Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA barcoding reveals species composition of sharks and rays in the Indian commercial fishery

Abstract DNA barcoding was successfully used for the accurate identification of chondrichthyans in the Indian commercial marine fishery. About 528 specimens of 111 chondrichthyan species and 34 families, collected from the Indian EEZ, were barcoded for a 655 bp region of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). Generally, five specimens per species were barcoded, but numbers ranged from 2 to 13. The average Kimura 2 parameter (K2P) distance separating individuals within species was 0.32%, and the average distance separating species within genera was 6.73%. Ten species were suggested as putative new species requiring formal descriptions. Based on the morphology and molecular support, 11 elasmobranch species were confirmed first records for Indian waters. The present study confirms the ability of DNA barcoding for the accurate identification of sharks, rays, and their products from Indian waters.
Influence of endogenous insulin secretion on splanchnic glucose and amino acid metabolism in man.

Splanchnic exchange of glucose, 20 individual amino acids, lactate, and pyruvate was studied in normal subjects in the postabsorptive state and after stimulation of endogenous insulin secretion by infusion of glucose at two dose levels. In the basal state, mean splanchnic glucose production was 3.4 mg/kg per min. A net uptake of lactate, pyruvate, and nine amino acids was observed, with alanine accounting for half of the total splanchnic-amino acid extraction. Infusion of glucose at 25 mg/kg per min for 20 min resulted in a fivefold increase in arterial insulin levels and in reversal of splanchnic glucose balance to a net uptake. Splanchnic uptake of alanine, glycine, phenylalanine, lactate, and pyruvate fell by 30-60% due to a reduction in fractional extraction of these substrates, inasmuch as their arterial concentrations did not decline.Administration of glucose at 2 mg/kg per min for 45 min resulted in a 19 mg/100 ml increase in arterial glucose concentration and a doubling of arterial insulin levels. Despite the small increment in insulin, hepatic glucose production fell by 85%. Splanchnic exchange of amino acids, lactate, and pyruvate was unaltered. Estimated total glucose utilization during the infusion was no greater than in the basal state, indicating lack of stimulation of peripheral glucose uptake. IT IS CONCLUDED THAT: (a) inhibition of hepatic glucose production associated with glucose infusion and large increments in insulin levels occurs in the absence of a decrease in the concentration of circulating gluconeogenic substrate, suggesting an hepatic rather than peripheral effect; (b) the liver is the primary target organ whereby glucose homeostasis is achieved with small increments in insulin; (c) the relatively greater sensitivity of the liver's response to insulin as compared with an effect of insulin on the peripheral tissues, may be a consequence of the higher levels of endogenous insulin in portal as compared with peripheral blood.
Role of chest CT in the follow-up of ovarian adenocarcinoma.

OBJECTIVE We describe the prevalence of metastatic chest disease in ovarian adenocarcinoma as seen on CT. We sought to determine whether routine chest CT added any pertinent information to the follow-up examination of patients with ovarian adenocarcinoma. MATERIALS AND METHODS Retrospective review of our tumor registry yielded 96 patients with ovarian adenocarcinoma who had only a single primary malignancy and at least one CT scan of the chest, abdomen, and pelvis. CT scans were reviewed to assess the presence of metastatic chest disease in relation to disease activity in the abdomen and pelvis. Chest CT findings were correlated with the physical examination findings and CA-125 levels and were reviewed in consultation with a gynecologic oncologist to select only those patients with chest abnormalities attributable to metastatic disease. RESULTS A total of 266 CT scans were obtained. Forty (41.7%) of the 96 patients had abnormalities attributable to metastatic chest disease on one or more scans. In the absence of disease progression in the abdomen and pelvis, chest disease progression was seen in only six (2.7%) of the 226 follow-up CT scans. Five of the six patients had rising CA-125 levels. CONCLUSION Correlation of the findings of abdominal and pelvic CT with the physical findings and the CA-125 levels serves as effective follow-up in patients with ovarian adenocarcinoma. The contribution of additional chest CT in these patients is small.
Recognition of the Different Structural Forms of the Capsid Protein Determines the Outcome following Infection with Porcine Circovirus Type 2

