Miracle-dz/UniFAR-FTUs huggingface dataset:
A revised set of potentials for β‐turn formation in proteins

Three thousand eight hundred ninety‐nine β‐turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive β‐turn positional potentials for turn types I' and II' for the first time and to provide updated potentials for formation of the more common types I, II, and VIII. Many of the sequence preferences for each of the 4 positions in turns can be rationalized in terms of the formation of stabilizing hydrogen bonds, preferences for amino acids to adopt a particular conformation in ϕ, ψ space, and the involvement of turn types I' and II' in β‐hairpins. Only 1,632 (42%) of the turns occur in isolation; the remainder have at least 1 residue in common with another turn and have hence been classified as multiple turns. Several types of multiple turn have been identified and analyzed.
Cyanobacteriochrome-based photoswitchable adenylyl cyclases (cPACs) for broad spectrum light regulation of cAMP levels in cells

Class III adenylyl cyclases generate the ubiquitous second messenger cAMP from ATP often in response to environmental or cellular cues. During evolution, soluble adenylyl cyclase catalytic domains have been repeatedly juxtaposed with signal-input domains to place cAMP synthesis under the control of a wide variety of these environmental and endogenous signals. Adenylyl cyclases with light-sensing domains have proliferated in photosynthetic species depending on light as an energy source, yet are also widespread in nonphotosynthetic species. Among such naturally occurring light sensors, several flavin-based photoactivated adenylyl cyclases (PACs) have been adopted as optogenetic tools to manipulate cellular processes with blue light. In this report, we report the discovery of a cyanobacteriochrome-based photoswitchable adenylyl cyclase (cPAC) from the cyanobacterium Microcoleus sp. PCC 7113. Unlike flavin-dependent PACs, which must thermally decay to be deactivated, cPAC exhibits a bistable photocycle whose adenylyl cyclase could be reversibly activated and inactivated by blue and green light, respectively. Through domain exchange experiments, we also document the ability to extend the wavelength-sensing specificity of cPAC into the near IR. In summary, our work has uncovered a cyanobacteriochrome-based adenylyl cyclase that holds great potential for the design of bistable photoswitchable adenylyl cyclases to fine-tune cAMP-regulated processes in cells, tissues, and whole organisms with light across the visible spectrum and into the near IR.
Nutritional Risk and Nutritional Status at Admission and Discharge among Chinese Hospitalized Patients: A Prospective, Nationwide, Multicenter Study

ABSTRACT Objective: The objective of this study was to assess nutritional risk and status of Chinese hospitalized patients at admission and discharge and relations with clinical outcomes. Methods: A prospective, nationwide, multicenter study was conducted from June to September 2014 in 34 large hospitals in 18 cities in China. Patients ≥ 18 years with a hospital stay of 7–30 days were recruited. Anthropometric and laboratory indicators, nutritional risk screening, and assessment by Nutritional Risk Screening 2002 (NRS 2002) and subjective global assessment (SGA) were performed within 24 hours of admission and discharge. Clinical data during hospitalization were collected. Results: A total of 6,638 patients met the criteria with a male: female ratio of 1.39:1 and an average age of 59.72 ± 15.40 years. At admission, the proportion of patients with nutritional risk, body mass index (BMI) < 18.5 kg/m2, and moderate to severe malnutrition was 40.12%, 8.92%, and 26.45%, respectively, whereas at discharge, these percentages were 42.28%, 8.91%, and 30.57%, respectively. The values of all of these indicators were higher in patients 65 years of age and older. Patients with nutritional risk at admission had a longer average hospital stay (14.02 ± 6.42 vs 13.09 ± 5.703 days), higher incidence of total complications (6.90% vs 1.52%), and greater total medical expenses (3.39 ± 7.50 vs 3.00 ± 3.38 million RMB; all p < 0.01) than patients without nutritional risk. Similar results were obtained for the patients with nutritional risk at discharge. Conclusion: The prevalence of nutritional risk and malnutrition, including moderate to severe malnutrition, at discharge is higher than that observed at admission; the clinical outcome of patients with nutritional risk is poor.
Learning an Optimizer for Image Deconvolution

