutions that become easy to use is essential to successful collaborative decision making adoption.
Pointer Networks

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence [1] and Neural Turing Machines [2], because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems - finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem - using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.
Analysis and optimisation of soft electroactive laminated composites

The aim of this study was to improve the overall electromechanical response of dielectric composite actuators. The microstructures of rank-1 and rank-2 laminates, composed of two materials of varying dielectric and shear moduli, were optimised for four types of actuation due to an applied nominal electric �eld. A homogenization theory, established in the literature in �nite electroelasticity for rank-1 layered composites, was specialized to the actuation types to develop a closed-form solution. A similar lamination methodology was then derived for rank-2 laminates to obtain a numerical solution. Expressions for speci�c sequentially laminated microstructures of rank-1 and rank-2 type were obtained so as to determine optimum microstructural con�gurations for maximum longitudinal stretch. These results were obtained iteratively using the Newton-Raphson method for a set of simultaneous equations. Results for rank-1 laminates obtained in �nite strain were found to produce actuation strains higher than those obtained by previous authors in small strain. Rank-2 laminates then presented an improvement in actuation strain compared to those obtained in small strain by the same authors. Ratios of shear and dielectric moduli were varied to obtain di�erent contrasts and four parameters were de�ned to contribute to rank-2 laminate performance, namely two lamination angles and two volume fractions. For all actuation types, rank-2 longitudinal stretch presented strong improvement from rank-1 laminates. Electromechanical instability was observed in rank-2 laminates for two of the four actuation types and a trade-o� requirement was demonstrated between applied nominal electric �eld, shear and laminate microstructure for optimum performance. At least a tenfold enhancement of phase electric �elds was obtained for rank-2 laminates and the current con�guration of lamination angles highlighted di�erences to the reference con�guration. The ratios of shear and dielectric moduli were lastly perturbed and further enhancement of maximum longitudinal stretch obtained as a foundation for future work.
Fertility in Obsessional Neurosis

Obsessional neurosis, inasfar as it comes to the attention of the psychiatrist, is a comparatively rare disorder, comprising not more than about 3 per cent of all cases of neurosis. Its rarity is reflected in the fact that the largest series so far described, that of Pollitt (1957), consisted of only 150 cases, though a limited amount of information has been available from the somewhat larger series of the Bethlem-Maudsley Hospital (Blacker and Gore, 1955) and of the Registrar General (1964).
Activated carbon of Babassu coconut impregnated with copper nanoparticles by green synthesis for the removal of nitrate in aqueous solution

ABSTRACT The present study was conducted to impregnate the surface of a carbon of vegetable origin with copper nanoparticles by the green synthesis method with the aqueous extract of Hibiscus sabdariffa flowers, rich in phenolic compounds, which are responsible for the reduction and impregnation of metal nanoparticles. Batch adsorption assays were conducted aimed at nitrate removal with pure (GAC) and impregnated (IGAC) carbon, for comparative purposes. It was found that impregnation increases the efficiency of the carbon by four times in terms of the maximum adsorption capacity, which was 10.13 mg g−1 at 45°C for GAC and 45.01 mg g−1 at 15°C for IGAC, indicating that this is a promising material for the removal of nitrate in waters with an excess of this ion.
Consumer reviews: reviewer avatar facial expression and review valence

Purpose – The purpose of this paper is to explore how the facial expression of the reviewer's avatar interacts with the valence of the consumer review to influence consumer purchase decisions.Design/methodology/approach – A 2 (facial expression of the reviewer's avatar)× 2 (valence of the consumer review) between‐subjects online experimental design was used.Findings – It was found that when the consumer review was positive, participants exposed to the reviewer's angry‐looking avatar were more likely to attribute the review to the product's performance than those exposed to the happy‐looking avatar. The causal attribution toward product performance, in turn, influenced the strength of intention to purchase the brand positively. When the consumer review was negative, however, there were no differential effects between the happy‐looking and the angry‐looking avatars.Originality/value – This study contributes to the literature on consumer reviews by identifying an important source characteristic that consumer.
Cyclopamine blocked the growth of colorectal cancer SW116 cells by modulating some target genes of Gli1 in vitro.

BACKGROUND/AIMS Hedgehog (Hh) pathway has been considered as a therapy target for various cancer entities. However, its mechanism in colorectal cancer is still unclear. METHODOLOGY We analyzed the expression of Hh pathway members in colorectal adenomas and cancer cell lines and then studied its relationship with survival of colorectal cancer cells through inhibiting Hh pathway by cyclopamine. Moreover, we studied the regulation of Gli1 on insulin-like growth factor binding protein 6 (IGFBP6) and B-cell CLL/lymphoma 2 (Bcl-2) genes at the level of transcription by XChIP and cyclopamine inhibition assay. RESULTS Sonic hedgehog (Shh), Smoothened (Smo), patched (Ptch) and Gli1 genes mRNA were expressed in SW116 cells. Gli1 bound to promoter regions of Bcl-2 and IGFBP6 genes, cyclopamine inhibited proliferation and induced apoptosis through inhibiting the transcriptions of IGFBP6 (p=0.003), proliferating cell nuclear antigen (PCNA) (p=0.014) and Bcl-2 (p=0.013), and increasing that of BCL2-associated X protein (Bax) and BCL2-antagonist/killer 1 (Bak1) (p=0.003 and 0.001, respectively) in SW116 cells. CONCLUSIONS Hh pathway is aberrant activation in part colorectal carcinomas cell lines and its inhibitor may be an effectual agent for colorectal cancer chemoprevention. It may be one of the mechanisms that Gli1 maintained cell survival by binding the promoter regions and facilitating transcription of IGFBP6 and Bcl-2 genes.
Developmental variation in lumbosacropelvic anatomy of thoroughbred racehorses.

