Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering Design Principles of Förster Resonance Energy Transfer-Based Protease Substrates: Thermolysin-Like Protease from Geobacillus stearothermophilus as a Test Case

Protease activity is frequently assayed using short peptides that are equipped with a Förster resonance energy transfer (FRET) reporter system. Many frequently used donor–acceptor pairs are excited in the ultraviolet range and suffer from low extinction coefficients and quantum yields, limiting their usefulness in applications where a high sensitivity is required. A large number of alternative chromophores are available that are excited in the visible range, for example, based on xanthene or cyanine core structures. These alternatives are not only larger in size but also more hydrophobic. Here, we show that the hydrophobicity of these chromophores not only affects the solubility of the resulting FRET-labeled peptides but also their kinetic parameters in a model enzymatic reaction. In detail, we have compared two series of 4–8 amino acid long peptides, designed to serve as substrates for the thermolysin-like protease (TLP-ste) from Geobacillus stearothermophilus. These peptides were equipped with a carboxyfluorescein donor and either Cy5 or its sulfonated derivative Alexa Fluor 647 as the acceptor. We show that the turnover rate kcat is largely unaffected by the choice of the acceptor fluorophore, whereas the KM value is significantly lower for the Cy5- than for the Alexa Fluor 647-labeled substrates. TLP-ste is a rather nonspecific protease with a large number of hydrophobic amino acids surrounding the catalytic site, so that the fluorophore itself may form additional interactions with the enzyme. This hypothesis is supported by the result that the difference between Cy5- and Alexa Fluor 647-labeled substrates becomes less pronounced with increasing peptide length, that is, when the fluorophore is positioned at a larger distance from the catalytic site. These results suggest that fluorophores may become an integral part of FRET-labeled peptide substrates and that KM and kcat values are generally only valid for a specific combination of the peptide sequence and FRET pair.
Green Space Visits among Adolescents: Frequency and Predictors in the PIAMA Birth Cohort Study

Background: Green space may influence health through several pathways, for example, increased physical activity, enhanced social cohesion, reduced stress, and improved air quality. For green space to increase physical activity and social cohesion, spending time in green spaces is likely to be important. Objectives: We examined whether adolescents visit green spaces and for what purposes. Furthermore, we assessed the predictors of green space visits. Methods: In this cross-sectional study, data for 1911 participants of the Dutch PIAMA (Prevention and Incidence of Asthma and Mite Allergy) birth cohort were analyzed. At age 17, adolescents reported how often they visited green spaces for physical activities, social activities, relaxation, and to experience nature and quietness. We assessed the predictors of green space visits altogether and for different purposes by log-binomial regression. Results: Fifty-three percent of the adolescents visited green spaces at least once a week in summer, mostly for physical and social activities. Adolescents reporting that a green environment was (very) important to them visited green spaces most frequently {adjusted prevalence ratio (PR) [95% confidence interval (CI)] very vs. not important: 6.84 (5.10, 9.17) for physical activities and 4.76 (3.72, 6.09) for social activities}. Boys and adolescents with highly educated fathers visited green spaces more often for physical and social activities. Adolescents who own a dog visited green spaces more often to experience nature and quietness. Green space visits were not associated with the objectively measured quantity of residential green space, i.e., the average normalized difference vegetation index (NDVI) and percentages of urban, agricultural, and natural green space in circular buffers around the adolescents’ homes. Conclusions: Subjective variables are stronger predictors of green space visits in adolescents than the objectively measured quantity of residential green space. https://doi.org/10.1289/EHP2429
A content-based retrieval of mammographic masses using the curvelet descriptor

