Miracle-dz/UniFAR-FTUs huggingface dataset:
Successful outcome for patients with streptococcal prosthetic joint infections – a retrospective population-based study

Abstract Background/Aim: Streptococci cause approximately 10% of prosthetic joint infections (PJIs). The aim of this study was to identify the characteristics of patients with streptococcal PJIs and to describe the treatment and outcome of streptococcal PJIs in Skåne county between 2011 and 2015. Methods: Patients with streptococcal PJIs with positive cultures or PCRs on samples from joint aspirate and/or periprosthetic tissue between 2011 and 2015 in Skåne county, were identified and medical records were studied. Results: Eighty-three PJI episodes treated at seven hospitals were identified. The median age was 70 years (IQR: 64–78) and there were more men (61%) than women. Hip joints were the most common site of isolation (54%). The most frequently isolated pathogens were beta-haemolytic streptococci of groups A, C and G (31%), group B (30%), and alpha-haemolytic streptococci (23%). Overall failure rate was 11% (n = 9), and lack of comorbidity was significantly associated with a favourable outcome. The most common treatment strategy was debridement, antibiotic treatment and implant retention (DAIR) (n = 64; 77%) and the initial success rate using this strategy was 84% (n = 53). Conclusion: This study indicates an acceptable success rate for the patients treated with DAIR strategy, and a high overall success rate for episodes suffering streptococcal PJIs.
Prioritization and Evaluation of Depression Candidate Genes by Combining Multidimensional Data Resources

Background Large scale and individual genetic studies have suggested numerous susceptible genes for depression in the past decade without conclusive results. There is a strong need to review and integrate multi-dimensional data for follow up validation. The present study aimed to apply prioritization procedures to build-up an evidence-based candidate genes dataset for depression. Methods Depression candidate genes were collected in human and animal studies across various data resources. Each gene was scored according to its magnitude of evidence related to depression and was multiplied by a source-specific weight to form a combined score measure. All genes were evaluated through a prioritization system to obtain an optimal weight matrix to rank their relative importance with depression using the combined scores. The resulting candidate gene list for depression (DEPgenes) was further evaluated by a genome-wide association (GWA) dataset and microarray gene expression in human tissues. Results A total of 5,055 candidate genes (4,850 genes from human and 387 genes from animal studies with 182 being overlapped) were included from seven data sources. Through the prioritization procedures, we identified 169 DEPgenes, which exhibited high chance to be associated with depression in GWA dataset (Wilcoxon rank-sum test, p = 0.00005). Additionally, the DEPgenes had a higher percentage to express in human brain or nerve related tissues than non-DEPgenes, supporting the neurotransmitter and neuroplasticity theories in depression. Conclusions With comprehensive data collection and curation and an application of integrative approach, we successfully generated DEPgenes through an effective gene prioritization system. The prioritized DEPgenes are promising for future biological experiments or replication efforts to discoverthe underlying molecular mechanisms for depression.
Transpiration of Eucalyptus woodlands across a natural gradient of depth-to-groundwater

Water resources and their management present social, economic and environmental challenges, with demand for human consumptive, industrial and environmental uses increasing globally. However, environmental water requirements, that is, the allocation of water to the maintenance of ecosystem health, are often neglected or poorly quantified. Further, transpiration by trees is commonly a major determinant of the hydrological balance of woodlands but recognition of the role of groundwater in hydrological balances of woodlands remains inadequate, particularly in mesic climates. In this study, we measured rates of tree water-use and sapwood 13C isotopic ratio in a mesic, temperate Eucalypt woodland along a naturally occurring gradient of depth-to-groundwater (DGW), to examine daily, seasonal and annual patterns of transpiration. We found that: (i) the maximum rate of stand transpiration was observed at the second shallowest site (4.3 m) rather than the shallowest (2.4 m); (ii) as DGW increased from 4.3 to 37.5 m, stand transpiration declined; (iii) the smallest rate of stand transpiration was observed at the deepest (37.5 m) site; (iv) intrinsic water-use efficiency was smallest at the two intermediate DGW sites as reflected in the Δ13C of the most recently formed sapwood and largest at the deepest and shallowest DGW sites, reflecting the imposition of flooding at the shallowest site and the inaccessibility of groundwater at the deepest site; and (v) there was no evidence of convergence in rates of water-use for co-occurring species at any site. We conclude that even in mesic environments groundwater can be utilized by trees. We further conclude that these forests are facultatively groundwater-dependent when groundwater depth is <9 m and suggest that during drier-than-average years the contribution of groundwater to stand transpiration is likely to increase significantly at the three shallowest DGW sites.
Effect of single‐dose DPP‐4 inhibitor sitagliptin on β‐cell function and incretin hormone secretion after meal ingestion in healthy volunteers and drug‐naïve, well‐controlled type 2 diabetes subjects

