Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of transforming growth factor β1 gene polymorphisms in patients with systemic sclerosis

Objectives: To determine the distribution of transforming growth factor β1 (TGFβ1) genotypes at codon 10 (+869 polymorphism) and codon 25 (+915 polymorphism) in patients with scleroderma (SSc). Differences between diffuse and limited SSc (dSSc and lSSc) were also investigated. Methods: Patients with lSSc (n=89) and dSSc (n=63) were compared with 147 controls. DNA was isolated from peripheral blood and polymorphisms at codons 10 (C/T) and 25 (G/C) of the TGFβ1 gene analysed by polymerase chain reaction and sequence specific oligonucleotide probing. Results: Significantly more patients with SSc than controls carried allele C at codon 10 (controls v SSc, 38% v 48%, χ2=8.2, 1df, p=0.004), OR=1.95 (95% CI 1.16 to 3.27). The difference remained when patients with SSc were split into those with limited or diffuse disease, (controls v dSSc, χ2=5, 1df, p=0.02 and controls v lSSc, χ2=6, 1df, p=0.013). The patients with SSc had significantly more subjects heterozygous at codon 10 (controls v SSc, χ2=45, 1df, p<0.0001). Possession of allele C at codon 10 gave an OR=4.8 (95% CI 2.8 to 8.4). No difference in allele frequency was seen between patients with SSc and controls at codon 25. More patients with SSc than controls carried the GG genotype (controls v SSc, 80% v 88%, χ2=7, 2df, p=0.027). Possession of allele G gave an OR=1.7 (95% CI 0.5 to 5.9). There was no difference between diffuse and limited disease at either codon. Conclusions: These results suggest that patients with SSc are genetically predisposed to high TGFβ1 production. These polymorphisms do not, however, explain the difference in the clinical phenotypes of limited and diffuse SSc.
Fast Distributed Algorithms for Connectivity and MST in Large Graphs

Motivated by the increasing need to understand the algorithmic foundations of distributed large-scale graph computations, we study a number of fundamental graph problems in a message-passing model for distributed computing where k ≥ 2 machines jointly perform computations on graphs with n nodes (typically, n gg k). The input graph is assumed to be initially randomly partitioned among the k machines, a common implementation in many real-world systems. Communication is point-to-point, and the goal is to minimize the number of communication rounds of the computation. Our main result is an (almost) optimal distributed randomized algorithm for graph connectivity. Our algorithm runs in ~O(n/k2) rounds (~O notation hides a polylog(n) factor and an additive polylog(n) term). This improves over the best previously known bound of ~O(n/k) [Klauck et al., SODA 2015], and is optimal (up to a polylogarithmic factor) in view of an existing lower bound of ~Ω(n/k2). Our improved algorithm uses a bunch of techniques, including linear graph sketching, that prove useful in the design of efficient distributed graph algorithms. We then present fast randomized algorithms for computing minimum spanning trees, (approximate) min-cuts, and for many graph verification problems. All these algorithms take ~O(n/k2) rounds, and are optimal up to polylogarithmic factors. We also show an almost matching lower bound of ~Ω(n/k2) for many graph verification problems using lower bounds in random-partition communication complexity.
Routine coagulation tests on ICU admission are associated with mortality in sepsis: an observational study

Low platelet count on admission to an intensive care unit (ICU) is associated with increased mortality and is thus included in some severity scoring systems such as the simplified acute physiologic score 3 (SAPS 3); however it is unclear whether other routine coagulation tests also predict mortality. The purpose of this retrospective single‐centre study was to investigate whether activated partial thromboplastin time (APTT) or prothrombin time – international normalized ratio (PT‐INR) measured on admission to the ICU in patients with severe sepsis or septic shock may be associated with mortality independent of SAPS 3 score.
Combining ConceptNet and WordNet for Word Sense Disambiguation

