Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear Magnetic Resonance Lipoprotein Abnormalities in Prediabetic Subjects in the Insulin Resistance Atherosclerosis Study

Background—Subjects with type 2 diabetes have smaller LDL and HDL particles in addition to higher levels of triglycerides and lower HDL cholesterol. Elevated insulin resistance, blood pressure, and dyslipidemia (including small dense LDL) predicted incident diabetes. In the Insulin Resistance Atherosclerosis Study (IRAS) we studied nuclear magnetic resonance (NMR) lipoprotein particle measures in prediabetic individuals, considering potentially modifying covariates, including insulin resistance, as directly measured using a frequently sampled intravenous glucose tolerance test. Methods and Results—Of 830 subjects who were nondiabetic at baseline, 130 (15.7%) developed diabetes after a mean follow-up of 5.2 years. Various lipoprotein abnormalities were found in prediabetic subjects compared with subjects who stayed nondiabetic at follow-up. In logistic regression analyses (demographically adjusted), VLDL particles, large VLDL, LDL particles, small LDL, large HDL, small HDL, VLDL size, LDL size, and HDL size were related to incident diabetes. The relation of VLDL size and small HDL to incident diabetes was independent of waist (odds ratio [OR] [95% CI], 1.43 [1.18 to 1.73] and 1.23 [1.01 to 1.51] for VLDL size and small HDL, respectively) and independent of conventionally (chemically) measured triglycerides and HDL cholesterol (OR [95% CI], 1.45 [1.18 to 1.78] and 1.30 [1.06 to 1.60], respectively). Insulin sensitivity attenuated the relation to incident diabetes of VLDL size (OR [95% CI], 1.25 [1.01 to 1.53]) but not of small HDL particles (OR [95% CI], 1.25 [1.02 to 1.54]). Conclusions—We have shown a range of lipoprotein abnormalities in prediabetic individuals, including compositional changes in HDL and VLDL. These findings extend previous work indicating a proatherogenic state in healthy, nondiabetic subjects who subsequently develop diabetes.
Decision Making Under Uncertainty

Often decision makers are uncertain about the consequences of their choices. Expected utility theory provides a model of decision making under such uncertainty. This theory deals with both objective and subjective uncertainty. It provides insights into actual decisions and it may be used as a guide for decision making. The theory has been extended to incorporate decisions made over time and the learning that results from these decisions. It also provides the basis for the analysis of interacting decision makers in a game.
Suppression of Rheumatoid Arthritis B Cells by XmAb5871, an Anti‐CD19 Antibody That Coengages B Cell Antigen Receptor Complex and Fcγ Receptor IIb Inhibitory Receptor

Engagement of Fcγ receptor IIb (FcγRIIb) suppresses B cell activation and represents a promising target for therapy in autoimmunity. The aim of this study was to characterize B cell immunosuppression mediated by the Fc‐engineered antibody, XmAb5871, which coengages FcγRIIb with the B cell antigen receptor (BCR) complex and that is currently in clinical development for the treatment of rheumatoid arthritis (RA). Because rheumatoid factor (RF) might interfere with the binding of XmAb5871 to FcγRIIb, we correlated RF titers with the potency of XmAb5871.
Correlation of Genomic and Physiological Traits of Thermoanaerobacter Species with Biofuel Yields

ABSTRACT Thermophilic anaerobic noncellulolytic Thermoanaerobacter species are of great biotechnological importance in cellulosic ethanol production due to their ability to produce high ethanol yields by simultaneous fermentation of hexose and pentose. Understanding the genome structure of these species is critical to improving and implementing these bacteria for possible biotechnological use in consolidated bioprocessing schemes (CBP) for cellulosic ethanol production. Here we describe a comparative genome analysis of two ethanologenic bacteria, Thermoanaerobacter sp. X514 and Thermoanaerobacter pseudethanolicus 39E. Compared to 39E, X514 has several unique key characteristics important to cellulosic biotechnology, including additional alcohol dehydrogenases and xylose transporters, modifications to pentose metabolism, and a complete vitamin B12 biosynthesis pathway. Experimental results from growth, metabolic flux, and microarray gene expression analyses support genome sequencing-based predictions which help to explain the distinct differences in ethanol production between these strains. The availability of whole-genome sequence and comparative genomic analyses will aid in engineering and optimizing Thermoanaerobacter strains for viable CBP strategies.
Device-free indoor localisation using radio tomography imaging in 800/900 MHz band