ABSTRACT Porcine circovirus type 2 (PCV2) capsid protein (CP) is the only protein necessary for the formation of the virion capsid, and recombinant CP spontaneously forms virus-like particles (VLPs). Located within a single CP subunit is an immunodominant epitope consisting of residues 169 to 180 [CP(169–180)], which is exposed on the surface of the subunit, but, in the structural context of the VLP, the epitope is buried and inaccessible to antibody. High levels of anti-CP(169–180) activity are associated with porcine circovirus-associated disease (PCVAD). The purpose of this study was to investigate the role of the immune response to monomer CP in the development of PCVAD. The approach was to immunize pigs with CP monomer, followed by challenge with PCV2 and porcine reproductive and respiratory syndrome virus (PRRSV). To maintain the CP immunogen as a stable monomer, CP(43–233) was fused to ubiquitin (Ub-CP). Size exclusion chromatography showed that Ub-CP was present as a single 33-kDa protein. Pigs immunized with Ub-CP developed a strong antibody response to PCV2, including antibodies against CP(169–180). However, only low levels of virus neutralizing activity were detected, and viremia levels were similar to those of nonimmunized pigs. As a positive control, immunization with baculovirus-expressed CP (Bac-CP) resulted in high levels of virus neutralizing activity, small amounts of anti-CP(169–180) activity, and the absence of viremia in pigs following virus challenge. The data support the role of CP(169–180) as an immunological decoy and illustrate the importance of the structural form of the CP immunogen in determining the outcome following infection.
Twin births: cesarean section or vaginal delivery?

Objective. To assess morbidity and mortality in twin pregnancy deliveries, according to chorionicity and mode of delivery. Design. Population‐based retrospective cohort. Setting. Fourteen obstetric departments in Denmark. Population. One thousand one hundred and seventy‐five twin pregnancies with two live fetuses at 36+0 weeks of gestation. Methods. Pregnancy outcomes assessed according to chorionicity and mode of delivery. Main outcome measures. Poor outcome defined as five min Apgar score ≤ 7, umbilical artery pH < 7.10, admission to neonatal unit for more than three days or death. Results. Dichorionic (DC) twins, delivered after 36 gestational weeks, with intended vaginal delivery (n= 689) compared with DC twins with planned cesarean section (n= 371) had an increased risk of poor outcome [odds ratio (OR) 1.47, p= 0.037] after adjustment for body mass index, parity and weight discordance. There was no increased risk for poor outcome in monochorionic (MC) twins with intended vaginal delivery (n= 63) compared with planned cesarean section (n= 52; OR 0.87, 95% confidence interval 0.26–2.96). Nulliparity increased the risk of poor outcome in DC (OR 1.5, p= 0.03) and in MC twins (OR 4.01, p= 0.02), as well as birthweight discordance >300 g (DC, OR 1.50, p= 0.02; and MC, OR 6.02, p= 0.002). For DC twins, we found a significantly higher risk of poor outcome of the second‐born twin compared with the first (OR 1.64, p= 0.001). Conclusions. Dichorionic twins born after 36 weeks of gestation had a higher risk of poor outcome by intended vaginal delivery than by planned cesarean section. For MC twins, statistical differences in outcome by mode of delivery could not be seen.
Hepatoprotective Effects of Sophoricoside against Fructose-Induced Liver Injury via Regulating Lipid Metabolism, Oxidation, and Inflammation in Mice.