To explore the effects of a single dose of the DPP‐4 inhibitor sitagliptin on glucose‐standardized insulin secretion and β‐cell glucose sensitivity after meal ingestion, 12 healthy and 12 drug‐naïve, well‐controlled type 2 diabetes (T2D) subjects (mean HbA1c 43 mmol/mol, 6.2%) received sitagliptin (100 mg) or placebo before a meal (525 kcal). β‐cell function was measured as the insulin secretory rate at a standardized glucose concentration and the β‐cell glucose sensitivity (the slope between glucose and insulin secretory rate). Incretin levels were also monitored. Sitagliptin increased standardized insulin secretion, in both healthy and T2D subjects, compared to placebo, but without increasing β‐cell glucose sensitivity. Sitagliptin also increased active glucose‐dependent insulinotropic polypeptide (GIP) and glucagon‐like peptide‐1 (GLP‐1) and reduced total (reflecting the secretion) GIP, but not total GLP‐1 levels. We conclude that a single dose of DPP‐4 inhibition induces dissociated effects on different aspects of β‐cell function and incretin hormones after meal ingestion in both healthy and well‐controlled T2D subjects.
Analysis and simulation of distributed T/H with averaging technique in folding and interpolating A/D converters

Distributed track‐and‐hold (T/H) circuit is widely used in folding and interpolating analog‐to‐digital (A/D) converters as a good candidate of single T/H circuits for an optimum overall system performance. But, rigorous analysis and method for design do not exist. This paper brings averaging network to suppress the random offset voltages of the differential difference pre‐amplifiers (DDPAs), which locate before T/H circuit featuring two differential inputs for the requirement of fully differential A/D converters. The first contribution of this work is to present the exact expressions for the output voltage and gain in S‐domain, the integral nonlinearity (INL) and differential nonlinearity (DNL) in DDPAs through the further insight into this architecture. Furthermore, distortion resulting from settling time limitation, interpolation error, folder offset, and all sources of mismatch in averaged DDPAs is considered. In addition, the figure of merit for INL and DNL is proposed to quantify the effectiveness of averaging and be served as the guideline for the optimum design. Finally, these theoretical results were verified against Hspice simulations from a design example of distributed T/H circuits for 8‐bit 250 MHz folding and interpolating A/D converter, which confirmed the accurate and exhaustive analysis and exhibited a good agreement. Copyright © 2009 John Wiley & Sons, Ltd.
Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations

