Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution and genetic diversity of atypical porcine pestivirus (APPV) from piglets with congenital tremor in Guangxi Province, Southern China

Abstract Atypical porcine pestivirus (APPV) was identified and associated with congenital tremor (CT) type A‐II in new born piglets and has been reported in many countries. In China, the first APPV identification in swine herds was reported in Guangdong province in 2016. To investigate the genetic characteristics of APPV in Guangxi province, 53 tissue samples from neonatal piglets with CT were collected and detected from October 2017 to May 2019. Five APPV strains which were named as GX04/2017, GX01‐2018, GX02‐2018, GX01‐2019 and GX02‐2019 were obtained. Sequence analysis revealed that all six APPV strains from Guangxi province, including five strains from this study and one from a previous report, shared 83.3%‐97.5% nucleotide identity of complete genome and 91.7%‐99.1% amino acid identity of the open reading frame (ORF), and shared 77.7%‐97.7% nucleotide identity of complete genome and 90.6%‐99.3% amino acid identity of ORF with reference strains. Phylogenetic analysis indicated that all APPV strains could be divided into three clades based on the complete genome, Npro, Erns and E2 gene sequences, respectively; and the APPV strains from Guangxi province distributed in two clades (clades I and II). No sign of recombination was observed from Guangxi strains. Evolution analysis performed on the complete genome of 58 APPV strains showed that America, Europe and Asia strains during 2006–2019 evolved at a mean rate of 1.37 × 10–4 substitutions/site/year, and the most recent common ancestor (tMRCA) of them was estimated as 1,700.5 years ago. The findings of this study indicated that there existed a high degree of genetic diversity of APPV from Guangxi province, Southern China, which provided important information on the epidemiological features and evolutionary relationships of APPV.
Seven traditional Chinese herbal extracts fermented by Lactobacillus rhamnosus provide anti‐pigmentation effects by regulating the CREB/MITF/tyrosinase pathway

Skin pigmentation is resulted from several processes, such as melanin synthesis transportation and abnormal melanin accumulation in keratinocytes. Various studies have suggested that seven traditional Chinese herbal extracts from Atractylodes macrocephala, Paeonia lactiflora, Bletilla striata, Poria cocos, Dictamnus dasycarpus, Ampelopsis japonica and Tribulus terrestris (which we collectively named ChiBai), show several protective effects toward skin‐related diseases. Lactobacillus rhamnosus, a lactic acid bacterium, has been reported to treat skin inflammation and atopic dermatitis. In this study, the broth produced by the cofermentation of ChiBai with Lactobacillus rhamnosus was studied for its effects on skin pigmentation through in vitro and in vitro experiments. In the in vitro experiments, we found that the fermented broth of ChiBai (FB‐ChiBai) suppressed alpha‐melanocyte stimulating hormone (α‐MSH)‐induced melanogenesis in B16F0 murine melanoma cells without any cytotoxicity at a concentration of 0.5%. FB‐ChiBai significantly attenuated melanin production, tyrosinase activities and melanogenesis‐related signaling pathways. Treatment with FB‐ChiBai also reduced the nuclear translocation and promoter binding activities of MITF. In the in vivo experiments, FB‐ChiBai was topically applied to the dorsal skin of C57BL/6J nude mice and concurrently irradiated with UVB, three times a week for 8 weeks. The results indicated that FB‐ChiBai alleviated UVB‐induced hyperpigmentation by reducing epidermal hyperplasia and inhibiting the CREB/MITF/tyrosinase pathway. In conclusion, our data indicated that the anti‐melanogenic effects of FB‐ChiBai are mediated by the inhibition of CREB/MITF/tyrosinase signaling pathway. The findings suggest that FB‐ChiBai can protect against UV‐B irradiation and that it might be used as an agent in cosmetic products to protect against UVB‐induced hyperpigmentation.
Analysis of energy and friction coefficient fluctuations of a Lennard-Jones liquid coupled to the Nosé–Hoover thermostat