Knowledge-based Word sense Disambiguation (WSD) methods heavily depend on knowledge. Therefore enriching knowledge is one of the most important issues in WSD. This paper proposes a novel idea of combining WordNet and ConceptNet for WSD. First, we present a novel method to automatically disambiguate the concepts in ConceptNet; and then we enrich WordNet with large amounts of semantic relations from the disambiguated ConceptNet for WSD. The evaluation experiments on the Semeval-2007 coarse-grained all-words disambiguation task show that the enriched WordNet can significantly improve the performance of knowledge-based WSD methods.
A particle system for interactive visualization of 3D flows

We present a particle system for interactive visualization of steady 3D flow fields on uniform grids. For the amount of particles we target, particle integration needs to be accelerated and the transfer of these sets for rendering must be avoided. To fulfill these requirements, we exploit features of recent graphics accelerators to advect particles in the graphics processing unit (GPU), saving particle positions in graphics memory, and then sending these positions through the GPU again to obtain images in the frame buffer. This approach allows for interactive streaming and rendering of millions of particles and it enables virtual exploration of high resolution fields in a way similar to real-world experiments. The ability to display the dynamics of large particle sets using visualization options like shaded points or oriented texture splats provides an effective means for visual flow analysis that is far beyond existing solutions. For each particle, flow quantities like vorticity magnitude and A2 are computed and displayed. Built upon a previously published GPU implementation of a sorting network, visibility sorting of transparent particles is implemented. To provide additional visual cues, the GPU constructs and displays visualization geometry like particle lines and stream ribbons.
The power of protein interaction networks for associating genes with diseases

Motivation: Understanding the association between genetic diseases and their causal genes is an important problem concerning human health. With the recent influx of high-throughput data describing interactions between gene products, scientists have been provided a new avenue through which these associations can be inferred. Despite the recent interest in this problem, however, there is little understanding of the relative benefits and drawbacks underlying the proposed techniques. Results: We assessed the utility of physical protein interactions for determining gene–disease associations by examining the performance of seven recently developed computational methods (plus several of their variants). We found that random-walk approaches individually outperform clustering and neighborhood approaches, although most methods make predictions not made by any other method. We show how combining these methods into a consensus method yields Pareto optimal performance. We also quantified how a diffuse topological distribution of disease-related proteins negatively affects prediction quality and are thus able to identify diseases especially amenable to network-based predictions and others for which additional information sources are absolutely required. Availability: The predictions made by each algorithm considered are available online at http://www.cbcb. umd.edu/DiseaseNet Contact: carlk@cs.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Model-Checking Parse Trees

Parse trees are fundamental syntactic structures in both computational linguistics and programming language design. We argue in this paper that, in both fields, there are good incentives for model-checking sets of parse trees for some word according to a context-free grammar. We put forward the adequacy of propositional dynamic logic (PDL) on trees in these applications, and study as a sanity check the complexity of the corresponding model-checking problem: although complete for exponential time in the general case, we find natural restrictions on grammars for our applications and establish complexities ranging from nondeterministic polynomial time to polynomial space in the relevant cases.
A review of allograft processing and sterilization techniques and their role in transmission of the human immunodeficiency virus

Human immunodeficiency virus (HIV) infection via vas cular organ and tissue transplantation is well docu mented. The majority of these transmissions occurred before the development of HIV antibody testing, which is now a routine screening tool used before organ and tissue procurement and transplantation. There exists what is commonly referred to as a "window" of sero negativity after HIV infection. Potential donors may be infectious with the HIV virus but not yet detected with available HIV antibody tests. Bone and soft tissue retrieval may be done in either a sterile or clean, non- sterile manner. Deep freezing and freeze-drying (lyoph ilization) are two commonly used modes of preserving bone and soft tissue allografts. In 1985, a screened donor who was in the window of seronegativity underwent vascular organ and mus culoskeletal tissue harvest. The bone and soft tissue procured underwent a variety of processing and pres ervation techniques. There have been no known cases of HIV transmission from the processed freeze-dried tissues. Evidence now exists that early HIV infection, before HIV antibody production, may be the most infectious period. The HIV antigen testing may allow earlier detec tion of an infectious donor, thus closing the window of seronegativity. It is unknown whether this nontransmis sion of HIV to the recipients of the processed and freeze-dried tissue was due to the processing or the nature of the tissue itself.
Cytokine Signaling in Splenic Leukocytes from Vaccinated and Non-Vaccinated Chickens after Intravenous Infection with Salmonella Enteritidis