The dried fruit of Sophora japonica L. is a traditional Chinese herb tea rich in sophoricoside that is an isoflavone glycoside. The aim of current study was to investigate the hepatic protective effect of sophoricoside in high fructose (HF) diet fed mice. Healthy male mice were fed 30% fructose water and treated 80 and 160 mg/kg·bw sophoricoside continuously for 8 wk. Our data showed that administration of sophoricoside at 80 and 160 mg/kg·bw observably decreased the body weight and liver weight in HF-fed mice. It was found that the treatment of sophoricoside decreased the hepatic cholesterol and triglyceride levels, and serum low-density lipoprotein-cholesterol and apolipoprotein-B levels, and elevated the serum high-density lipoprotein-cholesterol and apolipoprotein-A1 levels. Moreover, the administration of sophoricoside decreased the HF-caused elevations of hepatic malonaldehyde, interleukin-1 and tumor necrosis factor-α levels, while increased the HF-induced decreases of hepatic superoxide dismutase and glutathione peroxidase activities. Meanwhile, serum aspartate aminotransferase, alanine aminotransferase, and alkaline phosphatase activities were reduced by treatment of sophoricoside in HF-fed mice. Histopathology of hematoxylin and eosin (H&E) and oil red O staining of liver tissues also confirmed the beneficial effects of sophoricoside against liver injury induced by HF-diet in mice. These findings indicated that sophoricoside may be a novel natural isoflavone for alleviating HF-induced liver injury. PRACTICAL APPLICATION Fruit of Sophora japonica L. is a traditional herb tea and it recently becomes popular in China. Sophoricoside is an isoflavone glycoside (Genistein-4'-O-β-d-glucopyranoside) isolated from S. japonical L, and it possessed differential effects on the body health. The ingestion of sophoricoside or sophora fruit tea may be a novel strategy to prevent non-alcoholic fatty liver disease.
Long-Term Impact of the Kenya Postelection Crisis on Clinic Attendance and Medication Adherence for HIV-Infected Children in Western Kenya

Background:Kenya experienced a political and humanitarian crisis after presidential elections on December 27, 2007. We sought to describe both the immediate and long-term impact of this conflict for HIV-infected children in western Kenya. Methods:We conducted a retrospective study of a cohort of these children for 3 periods: period 1, before the election (October 26, 2007, to December 25, 2007); period 2, immediately after the election (December 26, 2007, to April 15, 2008); and period 3, long-term postelection (April 16, 2008, to December 31, 2008). Two outcome variables of loss-to-follow-up (LTFU) were assessed: initial LTFU and complete LTFU. We assessed clinic adherence by evaluating the difference between actual visits and expected visits. Among children on antiretroviral therapy (ART), we assessed overall medication adherence and changes in medication adherence. Results:Two thousand five hundred forty-nine HIV-infected children <14 years were seen in period 1. Children on ART had less initial LTFU (3.0% compared with 5.1%, P < 0.01) and less complete LTFU (2.6% compared with 6.8%, P < 0.001) than children not on ART. For children not on ART, clinic adherence improved in period 3 compared with period 2. For children on ART with a more strict measure of clinic adherence, clinic adherence declined over time. Orphans had better clinic adherence than nonorphans. Among children on ART, there were few demographic differences when comparing medication adherence between time. Conclusions:HIV-infected children are at risk for disruptions in clinic follow-up and medication adherence after a humanitarian crisis. Individual and contextual factors moderate the effects of these disruptions.
High-speed and high-power GaSb based photodiode for 2.5 μm wavelength operations

By using partially depleted Ga<inf>0.8</inf>In<inf>0.2</inf>As<inf>0.16</inf>Sb<inf>0.84</inf> absorber in GaSb based photodiodes for 2.5 pm wavelength operation, such device achieves high-speed and high-saturation current (3.6 mA/6 GHz) performances with low dark current (0.7μΑ at −2V). Device modeling results suggest that the internal carrier response time limits its dynamic performance.
Cytochrome P450-mediated metabolism in the human gut wall.

OBJECTIVE Although the human small intestine serves primarily as an absorptive organ for nutrients and water, it also has the ability to metabolise drugs. Interest in the small intestine as a drug-metabolising organ has been increasing since the realisation that it is probably the most important extrahepatic site of drug biotransformation. KEY FINDINGS Among the metabolising enzymes present in the small intestinal mucosa, the cytochromes P450 (CYPs) are of particular importance, being responsible for the majority of phase I drug metabolism reactions. Many drug interactions involving induction or inhibition of CYP enzymes, in particular CYP3A, have been proposed to occur substantially at the level of the intestine rather than exclusively within the liver, as originally thought. CYP3A and CYP2C represent the major intestinal CYPs, accounting for approximately 80% and 18%, respectively, of total immunoquantified CYPs. CYP2J2 is also consistently expressed in the human gut wall. In the case of CYP1A1, large interindividual variation in the expression levels has been reported. Data for the intestinal expression of the polymorphic CYP2D6 are conflicting. Several other CYPs, including the common hepatic isoform CYP2E1, are expressed in the human small intestine to only a very low extent, if at all. The distribution of most CYP enzymes is not uniform along the human gastrointestinal tract, being generally higher in the proximal regions of the small intestine. SUMMARY This article reviews the current state of knowledge of CYP enzyme expression in human small intestine, the role of the gut wall in CYP-mediated metabolism, and how this metabolism limits the bioavailability of orally administered drugs. Possible interactions between drugs and CYP activity in the small intestine are also discussed.
Deciphering and Targeting Oncogenic Mutations and Pathways in Breast Cancer.