We lack the understanding of why HIV-infected individuals in South Africa progress to AIDS. We hypothesised that in end-stage disease there is a shifting dynamic between T cell imposed immunity and viral immune escape, which, through both compensatory and reverting viral mutations, results in increased viral fitness, elevated plasma viral loads and disease progression. We explored how T cell responses, viral adaptation and viral fitness inter-relate in South African cohorts recruited from Bloemfontein, the Free State (n = 278) and Durban, KwaZulu-Natal (n = 775). Immune responses were measured by γ-interferon ELISPOT assays. HLA-associated viral polymorphisms were determined using phylogenetically corrected techniques, and viral replication capacity (VRC) was measured by comparing the growth rate of gag-protease recombinant viruses against recombinant NL4-3 viruses. We report that in advanced disease (CD4 counts <100 cells/µl), T cell responses narrow, with a relative decline in Gag-directed responses (p<0.0001). This is associated with preserved selection pressure at specific viral amino acids (e.g., the T242N polymorphism within the HLA-B*57/5801 restricted TW10 epitope), but with reversion at other sites (e.g., the T186S polymorphism within the HLA-B*8101 restricted TL9 epitope), most notably in Gag and suggestive of “immune relaxation”. The median VRC from patients with CD4 counts <100 cells/µl was higher than from patients with CD4 counts ≥500 cells/µl (91.15% versus 85.19%, p = 0.0004), potentially explaining the rise in viral load associated with disease progression. Mutations at HIV Gag T186S and T242N reduced VRC, however, in advanced disease only the T242N mutants demonstrated increasing VRC, and were associated with compensatory mutations (p = 0.013). These data provide novel insights into the mechanisms of HIV disease progression in South Africa. Restoration of fitness correlates with loss of viral control in late disease, with evidence for both preserved and relaxed selection pressure across the HIV genome. Interventions that maintain viral fitness costs could potentially slow progression.
Complete mitochondrial genome of the yellowbelly threadfin bream, Nemipterus bathybius (Perciformes, Nemipteridae)

Abstract The complete mitogenome of the yellowbelly threadfin bream, Nemipterus bathybius, has been reported for the first time in this study. The circular mtDNA molecule was 17 353 bp in size and the overall nucleotide composition of H-strand was 29.0% A, 28.3% T, 16.5% G, and 26.2% C, with an A + T bias. The complete mitogenome encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and 2 non-coding regions, as found in other typical vertebrate mitogenomes. The D-loop located between tRNAPro and tRNAPhe genes and the length was 1603 bp, rich in A + T (73.0%). The phylogenetic tree of complete mitogenome sequences of 12 families and 26 species showed that the family Nemipteridae was in the basal position of the suborder Percoidei, whereas its two associated families (Sparidae and Lethrinidae) were clustered together with other 7 families, which supported a non-monophyly of superfamily Sparoidea.
Medical Care Cost of Oropharyngeal Cancer among Texas Patients

Background: The incidence of oropharyngeal cancer is rising rapidly, with the majority of cases being attributable to human papillomavirus (HPV). Despite the availability of a vaccine, rates of HPV vaccination among Texas youth are low. The healthcare cost of oropharyngeal cancer in Texas is unknown. The aims of this study were to estimate the first 2-year cost of treating new cases of oropharyngeal cancer and determine the predictors of oropharyngeal cancer treatment cost in Texas. Methods: This study included a retrospective cohort of 467 Texas patients with commercial insurance claims data with oropharyngeal cancer diagnosed from 2011 to 2014 and a control group of 467 noncancer patients obtained with propensity score matching. Total healthcare cost during the first 2 years after the index date was measured. A generalized linear model was used to identify predictors of monthly cost during the 2 years after the index date. Results: The mean differential adjusted healthcare cost for oropharyngeal cancer cases was $139,749 in the first 2 years. The mean adjusted monthly cost in the first 2 years was $6,693 for cases and $870 for controls. Age, comorbidity, mental health, prediagnostic healthcare cost, and time index were significant predictors of monthly cost. Conclusions: Medical care cost was about $140,000 in the first 2 years after diagnosis of oropharyngeal cancer among commercially insured patients in Texas. Impact: The cost estimates provide important parameters for development of decision-analytic models to inform decision makers about the potential value of initiatives for increasing the HPV immunization rate in the state. Cancer Epidemiol Biomarkers Prev; 26(9); 1443–9. ©2017 AACR.
Local buckling of steel tubular columns.