As an integral component of blind image deblurring, non-blind deconvolution removes image blur with a given blur kernel, which is essential but difficult due to the ill-posed nature of the inverse problem. The predominant approach is based on optimization subject to regularization functions that are either manually designed, or learned from examples. Existing learning based methods have shown superior restoration quality but are not practical enough due to their restricted model design. They solely focus on learning a prior and require to know the noise level for deconvolution. We address the gap between the optimization-based and learning-based approaches by learning an optimizer. We propose a Recurrent Gradient Descent Network (RGDN) by systematically incorporating deep neural networks into a fully parameterized gradient descent scheme. A parameter-free update unit is used to generate updates from the current estimates, based on a convolutional neural network. By training on diverse examples, the Recurrent Gradient Descent Network learns an implicit image prior and a universal update rule through recursive supervision. Extensive experiments on synthetic benchmarks and challenging real-world images demonstrate that the proposed method is effective and robust to produce favorable results as well as practical for real-world image deblurring applications.
Endocrine, paracrine, and autocrine placental mediators in labor

Considering that preterm birth accounts for about 6–10% of all births in Western countries and of more than 65% of all perinatal deaths, elucidation of the particularly complicated mechanisms of labor is essential for determination of appropriate and effective therapeutic interventions. Labor in humans results from a complex interplay of fetal and maternal factors, which act upon the uterus to trigger pathways leading gradually to a coordinated cervical ripening and myometrial contractility. Although the exact mechanism of labor still remains uncertain, several components have been identified and described in detail. Based on the major role played by the human placenta in pregnancy and the cascade of labor processes activated via placental mediators exerting endocrine, paracrine, and autocrine actions, this review article has aimed at presenting the role of these mediators in term and preterm labor and the molecular pathways of their actions. some of the aforementioned mediators are involved in myometrial activation and preparation and others in myometrial stimulation leading to delivery. In the early stages of pregnancy, myometrial molecules, like progesterone, nitric oxide, and relaxin, contribute to the retention of pregnancy. At late stages of gestation, fetal hypothalamus maturation signals act on the placenta causing the production of hormones, including CRH, in an endocrine manner; the signals then enhance paracrinically the production of more hormones, such as estrogens and neuropeptides, that contribute to cervical ripening and uterine contractility. These molecules act directly on the myometrium through specific receptors, while cytokines and multiple growth factors are also produced, additionally contributing to labor. In situations leading to preterm labor, as in maternal stress and fetal infection, cytokines trigger placental signaling sooner, thus leading to preterm birth.
Sex differences in child and adolescent physical morbidity: cohort study

Background Evidence on sex differences in physical morbidity in childhood and adolescence is based largely on studies employing single/few physical morbidity measures and different informants. We describe sex differences in a wide range of parent/carer-reported physical morbidity measures between ages 4 and 13 years to determine evidence for a generalised pattern of an emerging/increasing female ‘excess’. Methods Parents/carers (approximately 90% mothers) of the population-based UK ALSPAC cohort provided data on general health, physical conditions/symptoms and infections in their child approximately annually between ages 4 and 13. Logistic regression analyses determined the odds of each morbidity measure being reported in respect of females (vs males) at each age and the sex-by-age interaction, to investigate any changing sex difference with age. Results Six measures (general health past year/month, high temperature, rash, eye and ear infections) demonstrated an emerging female ‘excess’, and six (earache, stomach-ache, headache, lice/scabies, cold sores, urinary infections) an increasing female ‘excess’; one (breathlessness) showed a disappearing male ‘excess’. Just two showed either an emerging or increasing male ‘excess’. Most changes were evident during childhood (prepuberty). Six measures showed consistent female ‘excesses’ and four consistent male ‘excesses’. Few measures showed no sex differences throughout this period of childhood/early adolescence. Conclusion Sex differences are evident for a wide range of parent-reported physical morbidity measures in childhood and early adolescence. Far more measures showed an emerging/increasing female ‘excess’ than an emerging/increasing male ‘excess’. Further studies are required to examine whether patterns differ across sociodemographic/cultural groups, and to explain this generalised pattern.
New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model