Thermal fluctuations of a many-body system coupled to a Nosé–Hoover thermostat depend on the strength of the coupling parameter τ*. A wrong choice may bring non-ergodic features and non-canonical fluctuations. Here, we analyse by means of molecular dynamics simulations both the energy fluctuations and the spectrum of the friction coefficient ζ* of an extended Lennard-Jones system in a wide range of τ* at liquid density. Three ranges of τ* are identified – small, intermediate and large, plus their transitions. For τ* values in the intermediate range, ζ* shows chaotic behaviour, and the particle system requires reasonable computing time for its thermalisation. As a result, the extended system is ergodic and energy fluctuations are canonical and stable in time. On the contrary, small and large ranges of τ* reveal clear evidence of periodicity in the thermostat variable, for instance by propagating the initial temperature condition. For these two ranges, the extended system shows non-ergodic features and energy fluctuations are non-canonical. For large τ*, micro-canonical fluctuations are occasionally obtained. For small to intermediate and intermediate to large ranges of τ*, the thermostat variable exhibits beat waves and is thus unable to reach equilibrium no matter how extended in time the simulations are. Here, we compare our results with previous work and explain the differences.
Impact of trophectoderm biopsy on obstetric and perinatal outcomes following frozen-thawed embryo transfer cycles.

STUDY QUESTION Does trophectoderm biopsy for preimplantation genetic testing (PGT) increase the risk of obstetric or perinatal complications in frozen-thawed embryo transfer (FET) cycles? SUMMARY ANSWER Trophectoderm biopsy may increase the risk of hypertensive disorders of pregnancy (HDP) in pregnancies following FET cycles. WHAT IS KNOWN ALREADY Trophectoderm biopsy has replaced blastomere biopsy as the standard of care to procure cells for PGT analysis. Recently, there has been concern that trophectoderm biopsy may adversely impact obstetric and perinatal outcomes. Previous studies examining this question are limited by use of inappropriate control groups, small sample size or reporting on data that no longer reflects current IVF practice. STUDY DESIGN, SIZE, DURATION This was a retrospective cohort study conducted at a single university-affiliated fertility center. A total of 756 patients who underwent FET with transfer of previously vitrified blastocysts that had either trophectoderm biopsy or were unbiopsied and resulted in a singleton live birth between 2013 and 2019 were included. PARTICIPANTS/MATERIALS, SETTING, METHODS Obstetric and perinatal outcomes for patients aged 20-44 years who underwent FET with transfer of previously vitrified blastocysts that were either biopsied (n = 241) or unbiopsied (n = 515) were analyzed. Primary outcome was odds of placentation disorders including HDP and rate of fetal growth restriction (FGR). Binary logistic regression was performed to control for potential covariates. MAIN RESULTS AND THE ROLE OF CHANCE The biopsy group was significantly older, had fewer anovulatory patients, was more often nulliparous and had fewer embryos transferred compared to the unbiopsied group. After controlling for potential covariates, the probability of developing HDP was significantly higher in the biopsy group compared with unbiopsied group (adjusted odds ratio (aOR) 1.943, 95% CI 1.072-3.521; P = 0.029). There was no significant difference between groups in the probability of placenta previa or placenta accreta. There was also no significant difference in the rate of FGR (aOR 1.397; 95% CI, 0.815-2.395; P = 0.224) or the proportion of low (aOR 0.603; 95% CI, 0.336-1.084; P = 0.091) or very low (aOR 2.948; 95% CI, 0.613-14.177; P = 0.177) birthweight infants comparing biopsied to unbiopsied groups. LIMITATIONS, REASON FOR CAUTION This was a retrospective study performed at a single fertility center, which may limit the generalizability of our findings. WIDER IMPLICATIONS OF THE FINDINGS Trophectoderm biopsy may increase the risk of HDP in FET cycles, however, a prospective multicenter randomized trial should be performed to confirm these findings. STUDY FUNDING/COMPETING INTEREST(S) No specific funding was obtained for this study. The authors declare no conflict of interest. TRIAL REGISTRATION NUMBER NA.
Examining Transdiagnostic Factors among Firefighters in Relation to Trauma Exposure, Probable PTSD, and Probable Alcohol Use Disorder

