Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of a second bacteriophage hyaluronidase gene from Streptococcus pyogenes: evidence for a third hyaluronidase involved in extracellular enzymatic activity

The hyaluronidase gene (hylP2) from a second group A streptococcal bacteriophage was isolated from ATCC T-type-22 hyaluronidase-producing strain 10403, a strain known to produce increased amounts of extracellular hyaluronidase. Sequence analysis of hylP2 and alignment with the previously described bacteriophage hyaluronidase gene (hylP) showed a high degree of similarity; however, hylP2 had deletions of regions specifying 34 amino acids. Twenty-eight of the deleted amino acids were in a region of HylP containing a series of collagen-like Gly-X-Y repeating units. By employing primers for both hylP and hylP2, PCR amplification resulted in fragments of appropriate sizes in 97% of the strains tested, with some strains producing two fragments, indicating the presence of at least two phages. When the hylP2 gene was introduced via a plasmid vector into a non-hyaluronidase-producing Streptococcus pyogenes strain, this strain was still unable to produce extracellular hyaluronidase, although intracellular hyaluronidase was present. These results, along with the absence of a typical N-terminal signal peptide, indicate that HylP2 is unable to be secreted into the extracellular milieu. Examination of more than 100 strains for production of hyaluronidase showed that only 23% of the strains produced extracellular hyaluronidase. One of these strains (strain 10403) contains a single bacteriophage hyaluronidase gene (hylP2) which, when inactivated by allelic replacement, still produces large amounts of extracellular hyaluronidase. These results suggest the presence of a different hyaluronidase gene encoding a protein that is actively secreted into the extracellular milieu.
Management of Incidental Findings in the Era of Next-generation Sequencing

Next-generation sequencing (NGS) technologies allow for the generation of whole exome or whole genome sequencing data, which can be used to identify novel genetic alterations associated with defined phenotypes or to expedite discovery of functional variants for improved patient care. Because this robust technology has the ability to identify all mutations within a genome, incidental findings (IF)- genetic alterations associated with conditions or diseases unrelated to the patient’s present condition for which current tests are being performed- may have important clinical ramifications. The current debate among genetic scientists and clinicians focuses on the following questions: 1) should any IF be disclosed to patients, and 2) which IF should be disclosed – actionable mutations, variants of unknown significance, or all IF? Policies for disclosure of IF are being developed for when and how to convey these findings and whether adults, minors, or individuals unable to provide consent have the right to refuse receipt of IF. In this review, we detail current NGS technology platforms, discuss pressing issues regarding disclosure of IF, and how IF are currently being handled in prenatal, pediatric, and adult patients.
Agency as a mediator in the pathway from transactional sex to HIV among pregnant women in Swaziland: a multigroup path analysis

Introduction: Transactional sex is a structural driver of HIV for women and girls in sub‐Saharan Africa. In transactional relationships, sexual and economic obligations intertwine and may have positive and negative effects on women's financial standing and social status. We conducted a clinic‐based survey with pregnant women in Swaziland using a locally validated transactional sex scale to measure the association between subjective social status, transactional sex, and HIV status, and to assess whether this association differed according to a woman's agency within her relationship.
2016 Ieee International Conference on Big Data (big Data) Detecting Fraud, Corruption, and Collusion in International Development Contracts: the Design of a Proof-of-concept Automated System

—International development banks provide low-interest loans to developing countries in an effort to stimulate social and economic development. These loans support key infrastructure projects including the building of roads, schools, and hospitals. However, despite the best efforts of development banks, these loan funds are often lost to fraud, corruption, and collusion. In an effort to sanction and deter this wrongdoing and to ensure proper use of funds, development banks conduct extensive, costly investigations that can take over a year to complete. This paper describes a proof-of-concept of a fully automated fraud, corruption, and collusion classification system for identifying risk in international development contracts. We developed this system in conjunction with the World Bank Group-the largest international development bank-to improve the time and cost efficiency of their investigation process. Using historical monetary award data and past investigation outcomes, our classifier assigns a " risk score " to World Bank contracts. This risk score is designed to enable World Bank investigators to identify the contracts most likely to lead to a substantiated investigation. If implemented, our automated system is predicted to successfully identify fraud, corruption, and collusion in 70% of cases.
A novel anti-inflammatory role for secretory phospholipase A2 in immune complex-mediated arthritis