In order to design a new Salmonella enterica vaccine, one needs to understand how naive and immune chickens interact differently when exposed to S. enterica. In this study we therefore determined the immune response of vaccinated and non-vaccinated chickens after intravenous infection with Salmonella enterica serovar Enteritidis (S. Enteritidis). Using flow cytometry we showed that 4 days post infection (DPI), counts of CD4 and B-lymphocytes did not change, CD8 and γδ T-lymphocytes decreased and macrophages and heterophils increased in the spleen. When vaccinated and non-vaccinated chickens were compared, only macrophages and heterophils were found in significantly higher counts in the spleens of the non-vaccinated chickens. The non-vaccinated chickens also expressed higher anti-LPS antibodies than the vaccinated chickens. The expression of interleukin (IL)1β, IL6, IL8, IL18, LITAF, IFNγ and iNOS did not exhibit any clear pattern in the cells sorted from the spleens of vaccinated or non-vaccinated chickens. Only IL17 and IL22 showed a differential expression in the CD4 T-lymphocytes of the vaccinated and non-vaccinated chickens at 4 DPI, both being expressed at a higher level in the non-vaccinated chickens. Due to a similar IFNγ expression in the CD4 T-lymphocytes in both the vaccinated and non-vaccinated chickens, and a variable IL17 expression oscillating around IFNγ expression levels, the IL17∶IFNγ ratio in CD4 T-lymphocytes was found to be central for the outcome of the immune response. When IL17 was expressed at higher levels than IFNγ in the non-vaccinated chickens, the Th17 immune response with a higher macrophage and heterophil infiltration in the spleen dominated. However, when the expression of IL17 was lower than that of IFNγ as in the vaccinated chickens, the Th1 response with a higher resistance to S. Enteritidis infection dominated.
Social software: E-learning beyond learning management systems

The article argues that it is necessary to move e-learning beyond learning management systems and engage students in an active use of the web as a resource for their self-governed, problem-based and collaborative activities. The purpose of the article is to discuss the potential of social software to move e-learning beyond learning management systems. An approach to use of social software in support of a social constructivist approach to e-learning is presented, and it is argued that learning management systems do not support a social constructivist approach which emphasizes self-governed learning activities of students. The article suggests a limitation of the use of learning management systems to cover only administrative issues. Further, it is argued that students' self-governed learning processes are supported by providing students with personal tools and engaging them in different kinds of social networks.
Enamel hypomineralization due to endocrine disruptors

Abstract There has been increasing concerns over last 20 years about the potential adverse effects of endocrine disruptors (EDs). Bisphenol A (BPA), genistein (G) and vinclozolin (V) are three widely used EDs having similar effects. Tooth enamel has recently been found to be an additional target of BPA that may be a causal agent of molar incisor hypomineralization (MIH). However, populations are exposed to many diverse EDs simultaneously. The purpose of this study was therefore to assess the effects of the combination of G, V and BPA on tooth enamel. Rats were exposed daily in utero and after birth to low doses of EDs mimicking human exposure during the critical fetal and suckling periods when amelogenesis takes place. The proportion of rats presenting opaque areas of enamel hypomineralization was higher when rats were treated with BPA alone than with a combination of EDs. The levels of mRNAs encoding the main enamel proteins varied with BPA treatment alone and did not differ significantly between controls and combined treatment groups. In vitro, rat ameloblastic HAT-7 cells were treated with the three EDs. BPA induced enamelin and reduced klk4 expression, G had no such effects and V reduced enamelin expression. These findings suggest that combinations of EDs may affect enamel less severely than BPA alone, and indicate that enamel hypomineralization may differ according to the characteristics of the ED exposure.
Recurrent Pregnancy Loss: Summary and Clinical Recommendations