Radio tomographic imaging (RTI) can be used as a method for device free localisation of persons in rooms. By measuring the signal strength of all links of a network of sensor nodes, one can estimate the position of an attenuating object with reasonable precision. The sub-GHz is shown to be suitable for an implementation. Such a design is more energy efficient than a 2.4 GHz implementation. We adapt, evaluate, and improve the device-free localization method of Wilson and Patwari to indoor environments using the 800/900 MHz band. The advantage of using 800/900 MHz is reduced reflections compared to 2.4 GHz. At the same time, the signal is attenuated less by objects in its path. Thus, the methods of Wilson and Patwari needed to be refined and parameters needed to be adapted. We evaluate some combinations of the most common choices of norms to perform a Tikhonov regularisation. The first difference gradient operator with H1 norm works best. We equipped a 5 m×5 m room with 20 wireless sensor nodes. We evaluated the influence of the distance to walls and the height of nodes. The radio tomographic image are post-processed by filters to make likely positions of objects more apparent. Additional parameters values suggested by Wilson and Patwari could not be used for the new frequency and hardware. For example, the ellipse excess path length has been experimentally determined to be close to 20 cm instead of 2 cm. In our experiments-up, we achieve an a maximum average localisation error below of 78 cm. With this work, we have reproduced the results of Wilson and Patwari, adapted it to a different frequency in the 800/900 MHz band and developed improvements to the original algorithms.
Linking Retinal Microvasculature Features With Severity of Diabetic Retinopathy Using Optical Coherence Tomography Angiography.

PURPOSE To correlate retinal vascular features with severity and systemic indicators of diabetic retinopathy (DR) using optical coherence tomography angiography (OCTA). METHODS A total of 209 eyes of 122 type 2 diabetes mellitus patients with DR and 60 eyes of 31 normal Indian subjects underwent OCTA imaging. The diabetic retinopathy patients were graded as having either nonproliferative diabetic retinopathy (NPDR: mild, moderate, and severe NPDR using Early Treatment Diabetic Retinopathy Study classification) or proliferative diabetic retinopathy (PDR). Local fractal analysis was applied to the superficial and deep retinal OCTA images. Foveal avascular zone area (FAZ in mm2); vessel density (%); spacing between large vessels (%); and spacing between small vessels (%) were analyzed. Sensitivity and specificity of vascular parameters were assessed with receiver operating characteristics (ROC) curve. RESULTS Normal eyes had a significantly lower FAZ area, higher vessel density, and lower spacing between large and small vessels compared with DR grades (P < 0.001). In the superficial layer, PDR and severe NPDR had higher spacing between large vessels than mild and moderate NPDR (P = 0.04). However, mild NPDR had higher spacing between the small vessels (P < 0.001). Spacing between the large vessels in the superficial retinal layer correlated positively with HbA1c (r = 0.25, P = 0.03); fasting (r = 0.23, P = 0.02); and postprandial (r = 0.26, P = 0.03) blood sugar. The same spacing in the deep retinal vascular plexus had the highest area under the ROC curve (0.99 ± 0.01) and was uniformly elevated in all diabetic eyes (P > 0.05). CONCLUSIONS Spacing between the large vessels in the superficial and deep retinal layers had superior diagnostic performance than overall vessel density.
Genotype Reconstruction of Paternity in European Lobsters (Homarus gammarus)

Decapod crustaceans exhibit considerable variation in fertilisation strategies, ranging from pervasive single paternity to the near-ubiquitous presence of multiple paternity, and such knowledge of mating systems and behaviour are required for the informed management of commercially-exploited marine fisheries. We used genetic markers to assess the paternity of individual broods in the European lobster, Homarus gammarus, a species for which paternity structure is unknown. Using 13 multiplexed microsatellite loci, three of which are newly described in this study, we genotyped 10 eggs from each of 34 females collected from an Atlantic peninsula in the south-western United Kingdom. Single reconstructed paternal genotypes explained all observed progeny genotypes in each of the 34 egg clutches, and each clutch was fertilised by a different male. Simulations indicated that the probability of detecting multiple paternity was in excess of 95% if secondary sires account for at least a quarter of the brood, and in excess of 99% where additional sire success was approximately equal. Our results show that multiple paternal fertilisations are either absent, unusual, or highly skewed in favour of a single male among H. gammarus in this area. Potential mechanisms upholding single paternal fertilisation are discussed, along with the prospective utility of parentage assignments in evaluations of hatchery stocking and other fishery conservation approaches in light of this finding.
Gravitational wave tests of general relativity with the parameterized post-Einsteinian framework