Phospholipase A2 (PLA2) catalyses the release of arachidonic acid for generation of lipid mediators of inflammation and is crucial in diverse inflammatory processes. The functions of the secretory PLA2 enzymes (sPLA2), numbering nine members in humans, are poorly understood, though they have been shown to participate in lipid mediator generation and the associated inflammation. To further understand the roles of sPLA2 in disease, we quantified the expression of these enzymes in the synovial fluid in rheumatoid arthritis and used gene‐deleted mice to examine their contribution in a mouse model of autoimmune erosive inflammatory arthritis. Contrary to expectation, we find that the group V sPLA2 isoform plays a novel anti‐inflammatory role that opposes the pro‐inflammatory activity of group IIA sPLA2. Mechanistically, group V sPLA2 counter‐regulation includes promotion of immune complex clearance by regulating cysteinyl leukotriene synthesis. These observations identify a novel anti‐inflammatory function for a PLA2 and identify group V sPLA2 as a potential biotherapeutic for treatment of immune‐complex‐mediated inflammation.
Crack Nucleation in β Titanium Alloys under High Cycle Fatigue Conditions - A Review

Beta titanium (β-Ti) alloys have emerged over the last 3 to 4 decades as an important class of titanium alloys. Many of the applications that they found, particularly in aerospace sector, are such that their high cycle fatigue (HCF) behavior becomes critical. In HCF regime, crack nucleation accounts for major part of the life. Consequently it becomes important to understand the mechanisms underlying the nucleation of cracks under HCF type loading conditions. The purpose of this review is to document the best understanding we have on date on crack nucleation in β-Ti alloys under HCF conditions. Role of various microstructural features encountered in β-Ti alloys in influencing the crack nucleation under HCF conditions has been reviewed. It has been brought out that changes in processing can result in changes in microstructure which in turn influence the time for crack nucleation/fatigue life and fatigue limit. While majority of fatigue failures originate at the surface, subsurface cracking is not uncommon with β-Ti alloys and the factors leading to subsurface cracking have been discussed in this review.
The role of the nose in the pathogenesis of obstructive sleep apnoea and snoring

Data from observational studies suggest that nasal obstruction contributes to the pathogenesis of snoring and obstructive sleep apnoea (OSA). To define more accurately the relationship between snoring, OSA and nasal obstruction, the current authors have summarised the literature on epidemiological and physiological studies, and performed a systematic review of randomised controlled trials in which the effects of treating nasal obstruction on snoring and OSA were investigated. Searches of bibliographical databases revealed nine trials with randomised controlled design. External nasal dilators were used in five studies, topically applied steroids in one, nasal decongestants in two, and surgical treatment in one study. Data from studies using nasal dilators, intranasal steroids and decongestants to relieve nasal congestion showed beneficial effects on sleep architecture, but only minor improvement of OSA symptoms or severity. Snoring seemed to be reduced by nasal dilators. Nasal surgery also had minimal impact on OSA symptoms. In conclusion, chronic nasal obstruction seems to play a minor role in the pathogenesis of obstructive sleep apnoea, and seems to be of some relevance in the origin of snoring. The impact of treating nasal obstruction in patients with snoring and obstructive sleep apnoea on long-term outcome remains to be defined through randomised controlled trials of medical and surgical therapies.
Dynamics of Ordinary and Recurrent Hopfield Networks: Novel Themes

In this research paper several interesting themes related to Hopfield network are explored and concrete results are derived. For instance, convergence in partial parallel mode of operation, convergence when synaptic weight matrix, W is row diagonally dominant case. Also, structured recurrent Hopfield network with companion matrix as W is studied. The dynamics when the activation function is a step function, the state space is asymmetric hypercube are also studied. Finally several experimental results are derived.
On the implementation of the probabilistic logic programming language ProbLog

Abstract The past few years have seen a surge of interest in the field of probabilistic logic learning and statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension of Prolog motivated by the mining of large biological networks. In ProbLog, facts can be labeled with probabilities. These facts are treated as mutually independent random variables that indicate whether these facts belong to a randomly sampled program. Different kinds of queries can be posed to ProbLog programs. We introduce algorithms that allow the efficient execution of these queries, discuss their implementation on top of the YAP-Prolog system, and evaluate their performance in the context of large networks of biological entities.
Economic burden of irritable bowel syndrome in China

AIM To estimate annual direct and indirect costs for patients diagnosed with irritable bowel syndrome (IBS) and subtypes. METHODS Patients completed a standardized questionnaire concerning usage of healthcare resources, travel costs, meals, and productivity loss of patients when seeking treatment for IBS. Total annual costs per patient were calculated as the sum of direct (including medical and nonmedical) and indirect costs. Total annual costs per patient among various IBS subtypes were compared. Analysis of variance and bootstrapped independent sample t-tests were performed to determine differences between groups after controlling for IBS subtypes. RESULTS A total of 105 IBS patients (64.80% female), mean age of 57.12 years ± 10.31 years), mean disease duration of 4.31 years ± 5.40 years, were included. Total annual costs per patient were estimated as CNY18262.84 (USD2933.08). Inpatient and outpatient healthcare use were major cost drivers, accounting for 46.41%and 23.36% of total annual costs, respectively. Productivity loss accounted for 25.32% of total annual costs. The proportions of direct and indirect costs were similar to published studies in other countries. Nationally, the total costs of managing IBS would amount to CNY123.83 billion (USD1.99 billion). Among the IBS subtypes, total annual costs per patient of IBS-M was highest at CNY18891.18 (USD3034). Furthermore, there was significant difference in productivity loss among IBS subtypes (P = 0.031). CONCLUSION IBS imposes a huge economic burden on patients and healthcare systems, which could account for 3.3% of the total healthcare budget for the entire Chinese nation. More than two-thirds of total annual costs of IBS consist of inpatient and outpatient healthcare use. Among the subtypes, IBS-M patients appear to have the greatest economic burden but require further confirmation.
GAMA/G10-COSMOS/3D-HST: the 0 < z < 5 cosmic star formation history, stellar-mass, and dust-mass densities