A new linear interaction energy (LIE) method based on a continuum solvent surface generalized Born (SGB) model is proposed for protein−ligand binding affinity calculations. The new method SGB-LIE is about 1 order of magnitude faster than previously published LIE methods based on explicit solvents. It has been applied to several binding sets: HEPT analogues binding to HIV-1 reverse transcriptase (20 ligands), sulfonamide inhibitors binding to human thrombin (seven ligands), and various ligands binding to coagulation factor Xa (eight ligands). The SGB-LIE predictions and cross-validation results show that about 1.0 kcal/mol accuracy is achievable for binding sets with as many as 20 ligands, e.g., for the HIV-1RT binding set, RMS errors of 1.07 and 1.20 kcal/mol are achieved for LIE fitting and leave-one-out cross validation, respectively, with correlation coefficients r2 equal to 0.774 and 0.717. We have also explored various techniques for the LIE underlying conformation space sampling, including molecula.
Comparison of the Natural History of Genital HPV Infection among Men by Country: Brazil, Mexico, and the United States

Background: Male genital human papillomavirus (HPV) prevalence and incidence has been reported to vary by geographical location. Our objective was to assess the natural history of genital HPV by country among men with a median of 48 months of follow-up. Methods: Men ages 18–70 years were recruited from United States (n = 1,326), Mexico (n = 1,349), and Brazil (n = 1,410). Genital specimens were collected every 6 months and HPV genotyping identified 37 HPV genotypes. Prevalence of HPV was compared between the three countries using the Fisher exact test. Incidence rates and 95% confidence intervals were calculated. The median time to HPV clearance among men with an incident infection was estimated using the Kaplan–Meier method. Results: The prevalence and incidence of the genital HPV types known to cause disease in males (HPV 16 and 6) was significantly higher among men from Brazil than men from Mexico. Prevalence and incidence of those genital HPV types in the United States varied between being comparable with those of Mexico or Brazil. Although genital HPV16 duration was significantly longer in Brazil (P = 0.04) compared with Mexico and the United States, HPV6 duration was shortest in Brazil (P = 0.03) compared with Mexico and the United States. Conclusions: Men in Brazil and Mexico often have similar, if not higher prevalence of HPV compared with men from the United States. Impact: Currently, there is no routine screening for genital HPV among males and while HPV is common in men, and most naturally clear the infection, a proportion of men do develop HPV-related diseases. Men may benefit from gender-neutral vaccine policies. Cancer Epidemiol Biomarkers Prev; 26(7); 1043–52. ©2017 AACR.
Soya bean meal increases litter moisture and foot pad dermatitis in maize and wheat based diets for turkeys but maize and non-soya diets lower body weight