OBJECTIVE To describe the incidence and types of gross osseous developmental variations and ages of physeal closure in the caudal portion of the thoracic and lumbosacral spine and the pelvis in a sample of Thoroughbred racehorses. ANIMALS Thoroughbred racehorses (n = 36) that died or were euthanatized at California racetracks between October 1993 and July 1994. PROCEDURE Lumbosacropelvic specimens were collected, and all soft tissues were removed. The osseous specimens were visually examined. RESULTS Only 22 (61%) specimens had the expected number of 6 lumbar and 5 sacral vertebrae. Eight (22%) specimens had thoracolumbar transitional vertebrae, and 13 (36%) had sacrocaudal transitional vertebrae. Articular process asymmetries were present at 1 or more vertebral segments in 30 (83%) specimens. Intertransverse joints (2 to 4 pairs/specimen) were bilaterally distributed in the caudal portion of the lumbar spine and the lumbosacral joint in 31 (86%) specimens. Five (14%) specimens had asymmetric distribution of the intertransverse joints. Intertransverse joint ankylosis was found in 10 (28%) specimens. Lumbosacral vertebral body physeal closure occurred between 4.9 and 6.7 years of age; pelvic physeal closure occurred between 5.2 and 5.8 years of age. Iliac crest and ischial arch epiphyseal formation was evaluated, using a grading system, and fusion to the underlying bone occurred at 7.2 years and 5.4 years of age, respectively. CONCLUSIONS Numerous vertebral anatomic variations were commonly found in a sample of Thoroughbred racehorses. CLINICAL RELEVANCE Normal anatomic variations and ages of skeletal maturity need to be considered in clinical evaluation of the equine spine and pelvis for differentiation from pathologic findings.
New and Improved Johnson-Lindenstrauss Embeddings via the Restricted Isometry Property

Consider an m by N matrix Phi with the Restricted Isometry Property of order k and level delta, that is, the norm of any k-sparse vector in R^N is preserved to within a multiplicative factor of 1 +- delta under application of Phi. We show that by randomizing the column signs of such a matrix Phi, the resulting map with high probability embeds any fixed set of p = O(e^k) points in R^N into R^m without distorting the norm of any point in the set by more than a factor of 1 +- delta. Consequently, matrices with the Restricted Isometry Property and with randomized column signs provide optimal Johnson-Lindenstrauss embeddings up to logarithmic factors in N. In particular, our results improve the best known bounds on the necessary embedding dimension m for a wide class of structured random matrices; for partial Fourier and partial Hadamard matrices, we improve the recent bound m = O(delta^(-4) log(p) log^4(N)) appearing in Ailon and Liberty to m = O(delta^(-2) log(p) log^4(N)), which is optimal up to the logarithmic factors in N. Our results also have a direct application in the area of compressed sensing for redundant dictionaries.
Cryo-electron microscopy of extracellular vesicles in fresh plasma

Introduction Extracellular vesicles (EV) are phospholipid bilayer-enclosed vesicles recognized as new mediators in intercellular communication and potential biomarkers of disease. They are found in many body fluids and mainly studied in fractions isolated from blood plasma in view of their potential in medicine. Due to the limitations of available analytical methods, morphological information on EV in fresh plasma is still rather limited. Objectives To image EV and determine the morphology, structure and size distribution in fresh plasma by cryo-electron microscopy (cryo-EM). Methods Fresh citrate- and ethylenediaminetetraacetic acid (EDTA)-anticoagulated plasma or EV isolated from these plasmas were rapidly cryo-immobilized by vitrification and visualized by cryo-EM. Results EV isolated from fresh plasma were highly heterogeneous in morphology and size and mostly contain a discernible lipid bilayer (lipid vesicles). In fresh plasma there were 2 types of particles with a median diameter of 30 nm (25–260 nm). The majority of these particles are electron dense particles which most likely represent lipoproteins. The minority are lipid vesicles, either electron dense or electron lucent, which most likely represent EV. Lipid vesicles were occasionally observed in close proximity of platelets in citrate and EDTA-anticoagulated platelet-rich plasma. Cryo-electron tomography (cryo-ET) was employed to determine the 3D structure of platelet secretory granules. Conclusions Cryo-EM is a powerful technique that enables the characterization of EV in fresh plasma revealing structural details and considerable morphological heterogeneity. Only a small proportion of the submicron structures in fresh plasma are lipid vesicles representing EV.
GWAPP: A Web Application for Genome-wide Association Mapping in A. thaliana

Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, together with other important features, such as small size, short generation time, small genome size, and wide geographic distribution, make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions, and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire Arabidopsis community. To facilitate this, we present GWAPP, an interactive web-based application for conducting GWAS in A. thaliana. Using an efficient Python implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with an efficient mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and a user-friendly interface that includes interactive manhattan plots and interactive local and genome-wide LD plots. It facilitates exploratory data analysis by implementing features such as the inclusion of candidate SNPs in the model as cofactors.
Bidirectional Recursive Neural Networks for Token-Level Labeling with Structure

Recently, deep architectures, such as recurrent and recursive neural networks have been successfully applied to various natural language processing tasks. Inspired by bidirectional recurrent neural networks which use representations that summarize the past and future around an instance, we propose a novel architecture that aims to capture the structural information around an input, and use it to label instances. We apply our method to the task of opinion expression extraction, where we employ the binary parse tree of a sentence as the structure, and word vector representations as the initial representation of a single token. We conduct preliminary experiments to investigate its performance and compare it to the sequential approach.