Abstract Objective Firefighters represent a distinct group of first responders that are at heightened risk of developing posttraumatic stress disorder (PTSD) and alcohol use disorder (AUD). Assessing the role of transdiagnostic factors that underlie PTSD-AUD associations can inform specialized interventions among this population. This study included urban firefighters (N = 657) with probable PTSD-AUD (n = 27), probable PTSD-alone (n = 35), probable AUD-alone (n = 125), and trauma-exposure-only (n = 470). Methods: All firefighters completed a self-report, online questionnaire battery. Between group differences in anxiety sensitivity (AS), distress tolerance (DT), mindfulness, and emotional regulation difficulties (ERD) were assessed. It was hypothesized that firefighters with probable PTSD-AUD would endorse elevated AS and ERD, and reduced DT and mindfulness in comparison to all other diagnostic groups. Relationship status was included as a covariate in all comparisons. Results: Firefighters with probable PTSD-AUD endorsed elevated AS and ERD, and reduced DT and mindfulness in comparison to firefighters with trauma-exposure-only and probable AUD-alone. Firefighters with probable PTSD-AUD and probable PTSD-alone did not significantly differ. Conclusions: Given these findings, this line of inquiry has great potential to inform specialized, evidence-based mental health programming among firefighter populations, who represent a unique population susceptible to trauma-exposure, PTSD symptomology, and problematic alcohol use.
Improved Pulse-Controlled Conductance Adjustment in Trilayer Resistors by Suppressing Current Overshoot

In this work, we demonstrate the enhanced synaptic behaviors in trilayer dielectrics (HfO2/Si3N4/SiO2) on highly doped n-type silicon substrate. First, the three dielectric layers were subjected to material and chemical analyses and thoroughly investigated via transmission electron microscopy and X-ray photoelectron spectroscopy. The resistive switching and synaptic behaviors were improved by inserting a Si3N4 layer between the HfO2 and SiO2 layers. The electric field within SiO2 was mitigated, thus reducing the current overshoot in the trilayer device. The reset current was considerably reduced in the trilayer device compared to the bilayer device without a Si3N4 layer. Moreover, the nonlinear characteristics in the low-resistance state are helpful for implementing high-density memory. The higher array size in the trilayer device was verified by cross-point array simulation. Finally, the multiple conductance adjustment was demonstrated in the trilayer device by controlling the gradual set and reset switching behavior.
Making it to the PhD: Gender and student performance in sub-Saharan Africa

Women’s underrepresentation in science, technology, engineering, and mathematics (STEM) impedes progress in solving Africa’s complex development problems. As in other regions, women’s participation in STEM drops progressively moving up the education and career ladder, with women currently constituting 30% of Africa’s STEM researchers. This study elucidates gender-based differences in PhD performance using new survey data from 227 alumni of STEM PhD programs in 17 African countries. We find that, compared to their male counterparts, sampled women had about one less paper accepted for publication during their doctoral studies and took about half a year longer to finish their PhD training. Negative binomial regression models provide insights on the observed differences in women’s and men’s PhD performance. Results indicate that the correlates of publication productivity and time to PhD completion are very similar for women and men, but some gender-based differences are observed. For publication output, we find that good supervision had a stronger impact for men than women; and getting married during the PhD reduced women’s publication productivity but increased that of men. Becoming a parent during the PhD training was a key reason that women took longer to complete the PhD, according to our results. Findings suggest that having a female supervisor, attending an institution with gender policies in place, and pursuing the PhD in a department where sexual harassment by faculty was perceived as uncommon were enabling factors for women’s timely completion of their doctoral studies. Two priority interventions emerge from this study: (1) family-friendly policies and facilities that are supportive of women’s roles as wives and mothers and (2) fostering broader linkages and networks for women in STEM, including ensuring mentoring and supervisory support that is tailored to their specific needs and circumstances.
Development and Compositional Analysis of Protien Rich Soyabean-maize Flour Blended Cookies

Bakery products are mainly prepared from wheat as its main ingredient. The present study was designed to blend soy flour and maize flour as a source of protein and fibre replacing refined flour to make protein rich cookies. Soyabean is limiting in sulphur amino acid methionine but higher in lysine, isoflavones and protein while maize protein is deficient in lysine and tryptophan and rich in methionine. Thereby blending soy and maize flour nutritional quality can be improved. Cookies were prepared by blending soy flour (SF) with maize flour (MF) from 0 to 100% levels using traditional creamery method. Cookies were evaluated for physico-chemical, functional and sensory quality parameters. Combinations of MF/SF significantly improved (p<0.05) the nutrient contents of the blends when compared to MF alone. The cookie containing maximum level of SF have high content of protein, crude fibre, ash and fat while the cookie containing maximum level of MF have high content of carbohydrate. The cookies with 10% soya flour and 90% maize flour scored maximum for all the sensory quality attributes. The use of soy flour/maize flour blends for cookie preparation is an advantage in a non traditional wheat producing country and in improving nutritional quality too.
The pro-migration and anti-apoptosis effects of HMGA2 in HUVECs stimulated by hypoxia