Recurrent pregnancy loss (RPL) is traditionally defined as three or more consecutive pregnancy losses before 20 weeks of gestation. This problem occurs in approximately 1% of all couples and is a frustrating problem for both the patient and physician. This article provides an overview of the problem, including causes, treatments, and recommendations. Among the numerous proposed causes of RPL, only parental karyotype abnormalities, antiphospholipid syndrome, uterine malformations, and cervical incompetence are universally accepted. There are numerous treatments for RPL, but only the efficacy of heparin and low-dose aspirin in women with antiphospholipid syndrome has been established with properly controlled trials. Even after undertaking a complete evaluation, the cause of RPL remains uncertain in over 50% of cases. These patients should understand that subsequent pregnancies have up to a 70% chance of success without treatment.
Infragravity Driven Suspended Sediment Transport in the Swash, Inner and Outer-Surf Zone

Nearbed suspended sediment concentration and velocity measurements from 3 field sites in the mid-outer surf zone (low energy), inner surf zone (high energy) and swash (high energy) are discussed. Calculation of net sediment particle flux at a single elevation is decomposed into steady and fluctuating components. The cospectrum of concentration and velocity is used to calculate the direction and magnitude of the fluctuating component of sediment flux as a function of frequency. Preliminary results indicate that the incident band contribution to the net flux of sediment is primarily directed onshore. The infragravity band contribution, however, can have both offshore and onshore directed fluxes depending on the relative phase between the velocity and sediment concentration. The net sediment flux due to the fluctuating components, the integral of the co-spectrum over all frequencies, is of the same order as the contribution due to the drift, or mean, velocities. In the swash and inner surf zone, particle flux due to the steady and the fluctuating components may act in opposite directions, and imply that net sediment transport in the surf zone is the result of several competing processes of comparable magnitude whose direction of transport can change with both cross-shore position and the overall energetics of the nearshore.
Arthroscopically assisted Medial Reefing without Routine Lateral Release for Patellar Instability

Background Patellofemoral instability in patients with normal alignment has been effectively treated with medial reefing procedures and a lateral release. Recent research suggests that a lateral release may not be necessary in patients without excessive patellar tilt. Hypothesis Arthroscopically assisted medial reefing without lateral release is as effective as techniques with a lateral release reported in the literature. Study Design Case series; Level of evidence, 4. Methods Twenty-four patients (25 knees) were observed for an average of 60 months. Preoperatively, patients underwent a history, physical examination, and radiographic evaluation. At follow-up, a physical examination and radiographic evaluation were repeated. Preoperative and postoperative Lysholm and Tegner scores were calculated. A subjective questionnaire was also completed. Comparative statistics were used for the preoperative and postoperative scores (P < .05). Results Ninety-six percent (24/25) were satisfied with their results, and all patients would have the same procedure performed again. Subjective symptom scores improved significantly. Lysholm knee scores improved from an average of 54 to 91 (P < .001). Tegner activity level improved from an average of 3.3 to 6.2 (P < .001). Significant improvement was seen in patellar mobility, apprehension, and patellofemoral tenderness with compression. Range of motion, muscle atrophy, and tilt did not change significantly. Congruence angles improved from 4.4° to —2.5° (P = .009), lateral patellofemoral angles improved from 5.5° to 8.7° (P = .011), and lateral patellar displacement improved from 2.0 to 0.2 mm (P < .044). There were no recurrent dislocations or subluxations. Conclusion Arthroscopically assisted medial reefing, without lateral release, is an effective treatment for patients with recurrent patellofemoral instability and normal alignment.
Search of S3 LIGO data for gravitational wave signals from spinning black hole and neutron star binary inspirals