The economical design of tubular steel columns against local buckling is handicapped by a rather wide variation among the current design rules . To promote a better understanding of the local buckling phenomenon, tests were conducted on seven specimens which were fabricated by cold-rolling and welding. The specimens were made from steel plate with static yield stresses ranging from 204 to 623 MPa (29.56 to 90.32 ksi). Thicknesses ranged from 2.02 to 9.94 mm (0.080 in. to 0.391 in.) and diameter-to-thickness ratios (D/t) from 59 to 294. The slenderness ratios (length-to-radius of gyration) were less than 9 to preclude the effect of overall column buckling. The ultimate stress was limited by the formation of the local buckles in five of the specimens. In the remaining two, stresses were reached slightly above those at which buckling was observed. The nondimensional buckling stresses ranged from 0.829 to 1.069 F/F and generally decreased with increasing D/t ratios. The initial geometric imperfections and the longitudinal welding residual stresses appeared to have no influence on either the location or the pattern of the local buckles. In the post-buckling range the specimens were able to reach capacities of 12 to 23% of their buckling strength. The test results were compared using several different design parameters and equations. Current American design equations were found to be conservative for all of the specimens. An equation is proposed to predict the local buckling strength of fabricated tubular members.
Dynamic Spyware Analysis

Spyware is a class of malicious code that is surreptitiously installed on victims' machines. Once active, it silently monitors the behavior of users, records their web surfing habits, and steals their passwords. Current anti-spyware tools operate in a way similar to traditional virus scanners. That is, they check unknown programs against signatures associated with known spyware instances. Unfortunately, these techniques cannot identify novel spyware, require frequent updates to signature databases, and are easy to evade by code obfuscation. In this paper, we present a novel dynamic analysis approach that precisely tracks the flow of sensitive information as it is processed by the web browser and any loaded browser helper objects. Using the results of our analysis, we can identify unknown components as spyware and provide comprehensive reports on their behavior. The techniques presented in this paper address limitations of our previouswork on spyware detection and significantly improve the quality and richness of our analysis. In particular, our approach allows a human analyst to observe the actual flows of sensitive data in the system. Based on this information, it is possible to precisely determine which sensitive data is accessed and where this data is sent to. To demonstrate the effectiveness of the detection and the comprehensiveness of the generated reports, we evaluated our system on a substantial body of spyware and benign samples.
Effects of low power microwave radiation on biological activity of L-Lactate dehydrogenase enzyme and growth rate of S. Cerevisiae yeast

Recently, microwave radiation, a type/subset of non-ionizing electromagnetic radiation (EMR) has been widely used in industry, medicine, as well as food technology and mobile communication. Use of mobile phones is rapidly growing. Four years from now, 5.1 billion people will be mobile phone users around the globe - almost 1 billion more mobile users than the 4.3 billion people worldwide using them now. Consequently, exposure to weak radiofrequency/microwave radiation generated by these devices is markedly increasing. Accordingly, public concern about potential hazards on human health is mounting [1]. Thermal effects of radiofrequency/microwave radiation are very well-known and extensively studied. Of particular interest are non-thermal effects of microwave exposures on biological systems. Nonthermal effects are described as changes in cellular metabolism caused by both resonance absorption and induced EMR and are often accompanied by a specific biological response. Non-thermal biological effects are measurable changes in biological systems that may or may not be associated with adverse health effects. In this study we studied non-thermal effects of low power microwave exposures on kinetics of Collagenase enzyme and growth rate of yeast Saccharomyces Cerevisiae strains type II. The selected model systems were continuously exposed to microwave radiation at the frequency of 968MHz and power of 10dBm using the designed and constructed (custom made) Transverse Electro- Magnetic (TEM) cell [2]. The findings reveal that microwave radiation at 968MHz and power of 10dBm inhibits Collagenase enzyme activity by 26% and increases significantly (15%) the proliferation rate of yeast cells.
Dynamic ensemble selection VS K-NN: Why and when dynamic selection obtains higher classification performance?