ABSTRACT High-mobility group AT-hook2 (HMGA2), serving as an architectural transcription factor, participates in plenty of biological processes. Our study is aimed at illustrating the effect of HMGA2 on hypoxia-induced HUVEC injury and the underlying mechanism. To induce hypoxia-related cell injury, HUVECs were exposed to hypoxic condition for 12–24 h. Molecular expression was determined by Western blot analysis, real-time PCR and immunofluorescence staining. Cell migration was monitored by wound healing assay and Transwell chamber assay. Cell proliferation and apoptosis were measured by MTT assay kits and TUNEL staining. In this study, we discovered that HMGA2 was upregulated in hypoxia-induced HUVECs. Overexpression of HMGA2 promoted cell migration, decreased the apoptosis ratio in response to hypoxia stimulation, while HMGA2 knockdown inhibited cell migration and accelerated apoptosis in HUVECs under hypoxic condition. Mechanistically, we found that HMGA2 induced increased expression of HIF-1α,VEGF, eNOS and AKT. eNOS knockdown significantly reduced HMGA2-mediated pro-migration effects, and AKT knockdown strikingly counteracted HMGA2-mediated anti-apoptotic effect. Hence, our data indicated that HMGA2 promoted cell migration by regulating HIF-1α/VGEF/eNOS signaling and prevented cell apoptosis by activating HIF-1α/VGEF/AKT signaling in HUVECs.
Comparison of endoscopic versus percutaneous drainage of symptomatic pancreatic necrosis in the early (< 4 weeks) phase of illness

Background and Objective: Pancreatic fluid collections in early phase of illness <4 weeks after onset of acute pancreatitis (AP) are usually treated with percutaneous drainage (PCD). There is a paucity of data comparing early (<4 weeks) endoscopic transluminal drainage (ETD) with PCD in patients with symptomatic pancreatic necrosis (PN). The objective of this study is to compare the safety and efficacy of early ETD with PCD in patients with symptomatic PN. Patients and Methods: Retrospective analysis of database of patients with symptomatic PN treated early (<4 weeks of onset of AP) with either ETD (encapsulated wall on EUS) or PCD. Results: Twenty-three patients (19 M; mean age: 36.1 years) were treated with ETD and 41 patients (29 M; mean age: 39.6 years) were treated with PCD, respectively. ETD and PCD were done 24.2 ± 2.3 and 24.2 ± 2.0 days after onset of AP, respectively (P = 0.84). In the ETD group, 35% of patients were treated with self-expanding metallic stents and 48% of patients required direct endoscopic necrosectomy. In the PCD group, 74% of patients were treated with multiple catheters and 91% of patients with either saline or streptokinase irrigation. As compared to the ETD group, patients in the PCD group took longer time for resolution (61.9 ± 22.9 days vs. 30.9 ± 5.6 days; P < 0.00001), increased need for surgery (30% vs. 4%; P = 0.01), and frequency of formation of external pancreatic fistula (EPF) (22% vs. nil; P = 0.02). Conclusions: ETD of PN in early phase of illness is associated with a shorter duration for resolution and infrequent need of salvage surgery compared to PCD. EPF formation is a significant adverse event with PCD.
Efficacy and safety of ruxolitinib in patients with myelofibrosis: a retrospective and multicenter experience in Turkey