Computer-aided diagnosis (CAD) that uses content based image retrieval (CBIR) strategies has became an important research area. This paper presents a retrieval strategy that automatically recovers mammography masses from a virtual repository of mammographies. Unlike other approaches, we do not attempt to segment masses but instead we characterize the regions previously selected by an expert. These regions are firstly curvelet transformed and further characterized by approximating the marginal curvelet subband distribution with a generalized gaussian density (GGD). The content based retrieval strategy searches similar regions in a database using the Kullback-Leibler divergence as the similarity measure between distributions. The effectiveness of the proposed descriptor was assessed by comparing the automatically assigned label with a ground truth available in the DDSM database.1 A total of 380 masses with different shapes, sizes and margins were used for evaluation, resulting in a mean average precision rate of 89.3% and recall rate of 75.2% for the retrieval task.
Career and Romantic Partnership Role Salience Between Sexual Minority Men Living With and Without a Chronic Illness/Disability (CID)

Ratings of career and romantic partnership life role salience were explored between sexual minority men in same-sex, dual-earner relationships living with and without chronic illness/disability (CID) conditions. Approximately 141 sexual minority men living in the United States completed questionnaires via the Internet. Results indicated that sexual minority men living with a CID scored higher on romantic partnership life role salience, but lower on career life role salience when compared with sexual minority men not living with a CID. Limitations and implications for practice and research are discussed.
Circulating and Adipose Tissue mRNA Levels of Zinc-α2-Glycoprotein, Leptin, High-Molecular-Weight Adiponectin, and Tumor Necrosis Factor-Alpha in Colorectal Cancer Patients With or Without Obesity

Objectives To explore zinc-α2-glycoprotein (ZAG), leptin, high-molecular-weight adiponectin (HMW-ADPN), and tumor necrosis factor-alpha (TNF-α) levels in serum and subcutaneous and visceral white adipose tissue (sWAT and vWAT) among normal weight (NW) and overweight/obese (OW/OB) patients with colorectal cancer (CRC). Methods A total of 76 Chinese CRC patients (42 NW + CRC, 34 OW/OB + CRC) and 40 healthy controls were recruited. Serum levels of the adipokines of interest were measured by an enzyme-linked immunosorbent assay method, and their mRNA levels in sWAT and vWAT were determined by reverse transcription quantitative PCR methods. Results Serum ZAG levels in the NW + CRC group were significantly increased by 11.7% compared with the healthy controls. Serum leptin levels in the OW/OB + CRC group were found to be increased by 57.7%, while HMW-ADPN levels were decreased by 23.5% when compared with the NW + CRC group of CRC patients. Additionally, ZAG mRNA levels in sWAT were significantly reduced by 78.8% in OB + CRC in comparison with NW + CRC patients. ZAG mRNA levels were negatively associated with body mass index (BMI) in sWAT but positively correlated with BMI in vWAT. TNF-α mRNA levels in vWAT of OB + CRC patients were significantly increased by 2.8-fold when compared with NW + CRC patients. In particular, CRC was independently associated with serum ZAG levels. The risk of CRC in participants with high tertile serum ZAG levels was 5.84-fold higher than in those with low tertile ZAG levels after adjusting for age, gender, and other confounders [odds ratio (OR) = 6.84, 95% confidence interval (CI) 1.70–27.54, P = 0.03]. The CRC risk in participants with high tertile leptin levels was only 10.7% of those with low tertile leptin levels (OR = 0.11, 95% CI 0.01–0.89, P = 0.04). The area under the receiver operating characteristic (ROC) curve of ZAG was 0.66 (95% CI 0.54–0.77, P < 0.05). At the cutoff value of 1.42 µg/mL serum ZAG, the sensitivity and specificity for differentiating patients with CRC from controls were 62.2 and 69.2%, respectively. Conclusion Serum ZAG levels were significantly increased in CRC patients. Subjects with higher circulating ZAG and lower leptin levels were more likely to have CRC than those with lower ZAG and higher leptin levels. Serum ZAG might be a potential diagnostic biomarker for CRC in the Chinese population.
The core effector Cce1 is required for early infection of maize by Ustilago maydis

Abstract The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host.
The transcription factor prospero homeobox protein 1 is a direct target of SoxC proteins during developmental vertebrate neurogenesis