UNLABELLED : Advances in DNA and RNA sequencing revealed substantially greater genomic complexity in breast cancer than simple models of a few driver mutations would suggest. Only very few, recurrent mutations or copy-number variations in cancer-causing genes have been identified. The two most common alterations in breast cancer are TP53 (affecting the majority of triple-negative breast cancers) and PIK3CA (affecting almost half of estrogen receptor-positive cancers) mutations, followed by a long tail of individually rare mutations affecting <1%-20% of cases. Each cancer harbors from a few dozen to a few hundred potentially high-functional impact somatic variants, along with a much larger number of potentially high-functional impact germline variants. It is likely that it is the combined effect of all genomic variations that drives the clinical behavior of a given cancer. Furthermore, entirely new classes of oncogenic events are being discovered in the noncoding areas of the genome and in noncoding RNA species driven by errors in RNA editing. In light of this complexity, it is not unexpected that, with the exception of HER2 amplification, no robust molecular predictors of benefit from targeted therapies have been identified. In this review, we summarize the current genomic portrait of breast cancer, focusing on genetic aberrations that are actively being targeted with investigational drugs. IMPLICATIONS FOR PRACTICE Next-generation sequencing is now widely available in the clinic, but interpretation of the results is challenging, and its impact on treatment selection is often limited. This work provides an overview of frequently encountered molecular abnormalities in breast cancer and discusses their potential therapeutic implications. This review emphasizes the importance of administering investigational targeted therapies, or off-label use of approved targeted drugs, in the context of a formal clinical trial or registry programs to facilitate learning about the clinical utility of tumor target profiling.
Population and lifestyle trend changes in China: implications for environmental quality

ABSTRACT Demographic changes have considerable impacts on a country’s long-term growth trajectory through the savings, consumption and labour market channels. Population changes, including ageing, migration and urbanization, as well as lifestyle shifts may affect growth for fast-growing countries like China. Rural population migrating to cities consumes more energy services and produces larger emissions since urban lifestyles are generally more energy- and carbon-intensive. Household structures also keep changing across the majority of Chinese cities. Migration and urbanization together drive China’s energy consumption, CO2 emissions upwards and environmental quality downwards if the current trend continues over time. It is, thus, necessary for China to draw useful lessons from experiences in other countries by reconciling population development and environmental changes. This study provides insights into the challenge of environmental sustainability, resulting jointly from population and lifestyle changes in China over the period 1978–2012. The empirical analysis generates empirical findings documenting that population changes and consumption behavioural changes contributed significantly to increased carbon emissions over the last three decades. The modelling results are highly relevant for policymakers who seek to adopt new policies to mitigate lifestyle change-driven environmental challenges that China has to cope with in the foreseeable future.
Daily impaired detachment and short-term effects of impaired sleep quality on next-day commuting near-accidents – an ambulatory diary study

Abstract This study investigated the short-term effects of daily recovery, that is, impaired psychological detachment from work and various actigraphical indicators of sleep quality, on near-accidents when commuting to work the next morning. Furthermore, the mediating effect of actigraphically assessed sleep quality on the relationship between impaired psychological detachment from work and near-accidents when commuting to work was analysed. Fifty-six full-time employees of a Swiss assurance company participated in the one-week study. Multilevel analyses revealed that impaired detachment was highly related to a decrease in sleep duration. Furthermore, impaired daily recovery processes, such as impaired psychological detachment from work and disturbed sleep quality, were related to commuting near-accidents. Impaired sleep quality mediated the effect of impaired psychological detachment from work on these near-accidents. Our results show that occupational safety interventions should address both impaired psychological detachment from work and sleep quality in order to prevent near accidents when commuting to work. Practitioner Summary: Commuting accidents occur frequently and have detrimental effects on employees, organisations and society. This study shows that daily lack of recovery, that is, impaired psychological detachment and impaired sleep quality, is related to near-accidents when commuting to work the next morning. Primary prevention of commuting accidents should therefore address daily lack of recovery.
A hybrid CRF framework for semantic 3D reconstruction