ABSTRACT 1. A 2 × 2 factorial experiment was conducted to compare the effects of wheat or maize based diets differing in dietary electrolyte balance (DEB) on litter moisture and foot pad dermatitis (FPD) at 4, 8 and 12 weeks of age in heavy-medium turkeys. A second objective was to investigate the effects on foot pad dermatitis of the interaction between dietary composition and artificially increasing litter moisture by adding water to the litter. 2. High DEB diets contained soya as the main protein source whereas low DEB diets did not contain soya bean meal. Diets were formulated to be iso-caloric and iso-nitrogenous in each of 3 successive 4-week phases following recommended dietary compositions. DEB concentrations were 330, 290 and 250 mEq/kg in high DEB diets and 230, 200 and 180 mEq/kg in low DEB diets. 3. Litter moisture and mean FPD score were higher in turkeys fed on high DEB diets compared with low DEB diets whereas there was no difference between maize and wheat. 4. Food intake was similar and body weight was lower after litter moisture was artificially raised in the wet compared with the dry litter treatment and there was no interaction with dietary composition. 5. Mean body weight and feed intake were higher in turkeys fed on wheat compared with maize and in high DEB compared with low DEB diets at 12 weeks of age. 6. Lowering dietary DEB for turkeys may improve litter moisture and lower the prevalence of FPD in commercial turkey flocks.
The E3 ubiquitin ligase RNF114 and TAB1 degradation are required for maternal‐to‐zygotic transition

The functional role of the ubiquitin‐proteasome pathway during maternal‐to‐zygotic transition (MZT) remains to be elucidated. Here we show that the E3 ubiquitin ligase, Rnf114, is highly expressed in mouse oocytes and that knockdown of Rnf114 inhibits development beyond the two‐cell stage. To study the underlying mechanism, we identify its candidate substrates using a 9,000‐protein microarray and validate them using an in vitro ubiquitination system. We show that five substrates could be degraded by RNF114‐mediated ubiquitination, including TAB1. Furthermore, the degradation of TAB1 in mouse early embryos is required for MZT, most likely because it activates the NF‐κB pathway. Taken together, our study uncovers that RNF114‐mediated ubiquitination and degradation of TAB1 activate the NF‐κB pathway during MZT, and thus directly link maternal clearance to early embryo development.
Oral Administration of a Select Mixture of Bacillus Probiotics Affects the Gut Microbiota and Goblet Cell Function following Escherichia coli Challenge in Newly Weaned Pigs of Genotype MUC4 That Are Supposed To Be Enterotoxigenic E. coli F4ab/ac Receptor Negative

ABSTRACT Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. Low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to piglets of genotype MUC4 that are supposed to be F4-expressing enterotoxigenic Escherichia coli strain (F4+ ETEC) F4ab/ac receptor negative (i.e., MUC4-resistant piglets) for 1 week before F4+ ETEC challenge. The luminal contents were collected from the mucosa of the colon on day 8 after F4+ ETEC challenge. The BLS mix attenuated E. coli-induced expansion of Bacteroides uniformis, Eubacterium eligens, Acetanaerobacterium, and Sporobacter populations. Clostridium and Turicibacter populations increased following F4+ ETEC challenge in pigs pretreated with low-dose BLS mix. Lactobacillusgasseri and Lactobacillus salivarius populations increased after administration of BLS mix during E. coli infection. The beneficial effects of BLS mix were due in part to the expansion of certain Clostridium, Lactobacillus, and Turicibacter populations, with a corresponding increase in the number of goblet cells in the ileum via upregulated Atoh1 expression, in turn increasing MUC2 production and thus preserving the mucus barrier and enhancing host defenses against enteropathogenic bacteria. However, excessive BLS mix consumption may increase the risk for enteritis, partly through disruption of colonic microbial ecology, characterized by expansion of Proteobacteria and impaired goblet cell function in the ileum. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis. IMPORTANCE The present study is important for improving our understanding of the protective role of probiotics against Escherichia coli infection in piglets. Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. In this study, low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to MUC4-resistant piglets for 1 week before the F4-expressing ETEC strain (F4+ ETEC) challenge. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis.
Different Levels of Expression of the Clock Protein PER and the Glial Marker REPO in Ensheathing and Astrocyte-Like Glia of the Distal Medulla of Drosophila Optic Lobe