Gravitational wave astronomy has tremendous potential for studying extreme astrophysical phenomena and exploring fundamental physics. The waves produced by binary black hole mergers will provide a pristine environment in which to study strong field, dynamical gravity. Extracting detailed information about these systems requires accurate theoretical models of the gravitational wave signals. If gravity is not described by General Relativity, analyses that are based on waveforms derived from Einstein's field equations could result in parameter biases and a loss of detection efficiency. A new class of "parameterized post-Einsteinian" (ppE) waveforms has been proposed to cover this eventuality. Here we apply the ppE approach to simulated data from a network of advanced ground based interferometers (aLIGO/aVirgo) and from a future spaced based interferometer (LISA). Bayesian inference and model selection are used to investigate parameter biases, and to determine the level at which departures from general relativity can be detected. We find that in some cases the parameter biases from assuming the wrong theory can be severe. We also find that gravitational wave observations will beat the existing bounds on deviations from general relativity derived from the orbital decay of binary pulsars by a large margin across a wide swath of parameter space.
Lack of Association between an XRCC1 Gene Polymorphism and Colorectal Cancer Survival in Thailand.

BACKGROUND Colorectal cancer (CRC) is one of the most common causes of death worldwide and in Thailand. The X-ray repair cross-complementary protein 1 (XRCC1) is required for efficient DNA repair. The effects of this gene on survival in colorectal cancer remain controversial and have not been reported in Thailand. The aim of this study was to investigate the association of the XRCC1 gene with survival of colorectal cancer patients in a Thai population. MATERIALS AND METHODS Data and blood samples were collected from 255 newly diagnosed and pathologically confirmed CRC patients who were recruited during the period 2002 to 2006 and whose vital status was followed up until 31 October, 2014. Real-time PCR-HRM was used for genotype identification. The Kaplan-Meier method, the log-rank test, and Cox proportional hazard regression were used to estimate cumulative survival curves and compare various survival distributions and adjusted hazard ratios. RESULTS Most of the cases were males, and the median age was 55 years. The median survival time was 2.43 years. The cumulative 1-, 3-, 5-, 7-, and 10 year survival rates were 76.70%, 39.25%, 26.50%, 16.60% and 3.56%, respectively. After adjustment, female gender, ages 50-59 and ≥ 60 years, tumour stage III+IV, a signet-ring cell carcinoma, and poor differentiation had significant associations with increased risk of CRC death. While the XRCC1 Arg/Arg homozygote appeared to be a risk factor for CRC death, the association was not significant. CONCLUSIONS The genetic variant in the XRCC1 may not be associated with the survival of CRC patients in Thailand. Further studies are needed to verify our findings.
A Cross-Sectional Survey of the Association between Bilateral Topical Prostaglandin Analogue Use and Ocular Adnexal Features

We studied the relation between prostaglandin analogue use and ocular adnexal features. We used a prospective, cross-sectional study involving 157 current, 15 past, and 171 never users of prostaglandin analogues. Patients 50 years of age or older and without conditions affecting ocular adnexal anatomy underwent glaucoma medication use history, external digital photography and systematic external adnexal exam. Two masked readers assessed the digital photos for upper lid dermatochalasis and lower lid steatoblepharon using a validated grading scheme. Another masked clinical examiner also assessed upper lid ptosis, levator muscle function, and inferior scleral show. We performed ordinal logistic regression analysis accounting for multiple covariates to assess the relation between prostaglandin analogue use and adnexal features. Multivariable analyses indicated there was a 230-fold increased risk of incremental involution of dermatochalasis (odds ratio (OR) = 2.30; 95% confidence interval (CI) 1.43–3.69; p = 5.44E-04) and a 249-fold increased risk of incremental loss of lower lid steatoblepharon (OR = 2.49; 95% CI, 1.54–4.03; p = 1.98E-04) associated with current prostaglandin analogue use (bimatoprost 0.03%, travoprost 0.005%, or latanoprost 0.004%) versus prostaglandin analogue never or past users. Upper lid ptosis (OR = 4.04; 95% CI, 2.43–6.72; p = 7.37E-08), levator dysfunction (OR = 7.51; 95% CI, 3.39–16.65; p = 6.74E-07) and lower lid retraction (OR = 2.60; 95% CI, 1.58–4.28; p = 1.72E-04) were highly associated with current prostaglandin analogue use versus prostaglandin analogue never or past users. The associations between prostaglandin analogue use and deepening of the upper lid sulci and between prostaglandin analogue use and loss of inferior periorbital fat are confirmed in this multivariable analysis. The associations between prostaglandin analogue use and levator muscle dysfunction and between prostaglandin analogue use and upper lid ptosis represent significant side effects that could impact visual function in glaucoma patients.
Collaboration of Antibody and Inflammation in Clearance of Rabies Virus from the Central Nervous System