Multiple classifier systems focus on the combination of classifiers to obtain better performance than a single robust one. These systems unfold three major phases: pool generation, selection and integration. One of the most promising MCS approaches is Dynamic Selection (DS), which relies on finding the most competent classifier or ensemble of classifiers to predict each test sample. The majority of the DS techniques are based on the K-Nearest Neighbors (K-NN) definition, and the quality of the neighborhood has a huge impact on the performance of DS methods. In this paper, we perform an analysis comparing the classification results of DS techniques and the K-NN classifier under different conditions. Experiments are performed on 18 state-of-the-art DS techniques over 30 classification datasets and results show that DS methods present a significant boost in classification accuracy even though they use the same neighborhood as the K-NN. The reasons behind the outperformance of DS techniques over the K-NN classifier reside in the fact that DS techniques can deal with samples with a high degree of instance hardness (samples that are located close to the decision border) as opposed to the K-NN. In this paper, not only we explain why DS techniques achieve higher classification performance than the K-NN but also when DS should be used.
TiO2 Nanoparticles Are Phototoxic to Marine Phytoplankton

Nanoparticulate titanium dioxide (TiO2) is highly photoactive, and its function as a photocatalyst drives much of the application demand for TiO2. Because TiO2 generates reactive oxygen species (ROS) when exposed to ultraviolet radiation (UVR), nanoparticulate TiO2 has been used in antibacterial coatings and wastewater disinfection, and has been investigated as an anti-cancer agent. Oxidative stress mediated by photoactive TiO2 is the likely mechanism of its toxicity, and experiments demonstrating cytotoxicity of TiO2 have used exposure to strong artificial sources of ultraviolet radiation (UVR). In vivo tests of TiO2 toxicity with aquatic organisms have typically shown low toxicity, and results across studies have been variable. No work has demonstrated that photoactivity causes environmental toxicity of TiO2 under natural levels of UVR. Here we show that relatively low levels of ultraviolet light, consistent with those found in nature, can induce toxicity of TiO2 nanoparticles to marine phytoplankton, the most important primary producers on Earth. No effect of TiO2 on phytoplankton was found in treatments where UV light was blocked. Under low intensity UVR, ROS in seawater increased with increasing nano-TiO2 concentration. These increases may lead to increased overall oxidative stress in seawater contaminated by TiO2, and cause decreased resiliency of marine ecosystems. Phototoxicity must be considered when evaluating environmental impacts of nanomaterials, many of which are photoactive.
Cd2+ Toxicity to a Green Alga Chlamydomonas reinhardtii as Influenced by Its Adsorption on TiO2 Engineered Nanoparticles

In the present study, Cd2+ adsorption on polyacrylate-coated TiO2 engineered nanoparticles (TiO2-ENs) and its effect on the bioavailability as well as toxicity of Cd2+ to a green alga Chlamydomonas reinhardtii were investigated. TiO2-ENs could be well dispersed in the experimental medium and their pHpzc is approximately 2. There was a quick adsorption of Cd2+ on TiO2-ENs and a steady state was reached within 30 min. A pseudo-first order kinetics was found for the time-related changes in the amount of Cd2+ complexed with TiO2-ENs. At equilibrium, Cd2+ adsorption followed the Langmuir isotherm with the maximum binding capacity 31.9, 177.1, and 242.2 mg/g when the TiO2-EN concentration was 1, 10, and 100 mg/l, respectively. On the other hand, Cd2+ toxicity was alleviated in the presence of TiO2-ENs. Algal growth was less suppressed in treatments with comparable total Cd2+ concentration but more TiO2-ENs. However, such toxicity difference disappeared and all the data points could be fitted to a single Logistic dose-response curve when cell growth inhibition was plotted against the free Cd2+ concentration. No detectable amount of TiO2-ENs was found to be associated with the algal cells. Therefore, TiO2-ENs could reduce the free Cd2+ concentration in the toxicity media, which further lowered its bioavailability and toxicity to C. reinhardtii.