Circadian plasticity of the visual system of Drosophila melanogaster depends on functioning of both the neuronal and glial oscillators. The clock function of the former is already quite well-recognized. The latter, however, is much less known and documented. In this study we focus on the glial oscillators that reside in the distal part of the second visual neuropil, medulla (dMnGl), in vicinity of the PIGMENT-DISPERSING FACTOR (PDF) releasing terminals of the circadian clock ventral Lateral Neurons (LNvs). We reveal the heterogeneity of the dMnGl, which express the clock protein PERIOD (PER) and the pan-glial marker REVERSED POLARITY (REPO) at higher (P1) or lower (P2) levels. We show that the cells with stronger expression of PER display also stronger expression of REPO, and that the number of REPO-P1 cells is bigger during the day than during the night. Using a combination of genetic markers and immunofluorescent labeling with anti PER and REPO Abs, we have established that the P1 and P2 cells can be associated with two different types of the dMnGl, the ensheathing (EnGl), and the astrocyte-like glia (ALGl). Surprisingly, the EnGl belong to the P1 cells, whereas the ALGl, previously reported to play the main role in the circadian rhythms, display the characteristics of the P2 cells (express very low level of PER and low level of REPO). Next to the EnGl and ALGl we have also observed another type of cells in the distal medulla that express PER and REPO, although at very low levels. Based on their morphology we have identified them as the T1 interneurons. Our study reveals the complexity of the distal medulla circadian network, which appears to consist of different types of glial and neuronal peripheral clocks, displaying molecular oscillations of higher (EnGl) and lower (ALGl and T1) amplitudes.
Research and development of interfacial bond property between synthetic fiber and concrete

This paper presents the research ideas of interfacial bond property between synthetic fiber and concrete,and summarizes the latest research works and developments.It emphasized on discussing the effect factors and improving measures on interfacial bond between synthetic fiber and concrete.Mechanical model for interfacial bond is analyzed.In addition,the author briefly analyzes their development prospects and tendency.
A Modified Tracheal Transaction Approach for the Repair of Nonmalignant Tracheoesophageal Fistulas: A Report of 5 Cases

Background: A postintubation tracheoesophageal fistula is a rare complication of a tracheotomy. Surgical repair is the only viable option for these patients, but the repair techniques presented in the literature vary. Methods: We used a modified tracheal transaction approach to repair 5 cases of nonmalignant tracheoesophageal fistulas. The procedure was performed with a low cervical collar incision, and the trachea was transected directly. All the procedures were only carried out in the surgical field created by tracheostomy and paratracheal and esophageal dissection was no longer necessary. The esophageal and tracheal walls were separated. Then, a 2-layer longitudinal suture was used for esophageal reconstruction, and end-to-end anastomosis with excessive cartilage resection was used for tracheal reconstruction. Results: A successful 1-stage repair of both the esophagus and the trachea was achieved in 4 cases. The remaining case had a tracheostomy fistula and required a second-stage reconstruction for a long (5.5 cm) defect of the tracheal membrane. No perioperative complications occurred, and all gastric tubes and tracheostomies were removed within 3 months of surgery. Conclusion: Based on our primary experience, this modified tracheal transection approach can be considered an appropriate choice for the reconstruction of nonmalignant tracheal fistulas.
Seroprevalence of Toxoplasma gondii in free-living European mouflon (Ovis orientalis musimon) hunted in central Germany

Despite increasing consumption of mouflon (Ovis orientalis musimon) meat in Germany, there is currently no surveillance of Toxoplasma gondii infection in populations of these animals and generally little knowledge about the prevalence of this protozoan in German wild ungulates. Between 2011 and 2015, we collected 138 blood samples from a free-living mouflon population in central German and tested sera for the presence of T. gondii antibodies using a modified agglutination test (MAT, cut-off 1:20). Antibodies were detected in 31 of the 138 samples (22.46%). There was a significant difference in seroprevalence between the different age classes, with antibodies to T. gondii more frequent in adults. In contrast, there was no significant difference in seroprevalence depending on sex and year of sample collection. Game meat is frequently consumed as raw or undercooked meat and may therefore represent a potential source of human infection with T. gondii.