ABSTRACT To investigate the involvement of various cellular and humoral aspects of immunity in the clearance of rabies virus from the central nervous system, (CNS), we studied the development of clinical signs and virus clearance from the CNS in knockout mice lacking either B and T cells, CD8+ cytotoxic T cells, B cells, alpha/beta interferon (IFN-α/β) receptors, IFN-γ receptors, or complement components C3 and C4. Following intranasal infection with the attenuated rabies virus CVS-F3, normal adult mice of different genetic backgrounds developed a transient disease characterized by loss of body weight and appetite depression which peaked at 13 days postinfection (p.i.). While these animals had completely recovered by day 21 p.i. , mice lacking either B and T cells or B cells alone developed a progressive disease and succumbed to infection. Mice lacking either CD8+ T cells, IFN receptors, or complement components C3 and C4 showed no significant differences in the development of clinical signs by comparison with intact counterparts having the same genetic background. However, while infectious virus and viral RNA could be detected in normal control mice only until day 8 p.i. , in all of the gene knockout mice studied except those lacking C3 and C4, virus infection persisted through day 21 p.i. Analysis of rabies virus-specific antibody production together with histological assessment of brain inflammation in infected animals revealed that clearance of CVS-F3 by 21 days p.i. correlated with both a strong inflammatory response in the CNS early in the infection (day 8 p.i.), and the rapid (day 10 p.i.) production of significant levels of virus-neutralizing antibody (VNA). These studies confirm that rabies VNA is an absolute requirement for clearance of an established rabies virus infection. However, for the latter to occur in a timely fashion, collaboration between VNA and inflammatory mechanisms is necessary.
A Market Impact Analysis of Soybean Technology Adoption

This article analyzes the welfare benefits of the adoption of Roundup Ready (RR) technology by producers and consumers in the United States and the ROW. Based on a survey data and other secondary data sources we calculated economic surpluses that revealed that while producers and consumers in the U.S. gain some welfare benefits from the adoption, the economic surplus accrued by consumers is offset by producer losses. Our estimates also show that consumers in the rest of the world (ROW) gained economics surpluses while producers in the ROW lost economic surplus due to the non-adoption of RR soybean technology. The estimated total surplus for the pivotal supply shift ($4.64 million) was about half that of the parallel shift ($8.21 million).
Predicting Subsequent Infection in Patients Attending Sexually Transmitted Disease Clinics

Objective/Goal: The objective of this study was to identify characteristics associated with subsequent infection in patients attending a sexually transmitted disease (STD) clinic. Study Design: Records were retrospectively reviewed for patients from public STD clinics in 4 cities for 12 months after their initial visit to assess subsequent infection with gonorrhea, chlamydia, mucopurulent cervicitis, nongonococcal urethritis, pelvic inflammatory disease, primary or secondary syphilis, or trichomoniasis. Results: Among 64,463 patients, 33.9% had an initial STD and 7.0% had a subsequent STD. Patients with an initial STD had significantly higher probability of a subsequent STD than patients without (12.0% vs. 4.4%). A subsequent STD was significantly more likely for both sexes for those with an initial STD, who were symptomatic at initial visit, reporting exchange of sex, or under age 20 as well as for men reporting sex with men. Conclusions: Patients with an initial STD were more likely to return with a subsequent STD. Routinely collected information such as initial diagnosis or age can help identify patients at increased risk of a subsequent STD.
Endosomal-sorting complexes required for transport (ESCRT) pathway-dependent endosomal traffic regulates the localization of active Src at focal adhesions