We report on the methods and results of the first dedicated search for gravitational waves emitted during the inspiral of compact binaries with spinning component bodies. We analyze 788 hours of data collected during the third science run (S3) of the LIGO detectors. We searched for binary systems using a detection template family specially designed to capture the effects of the spin-induced precession of the orbital plane. We present details of the techniques developed to enable this search for spin-modulated gravitational waves, highlighting the differences between this and other recent searches for binaries with nonspinning components. The template bank we employed was found to yield high matches with our spin-modulated target waveform for binaries with masses in the asymmetric range 1.0M⊙<m1<3.0M⊙ and 12.0M⊙<m2<20.0M⊙ which is where we would expect the spin of the binary’s components to have a significant effect. We find that our search of S3 LIGO data has good sensitivity to binaries in the Milky Way and to a small fraction of binaries in M31 and M33 with masses in the range 1.0M⊙<m1, m2<20.0M⊙. No gravitational wave signals were identified during this search. Assuming a binary population with spinning components and Gaussian distribution of masses representing a prototypical neutron star–black hole system with m1≃1.35M⊙ and m2≃5M⊙, we calculate the 90%-confidence upper limit on the rate of coalescence of these systems to be 15.9 yr−1L−110, where L10 is 1010 times the blue light luminosity of the Sun.
Maximizing Data Extraction in Energy-Limited Sensor Networks

We examine the problem of maximizing data collection from an energy-limited store-and-extract wireless sensor network, which is analogous to the maximum lifetime problem of interest in continuous data-gathering sensor networks. One significant difference is that this problem requires attention to “data-awareness” in addition to “energy-awareness”. We formulate the maximum data extraction problem as a linear program and present a 1 + ω iterative approximation algorithm for it. As a practical distributed implementation we develop a faster greedy heuristic for this problem that uses an exponential metric based on the approximation algorithm. We then show through simulation results that the greedy heuristic incorporating this exponential metric performs near-optimally (within 1 to 10% of optimal, with low overhead) and significantly better than other energy aware routing approaches (developed mainly through intuition), particularly when nodes are heterogeneous in their energy and data availability.
Basophil Responses to Chemokines Are Regulated by Both Sequential and Cooperative Receptor Signaling1

To investigate human basophil responses to chemokines, we have developed a sensitive assay that uses flow cytometry to measure leukocyte shape change as a marker of cell responsiveness. PBMC were isolated from the blood of volunteers. Basophils were identified as a single population of cells that stained positive for IL-3Rα (CDw123) and negative for HLA-DR, and their increase in forward scatter (as a result of cell shape change) in response to chemokines was measured. Shape change responses of basophils to chemokines were highly reproducible, with a rank order of potency: monocyte chemoattractant protein (MCP) 4 (peak at <1 nM) ≥ eotaxin-2 = eotaxin-3 ≥ eotaxin > MCP-1 = MCP-3 > macrophage-inflammatory protein-1α > RANTES = MCP-2 = IL-8. The CCR4-selective ligand macrophage-derived chemokine did not elicit a response at concentrations up to 10 nM. Blocking mAbs to CCR2 and CCR3 demonstrated that responses to higher concentrations (>10 nM) of MCP-1 were mediated by CCR3 rather than CCR2, whereas MCP-4 exhibited a biphasic response consistent with sequential activation of CCR3 at lower concentrations and CCR2 at 10 nM MCP-4 and above. In contrast, responses to MCP-3 were blocked only in the presence of both mAbs, but not after pretreatment with either anti-CCR2 or anti-CCR3 mAb alone. These patterns of receptor usage were different from those seen for eosinophils and monocytes. We suggest that cooperation between CCRs might be a mechanism for preferential recruitment of basophils, as occurs in tissue hypersensitivity responses in vivo.