Background/aim The aim of this study is to assess the efficacy and safety of ruxolitinib in patients with myelofibrosis. Materials and methods From 15 centers, 176 patients (53.4% male, 46.6% female) were retrospectively evaluated. Results The median age at ruxolitinib initiation was 62 (28–87) and 100 (56.8%) of all were diagnosed as PMF. Constitutional symptoms were observed in 84.7%. The median initiation dose of ruxolitinib was 30 mg (10–40). Dose change was made in 69 (39.2%) patients. Forty seven (35.6%) and 20 (15.2%) of 132 patients had hematological and nonhematological adverse events, respectively. The mean spleen sizes before and after ruxolitinib treatment were 219.67 ± 46.79 mm versus 199.49 ± 40.95 mm, respectively (p < 0.001). There was no correlation between baseline features and subsequent spleen response. Overall survival at 1-year was 89.5% and the median follow up was 10 (1–55) months. We could not show any relationship between survival and reduction in spleen size (p = 0.73). Conclusion We found ruxolitinib to be safe, well tolerated, and effective in real-life clinical practice in Turkey. Ruxolitinib dose titration can provide better responses in terms of not only clinical benefit but also for long term of ruxolitinib treatment.
Loss to follow up of pregnant women with HIV and infant HIV outcomes in the prevention of maternal to child transmission of HIV programme in two high-burden provinces in Papua New Guinea: a retrospective clinical audit

Introduction Despite early adoption of the WHO guidelines to deliver lifelong antiretroviral (ARV) regimen to pregnant women on HIV diagnosis, the HIV prevention of mother to child transmission programme in Papua New Guinea remains suboptimal. An unacceptable number of babies are infected with HIV and mothers not retained in treatment. This study aimed to describe the characteristics of this programme and to investigate the factors associated with programme performance outcomes. Methods We conducted a retrospective analysis of clinical records of HIV-positive pregnant women at two hospitals providing prevention of mother to child transmission services. All women enrolled in the prevention of mother to child transmission programme during the study period (June 2012–June 2015) were eligible for inclusion. Using logistic regression, we examined the factors associated with maternal loss to follow-up (LTFU) before birth and before infant registration in a paediatric ARV programme. Results 763 of women had records eligible for inclusion. Demographic and clinical differences existed between women at the two sites. Almost half (45.1%) of the women knew their HIV-positive status prior to the current pregnancy. Multivariate analysis showed that women more likely to be LTFU by the time of birth were younger (adjusted OR (AOR)=2.92, 95% CI 1.16 to 7.63), were newly diagnosed with HIV in the current/most recent pregnancy (AOR=3.50, 95% CI 1.62 to 7.59) and were in an HIV serodiscordant relationship (AOR=2.94, 95% CI 1.11 to 7.84). Factors associated with maternal LTFU before infant registration included being primipara at the time of enrolment (AOR=3.13, 95% CI 1.44 to 6.80) and being newly diagnosed in that current/most recent pregnancy (AOR=2.49, 95% CI 1.31 to 4.73). 6.6% (50 of 763) of exposed infants had a positive HIV DNA test. Conclusions Our study highlighted predictors of LTFU among women. Understanding these correlates at different stages of the programme offers important insights for targets and timing of greater support for retention in care.
Deep Learning Predicts Underlying Features on Pathology Images with Therapeutic Relevance for Breast and Gastric Cancer

Simple Summary DNA repair deficiency (DRD) is common in many cancers. This deficiency contributes to pathogenesis of the disease, but it also presents an opportunity for therapeutic targeting. However, current DRD identification assays are not available for all patients. We propose an efficient machine learning algorithm which can predict DRD from histopathological images. The utility of our method was shown by considering the detection of homologous recombination deficiency (HRD) and mismatch repair deficiency (MMRD) in breast and gastric cancer respectively. Our findings demonstrate that machine-learning approaches can be used in advanced applications to assist therapy decisions. Abstract DNA repair deficiency (DRD) is an important driver of carcinogenesis and an efficient target for anti-tumor therapies to improve patient survival. Thus, detection of DRD in tumors is paramount. Currently, determination of DRD in tumors is dependent on wet-lab assays. Here we describe an efficient machine learning algorithm which can predict DRD from histopathological images. The utility of this algorithm is demonstrated with data obtained from 1445 cancer patients. Our method performs rather well when trained on breast cancer specimens with homologous recombination deficiency (HRD), AUC (area under curve) = 0.80. Results for an independent breast cancer cohort achieved an AUC = 0.70. The utility of our method was further shown by considering the detection of mismatch repair deficiency (MMRD) in gastric cancer, yielding an AUC = 0.81. Our results demonstrate the capacity of our learning-base system as a low-cost tool for DRD detection.