Nowadays, in order to achieve an immersive experience, virtual reality systems usually require vivid 3D models and a good understanding of particular scenes. The limitations of separately optimizing image segmentation and 3D modeling from images have gradually been seen by more and more researchers, so plenty of novel methods on how to combine them for a better result begin to be put forward widely. In this paper, we propose a new hybrid framework to generate semantic 3D dense models from monocular images. Based on the available hierarchical CRFs model, we make full use of the correlation between voxels and their corresponding pixels from different images. Naturally, valuable information from 3D space can be added as one of the important energy items in the model. Either pixels, segments or voxles are all regarded as a node in the huge graph we build. Our ultimate goal is to realize a joint optimization for both 3D dense reconstruction and image segmentation. Experiments have been done on four real challenging datasets and all of the results prove the efficiency of our proposed hybrid framework.
Stage-specific expression of androgen receptor, follicle-stimulating hormone receptor, and anti-Müllerian hormone type II receptor in single, isolated, human preantral follicles: relevance to polycystic ovaries.

CONTEXT Recent evidence indicates that the increase in follicle numbers seen in polycystic ovary syndrome occurs early in folliculogenesis, with androgens being a likely causative candidate. In primates and sheep, androgen excess in utero results in ovarian changes similar to those in polycystic ovary syndrome. There is also increasing interest in the role of anti-Müllerian hormone (AMH) in early folliculogenesis because AMH knockout mice have an early depletion of their stock of primordial follicles. Initiation and early folliculogenesis may therefore be under negative control by AMH and positive control by androgens. OBJECTIVE Because AMH signals exclusively through its type II receptor (AMHRII), the aim of this study was to determine and colocalize the stage-specific expression of AMHRII, androgen receptor (AR), and FSH receptor (FSHR) mRNA in individual, well-characterized preantral follicles. METHOD Follicles were isolated from human ovarian cortex obtained from either oophorectomies or cortical biopsies at cesarean section. Expression of AR, FSHR, and AMHRII mRNA was determined using a nested RT-PCR protocol. RESULTS AR mRNA was not detected in any primordial follicles but was from the transitional stage onward. The number of AR-positive follicles increased at each progressive growth stage. The expression of AR preceded that of FSHR, and only a small percentage of primary follicles expressed FSHR. AMHRII expression was rarely detected. CONCLUSIONS This is the first study to identify the expression of AR in human transitional follicles. Results suggest a role for androgens in promoting early follicle growth and challenging the hypothesis that AMH exerts a direct, inhibitory effect on follicles at this stage.
Time to pregnancy in relation to semen quality assessed by CASA before and after sperm separation.

BACKGROUND In order to provide a reference for infertile men, we defined normal values of semen quality in a population of fertile men, using computer-assisted semen analysis (CASA) before and after sperm separation. Additionally, we investigated the relationship between semen quality and time to pregnancy (TTP). METHODS AND RESULTS Semen samples were obtained from 315 proven fertile men. The median sperm concentration in fresh samples was 107 x 10(6)/ml (5-95 percentiles: 16-322 x 10(6)/ml), the median percentage of motile sperm cells was 65% (14-87%) and the median percentage of progressively motile cells was 37% (5-64%). After density gradient sperm separation, the median total sperm count was 46 x 10(6) (4-350 x 10(6)), the median percentage of motile sperm cells was 77% (16-95%) and the median percentage of progressively motile cells was 63% (11-84%). No significant associations were found between TTP and sperm counts or sperm motility, either before or after sperm separation. This may be due in part to the fact that the study comprised couples with proven fertility. CONCLUSION We have defined semen parameters, including the results of density gradient separation, in a population of normal fertile men which may be of interest in the evaluation of semen samples from infertile men.