We use the energy-balance code MAGPHYS to determine stellar and dust masses, and dust corrected star-formation rates for over 200,000 GAMA galaxies, 170,000 G10-COSMOS galaxies and 200,000 3D-HST galaxies. Our values agree well with previously reported measurements and constitute a representative and homogeneous dataset spanning a broad range in stellar mass (10^8---10^12 Msol), dust mass (10^6---10^9 Msol), and star-formation rates (0.01---100 Msol per yr), and over a broad redshift range (0.0 < z < 5.0). We combine these data to measure the cosmic star-formation history (CSFH), the stellar-mass density (SMD), and the dust-mass density (DMD) over a 12 Gyr timeline. The data mostly agree with previous estimates, where they exist, and provide a quasi-homogeneous dataset using consistent mass and star-formation estimators with consistent underlying assumptions over the full time range. As a consequence our formal errors are significantly reduced when compared to the historic literature. Integrating our cosmic star-formation history we precisely reproduce the stellar-mass density with an ISM replenishment factor of 0.50 +/- 0.07, consistent with our choice of Chabrier IMF plus some modest amount of stripped stellar mass. Exploring the cosmic dust density evolution, we find a gradual increase in dust density with lookback time. We build a simple phenomenological model from the CSFH to account for the dust mass evolution, and infer two key conclusions: (1) For every unit of stellar mass which is formed 0.0065---0.004 units of dust mass is also formed; (2) Over the history of the Universe approximately 90 to 95 per cent of all dust formed has been destroyed and/or ejected.
Astrocytes and Müller Cell Alterations During Retinal Degeneration in a Transgenic Rat Model of Retinitis Pigmentosa

Purpose: Retinitis pigmentosa includes a group of progressive retinal degenerative diseases that affect the structure and function of photoreceptors. Secondarily to the loss of photoreceptors, there is a reduction in retinal vascularization, which seems to influence the cellular degenerative process. Retinal macroglial cells, astrocytes, and Müller cells provide support for retinal neurons and are fundamental for maintaining normal retinal function. The aim of this study was to investigate the evolution of macroglial changes during retinal degeneration in P23H rats. Methods: Homozygous P23H line-3 rats aged from P18 to 18 months were used to study the evolution of the disease, and SD rats were used as controls. Immunolabeling with antibodies against GFAP, vimentin, and transducin were used to visualize macroglial cells and cone photoreceptors. Results: In P23H rats, increased GFAP labeling in Müller cells was observed as an early indicator of retinal gliosis. At 4 and 12 months of age, the apical processes of Müller cells in P23H rats clustered in firework-like structures, which were associated with ring-like shaped areas of cone degeneration in the outer nuclear layer. These structures were not observed at 16 months of age. The number of astrocytes was higher in P23H rats than in the SD matched controls at 4 and 12 months of age, supporting the idea of astrocyte proliferation. As the disease progressed, astrocytes exhibited a deteriorated morphology and marked hypertrophy. The increase in the complexity of the astrocytic processes correlated with greater connexin 43 expression and higher density of connexin 43 immunoreactive puncta within the ganglion cell layer (GCL) of P23H vs. SD rat retinas. Conclusions: In the P23H rat model of retinitis pigmentosa, the loss of photoreceptors triggers major changes in the number and morphology of glial cells affecting the inner retina.
Exploiting uniform vector instructions for GPGPU performance, energy efficiency, and opportunistic reliability enhancement

State-of-art graphics processing units (GPUs) employ the single-instruction multiple-data (SIMD) style execution to achieve both high computational throughput and energy efficiency. As previous works have shown, there exists significant computational redundancy in SIMD execution, where different execution lanes operate on the same operand values. Such value locality is referred to as uniform vectors. In this paper, we first show that besides redundancy within a uniform vector, different vectors can also have the identical values. Then, we propose detailed architecture designs to exploit both types of redundancy. For redundancy within a uniform vector, we propose to either extend the vector register file with token bits or add a separate small scalar register file to eliminate redundant computations as well as redundant data storage. For redundancy across different uniform vectors, we adopt instruction reuse, proposed originally for CPU architectures, to detect and eliminate redundancy. The elimination of redundant computations and data storage leads to both significant energy savings and performance improvement. Furthermore, we propose to leverage such redundancy to protect arithmetic-logic units (ALUs) and register files against hardware errors. Our detailed evaluation shows that our proposed design has low hardware overhead and achieves performance gains, up to 23.9% and 12.0% on average, along with energy savings, up to 24.8% and 12.6% on average, as well as a 21.1% and 14.1% protection coverage for ALUs and register files, respectively.
Matched regulation of gastrointestinal performance in the Burmese python, Python molurus