The high‐mobility‐group domain containing SoxC transcription factors Sox4 and Sox11 are expressed and required in the vertebrate central nervous system in neuronal precursors and neuroblasts. To identify genes that are widely regulated by SoxC proteins during vertebrate neurogenesis we generated expression profiles from developing mouse brain and chicken neural tube with reduced SoxC expression and found the transcription factor prospero homeobox protein 1 (Prox1) strongly down‐regulated under both conditions. This led us to hypothesize that Prox1 expression depends on SoxC proteins in the developing central nervous system of mouse and chicken. By combining luciferase reporter assays and over‐expression in the chicken neural tube with in vivo and in vitro binding studies, we identify the Prox1 gene promoter and two upstream enhancers at −44 kb and −40 kb relative to the transcription start as regulatory regions that are bound and activated by SoxC proteins. This argues that Prox1 is a direct target gene of SoxC proteins during neurogenesis. Electroporations in the chicken neural tube furthermore show that Prox1 activates a subset of SoxC target genes, whereas it has no effects on others. We propose that the transcriptional control of Prox1 by SoxC proteins may ensure coupling of two types of transcription factors that are both required during early neurogenesis, but have at least in part distinct functions.
Resistance of native oak to recurrent drought conditions simulating predicted climatic changes in the Mediterranean region.

The capacity of a Quercus pubescens forest to resist recurrent drought was assessed on an in situ experimental platform through the measurement of a large set of traits (ecophysiological and metabolic) studied under natural drought (ND) and amplified drought (AD) induced by partial rain exclusion. This study was performed during the third and fourth years of AD, which correspond to conditions of moderate AD in 2014 and harsher AD in 2015, respectively. Although water potential (Ψ) and net photosynthesis (Pn) were noticeably reduced under AD in 2015 compared to ND, trees showed similar growth and no oxidative stress. The absence of oxidative damage could be due to a strong accumulation of α-tocopherol, suggesting that this compound is a major component of the Q. pubescens antioxidant system. Other antioxidants were rather stable under AD in 2014, but slight changes started to be observed in 2015 (carotenoids and isoprene) due to harsher conditions. Our results indicate that Q. pubescens could be able to cope with AD, for at least 4 years, likely due to its antioxidant system. However, growth decrease was observed during the fifth year (2016) of AD, suggesting that this resistance could be threatened over longer periods of recurrent drought.
Multicast Networks Solvable over Every Finite Field

In this work, it is revealed that an acyclic multicast network that is scalar linearly solvable over Galois Field of two elements, G $F$(2), is solvable over all higher finite fields. An algorithm which, given a G $F$(2) solution for an acyclic multicast network, computes the solution over any arbitrary finite field is presented. The concept of multicast matroid is introduced in this paper. Gammoids and their base-orderability along with the regularity of a binary multicast matroid are used.
BREEDING SYSTEM AND POLLINATION BIOLOGY OF PAEONIA DELAVAYI ( PEAONIACEAE ) , AN ENDANGERED PLANT IN THE SOUTHWEST OF CHINA