Active Src localization at focal adhesions (FAs) is essential for cell migration. How this pool is linked mechanistically to the large pool of Src at late endosomes (LEs)/lysosomes (LY) is not well understood. Here, we used inducible Tsg101 gene deletion, TSG101 knockdown, and dominant-negative VPS4 expression to demonstrate that the localization of activated cellular Src and viral Src at FAs requires the endosomal-sorting complexes required for transport (ESCRT) pathway. Tsg101 deletion also led to impaired Src-dependent activation of STAT3 and focal adhesion kinase and reduced cell migration. Impairment of the ESCRT pathway or Rab7 function led to the accumulation of active Src at aberrant LE/LY compartments followed by its loss. Analyses using fluorescence recovery after photo-bleaching show that dynamic mobility of Src in endosomes is ESCRT pathway-dependent. These results reveal a critical role for an ESCRT pathway-dependent LE/LY trafficking step in Src function by promoting localization of active Src to FAs.
Endoscopic management of anastomotic leakage after gastrectomy for gastric cancer: how efficacious is it?

Abstract Background. Anastomotic leak is a dreadful complication with a high mortality rate. The authors aimed to evaluate the efficacy of endoscopic closure of anastomotic dehiscence after gastrectomy in patients with gastric cancer. Methods. The authors retrospectively reviewed 33 patients with anastomotic leakage who had underdone endoscopic treatment among 5249 patients with gastric cancer who underwent radical total or subtotal gastrectomy. Methods of endoscopic closure included clipping with or without detachable snare, fibrosealant, Histoacryl® or stent insertion. Results of endoscopic treatment were categorized as complete, partial closure and failure. Results. The size of the tissue defect was the only factor that had statistically significant differences among the cases with complete closure, partial closure and failure (p = 0.005). For tissue defects smaller than 2 cm in size, complete closure was achieved in 19 (73.1%), partial closure in 5 patients (19.2%) and 2 failed (7.6%). For those larger than 2 cm in size, one (14.3%) was completely closed, four (57.1%) were partially closed and two (28.6%) failed. Conclusions. Endoscopic treatment for anastomotic dehiscence smaller than 2 cm in size had excellent success rate in this study.
Daily temporal organization of laying in Japanese quail: variability and heritability

In birds, many behavioral and physiological processes that occur during reproduction show daily rhythms in response to environmental temporal constraints. In this study, the individual daily organization of laying and its genetic determinant in Japanese quail (Coturnix coturnix japonica) were analyzed. For this purpose, the oviposition time of 102 randomly chosen females, maintained in long-day photoperiodic conditions (LD 14h:10h) for 1 mon was observed and extreme phenotypes selected. Laying is characterized by two parameters: oviposition interval and laying hour. The birds showed a specific time of laying during 24 h. All eggs were laid in the afternoon between 6.5 and 14 h after lights on (HALO). Two laying profiles were determined: 20% of females with an oviposition interval greater than 24 h (24.7±0.2 h) (the “delayed” profile) laid progressively later each day until a pause day. The remaining 80% of the females laid at the same time each day, with few pause days and an oviposition interval close to 24 h (24.0±0.2 h) (the “stable” profile). Among the females, showing this last profile, an intra-individual stability and an inter-individual variability of laying hour was established. Two extreme laying phenotypes were then determined: the “early” phenotype (E) for females laying on average between 7.5 and 9.5 HALO and the “late” phenotype (L) for females laying between 12.5 and 14 HALO. In order to study the genetic basis of the laying hour, three females of each extreme phenotype were selected and crossed with two different males. The E and L females produced 57 F1E and 42 F1L daughters, respectively. F1 females displayed both laying profiles. However, the proportion of females displaying a “delayed” profile was higher in the L line (50%) than in the E line (29.8%). For the “stable” daughters, artificial selection induced an advance in laying hour of 4.7% for the E line and a delay of 4.7% for the L line. Realized heritability was estimated at 0.5. Moreover, the laying hour of the daughters was correlated positively to that of the mothers (N=61;r=0.45). These results support the notion of heritability of oviposition time in Japanese quail.