SUMMARY In Burmese pythons fasting and feeding cause dramatic regulation of gastric acid production and intestinal nutrient uptake. Predictably, other components of their gastrointestinal tract are similarly regulated with each meal. We therefore assessed the matched regulation of gastrointestinal performance by comparing the postprandial activities and capacities of gastric (pepsin), pancreatic (amylase and trypsin) and intestinal (aminopeptidase-N and maltase) enzymes, and intestinal nutrient uptake. Tissue samples were collected from pythons fasted and at 0.25, 0.5, 1, 2, 3, 4, 6, 10 and 15 days following their consumption of rodent meals equaling 25% of snake body mass. With feeding, pythons experience no significant change in stomach mass, whereas both the pancreas and small intestine doubled in mass. Feeding also triggered a depletion of gastric mucosal pepsinogen, a respective 5.7- and 20-fold increase in the peak activities of pancreatic trypsin and amylase, and a respective 2.3- and 5.5-fold increase in the peak activities of intestinal maltase and aminopeptidase-N. Enzyme activities peaked between 2 and 4 days postfeeding and returned to fasting levels by day 10. Independent of digestive stage, python intestine exhibited a proximal to distal decline in enzyme activity. For both sugars and proteins, intestinal capacities for enzyme activity were significantly correlated with nutrient uptake capacities. The concomitant postprandial upregulation of tissue morphology, intestinal nutrient transport rates and enzyme activities illustrate, for the python, the matched regulation of their gastrointestinal performance with each meal.
QUANTITATIVE STUDIES OF THE IMMUNOGLOBULIN SEQUENCE IN THE RESPONSE OF THE RABBIT TO A SOMATIC ANTIGEN

Employing a sensitive and immunoglobulin-specific assay method based upon antiglobulin augmentation, quantitative and qualitative aspects of the primary and secondary response of the rabbit to Salmonella typhimurium O antigens have been evaluated. These studies examine the validity of the method of assay for detecting and measuring γG- and γM-antibodies produced in response to whole organisms or its lipopolysaccharide. The results show that during the primary response γG-antibodies, not detectable by usual techniques, are produced in a pattern similar to that reported in animals stimulated by other classes of antigens. Moreover, the γG response following reinjection is characteristic of a secondary-type response. In contrast, γM-antibody levels after both primary and secondary stimulation rose equally to levels between 1 and 4 mg/ml. Despite increased sensitivity of detection and quantitative estimates of the actual molar concentration of each immunoglobulin, the minimal interval between γM and γG appearance in serum was not less than 1.5 days. The variable degree of augmentation of agglutination by antiglobulin reagent found during the immune response severely limits the quantitative usefulness of the methods developed. However, the data suggest that qualitative changes in anti-O antibodies interpretable as changes in avidity occur regularly during the immune response.
Clinical outcomes of stereotactic ablative radiotherapy in patients with pulmonary metastasis

Backgrounds In addition to its curative use for early stage lung cancer, stereotactic ablative radiotherapy is also indicated for pulmonary metastatic disease. Aims of this study were to retrospectively analyze treatment outcomes and to find prognostic factors for survivals. Methods Treatment outcomes and toxicities of 85 cases of SABR in 72 patients were retrospectively reviewed from September 2012 to April 2015. Prognostic factors were analyzed using Cox proportional hazards regression. Results The local failure-free survival rate at 2 years was 98%. Of the case, 1-year and 2-year progression-free survival rates were 62% and 48%, and overall survival rates were 90% and 72%, respectively. Multivariate analyses demonstrated that controlled primary cancer (P = 0.01), absence of extra-pulmonary metastatic disease (P < 0.01) and disease-free interval longer than 1 year (P < 0.01) favorably affected progression-free survival. Furthermore, the absence of extra-pulmonary metastatic disease (P < 0.01) increased overall survival as well. Grade 1 or 2 radiation pneumonitis was found in 37 cases, and Grade 1 chest wall pain was found in 1 case. Conclusions Stereotactic ablative radiotherapy demonstrated good local control with tolerable adverse effects for pulmonary metastasis. The presence or absence of extra-pulmonary metastasis was found to be prognostic factor of mortality after stereotactic ablative radiotherapy treatment.