Breeding system and pollination biology of Paeonia delavayi (Peaoniaceae) from Shangri-La, Yunnan Province, southwest of China were studied. Flowering phenologies and flower visitors were observed or collected from 2008 to 2011. The pollen viability, stigma receptivity and pollination efficiency of different visitors were detected and tested. The florescence lasted for 69d in a single flower from mid-May to late June. A high percentage of flower damage promoted early anther dehiscence. Flowers started disseminating pollen at 1-2 d after flowering, and lasted for 5-6 d. Pollen viability could be preserved for more than 10 d at normal temperature. High seed rate from the stigma was observed at 1 d before flowering to 3d after flowering, and the dissemination hysteresis was defined as protogyny. The P/O ratios were 6,124 to 9,713:1, suggesting that the larger quantity of pollen to increased the seed setting rate. Three species of bees, eight species of beetles, seven species of syrphid flies, four species of ants, and three species of butterflies were observed on the flowers. P. delavayi rewarded to the visitors by releasing fragrance, providing pollen and nectar. On the bodies of the visitors under stereomicroscope and scanning electron microscope (SEM), much pollen from the plants of similar flowering period inner community were found which indicated that these incompatible visitors were not species-specific pollinators. The bagging experiments showed that P. delavayi was selfincompatible and no apomixes. Anemophily only played a minor role in the fertilization. A few seeds with poor plumpness can be produced by geitonogamy. Seed setting rate of artificial xenogamy was higher than natural pollination. Artificial control of the visitors’ species showed bees being the most important pollinators. Beetles and ants participated in pollination to some extent and were unstable. Syrphid flies and butterflies were very unreliable with low pollination efficiency. Reproductive success depended largely on cross-pollination assisted by pollinator activities, especially the bees.
The Influence of Instructor Self-disclosure on Students' Evaluations: An Intercultural Comparison

A considerable amount of literature studied self-disclosing communication. Self-disclosure is defined as “any information about himself which Person A communicates verbally to a Person B” (Cozby, 1973, p. 73). Other terms such as “verbal accessibility” (Polansky, 1965) and “social accessibility” (Rickers-Ovsiankina, 1956) were used to describe the same concept. Self-disclosure was found to be multidimensional in both Altman and Taylor’s (1973) study and Wheeless and Grotz’s (1976) study. Based on the multidimensional nature of self-disclosure, the Revised Self-Disclosure Scale was created and has been widely used to analyze self-disclosure differences (Wheeless, 1978; Wheeless & Grotz, 1976).
A Link Heterogeneity-Aware On-Demand Routing (LHAOR) Protocol Utilizing Local Update and RSSI Information

Many routing protocols have been proposed for mobile ad hoc networks. Among these protocols, the on-demand routing protocols are very attractive because they have low routing overhead. However, few of the existing on-demand routing protocols have considered the link heterogeneity, such as the different communication rate, different Packet Error Ratio (PER). As a result, the routes tend to have the shortest hop count and contain weak links, which usually provide low performance and are susceptible to breaks in the presence of mobility. In this paper, we analyze the existing on-demand routing protocols and propose a Link Heterogeneity Aware On-demand Routing (LHAOR) protocol, where the link quality and mobility are considered. Specifically, the Local Update (LU) is proposed and the link metric is inversely related with the Received Signal Strength Indicator (RSSI). By using the LU method and RSSI information, the routes adapt to the topology variation and link quality changes, and reach the local optimum quickly, which contains strong links and has a small metric. Simulation and experiment results show that our LHAOR protocol achieves much higher performance than the classical on-demand routing protocols.
A Systematic Review and Meta-Analysis of Laparoscopic and Open Distal Pancreatectomy of Nonductal Adenocarcinomatous Pancreatic Tumor (NDACPT) in the Pancreatic Body and Tail

Background: Currently, laparoscopic distal pancreatectomy is regarded as a safe and effective surgical approach for lesions in the body and tail of the pancreas. This review examined the evidence from published data of comparative studies of laparoscopic versus open distal pancreatectomy of nonductal adenocarcinomatous pancreatic tumor in pancreatic body and tail. Methods: A systematic review of the studies comparing laparoscopic and open distal pancreatectomy was conducted. Comparative studies published between January 1996 and June 2016 were included. Studies were selected on the basis of specific inclusion and exclusion criteria. These 2 techniques were compared regarding several outcomes of interest, which were divided into preoperative, operative, postoperative, and pathologic characteristics, postoperative biomarker, and hospital stay cost. Sensitivity and subgroup analysis partially confirmed the robustness of these data. Results: Ten comparative case-control studies involving 712 patients (53.7% laparoscopic and 46.3% open), who underwent a distal pancreatectomy were included. The results favored laparoscopy with regard to intraoperative blood loss (P=0.0001), the rate of blood transfusion (P=0.02), total hospital stay (P=0.004), postoperative hospital stay (P<0.0001), overall morbidity (P=0.0002), the rate of wound infection (P=0.05), time to initial feeds (P<0.0001), first flatus time (P=0.008), duration of pain-killer intake (P=0.0003), and C-reactive protein on postoperative day 1 (P=<0.0001). In the subgroup analysis, excluding western country studies, operation time changed to have a statistically significant difference between these 2 groups (P=0.02). Conclusions: Laparoscopic resection results in improved operative and postoperative outcomes compared with open surgery according to the results of the present meta-analysis. It may be a safe and feasible option for nonductal adenocarcinomatous pancreatic tumor patients in pancreatic body and tail. However, randomized controlled trials should be undertaken to confirm the relevance of these findings.
Averaging for some simple constrained Markov processes

In this paper, a class of piecewise deterministic Markov processes with underlying fast dynamic is studied. By using a “penalty method”, an averaging result is obtained when the underlying dynamic is infinitely accelerated. The features of the averaged process, which is still a piecewise deterministic Markov process, are fully described.
Multigrid for an HDG method

We analyze the convergence of a multigrid algorithm for the Hybridizable Discontinuous Galerkin (HDG) method for diffusion problems. We prove that a non-nested multigrid V-cycle, with a single smoothing step per level, converges at a mesh independent rate. Along the way, we study conditioning of the HDG method, prove new error estimates for it, and identify an abstract class of problems for which a nonnested two-level multigrid cycle with one smoothing step converges even when the prolongation norm is greater than one. Numerical experiments verifying our theoretical results are presented.
Current, experimental, and future treatments in inflammatory bowel disease: a clinical review

Abstract Inflammatory bowel diseases (IBDs) may result from dysregulated mucosal immune responses directed toward the resident intestinal microbiota. This review describes the hallmark immunobiology of Crohn’s disease and ulcerative colitis as well as therapeutic targets and mechanisms of action for current, experimental, and future treatments in IBD. Conventional therapies include 5-aminosalicylic acid, glucocorticosteroids, thiopurines, and methotrexate. Since 1997, monoclonal antibodies have gained widespread use. These consist of antibodies directed against pro-inflammatory cytokines such as tumor necrosis factor α, interleukin (IL)-12, and IL-23, or anti-homing antibodies directed against α4β7 integrin. Emerging oral therapies include modulators of intracellular signal transduction such as Janus kinase inhibitors. Vitamin D may help to regulate innate and adaptive immune responses. Modulation of the intestinal microbiota, using live microorganisms (probiotics), substrates for the colonic microbiota (prebiotics), or fecal microbiota transplantation (FMT), is in development. Dietary supplements are in widespread use, but providing evidence for their benefit is challenging. Stem cell treatment and nervous stimulation are promising future treatments.
IN HARBOUR PORPOISES PHOCOENA PHOCOENA

Sound plays an important role for toothed whales in foraging and communication. However, little is known about acoustic communication in the toothed whale species that only produce narrow band high frequency (NBHF) clicks, such as the harbour porpoise Phocoena phocoena. To study acoustic behaviour and to quantify the source parameters of porpoise communication signals, the acoustic and swimming behaviour of three adults and one calf were recorded using an array of hydrophones, acoustic tags and an overhead video camera. We tested the hypothesis that different behavioural interactions between porpoises involve specific click patterns for communication and measured the source characteristics of these click patterns to estimate the active space of porpoise click communication. Our results provide strong evidence that porpoises communicate acoustically using specific patterns of clicks with source properties comparable to normal echolocation clicks, and that they employ stereotyped aggressive click patterns, exposing conspecifics to received levels of up to 180 dB re 1 μPa (pp). The measured source properties render estimated active spaces of less than 000 meters for porpoises’ communication sounds. Compared to other cetaceans, porpoises must therefore remain much closer to be able to communicate acoustically.