Miracle-dz/UniFAR-FTUs huggingface dataset:
Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species

The aim of this study was to perform an in silico analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to Salmonella genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as Vibrio, Shewanella, Halomonas, Idiomarina, Marinobacter, and Pseudohongiella. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from attL to the origin of transfer (oriT) harbored the DNA recombination, transfer, and mobilization genes, and the part from oriT to attR differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The oriT appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in Vibrio, Shewanella, and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.
Effects of a Single Sub-Anesthetic Dose of Ketamine on Postoperative Emotional Responses and Inflammatory Factors in Colorectal Cancer Patients

Objective: To investigate the effect of a single sub-anesthetic dose of ketamine on postoperative anxiety, depression, and inflammatory factors in patients with colorectal cancer. Methods: A total of 104 patients undergoing selective colorectal surgery in our hospital from Jan 2015 to Oct 2017 were included and randomly assigned (1:1:1:1) into a 0.1 mg kg−1 ketamine group (K1 group), 0.2 mg kg−1 ketamine group (K2 group), 0.3 mg kg−1 ketamine group (K3 group), or control group (C group). Corresponding doses of ketamine were given intravenously in the K groups (K1, K2, and K3 groups) 5 min before operation, and the same amount of normal saline was given in the C group. The intravenous analgesia program was identical in the four groups. The patients’ emotional reactions (anxiety and depression) were assessed by the Hospital Anxiety and Depression Scale (HAD), the quality of postoperative recovery was evaluated by the Quality of Recovery-40 (QoR-40) questionnaire, and the levels of IL-6, IL-8, and TNF-α in peripheral blood were detected by enzyme-linked immunosorbent assay (ELISA) on the day before operation and within 24, 48, and 72 h post-operation respectively. Pain was estimated by the visual analog scale (VAS), and sedation was assessed with Ramsay score 30 min after extubation. The time points of anesthetic end and extubation were recorded. The complications during anesthesia and recovery such as cough and agitation 30 min after extubation were recorded. Results: The anxiety score (HAD-A) and depression score (HAD-D) of the K3 group were significantly lower than those of the C group post-operation (p < 0.05). The QoR-40 score of the K3 group was significantly higher than that of the C group (p < 0.05). The serum levels of IL-6, IL-8, and TNF-α in the K3 group were significantly lower than those in the C group (p < 0.05 and p < 0.01). There were no significant differences in HAD-A, HAD-D, and QoR-40 scores or serum levels of IL-6, IL-8, and TNF-α between the K1 and K2 groups and the C group. There were no significant differences in VAS pain score or Ramsay sedation score among the four groups 30 min after extubation. There were no significant differences in extubation time, postoperative cough, emergence agitation, or delirium among the four groups. Dizziness, nausea, vomiting, diplopia, or other adverse reactions were not found 30 min after extubation. Conclusion: A single sub-anesthetic dose (0.3 mg kg−1) of ketamine can significantly improve the postoperative anxiety and depression of colorectal cancer patients and reduce the levels of IL-6, IL-8, and TNF-α.
β-Catenin Signaling Evokes Hair Follicle Senescence by Accelerating the Differentiation of Hair Follicle Mesenchymal Progenitors

Rationale: β-catenin signaling controls multiple fibroblast subsets, with its overactivity promoting the differentiation of hair follicle dermal stem cells (hfDSCs) and the hyperactivation of interfollicular fibroblasts. Understanding the concept of hfDSC activation and modulation offers hope towards the therapeutic armamentarium in dermatology and related comorbidities, as well as their potential applications in gerontology (the study of physiological aging). Having a comprehensive understanding in this stochastic process could also further yield important, novel insights into the molecular basis of skin aging to improve lifespan and preventing aging-related diseases. Methods: A new CD34CrePGR mouse line was generated. Through fate-tracing models and a series of β-catenin genetic experiments, our study depicts how the wound environment increases phosphorylated β-catenin in hfDSCs and facilitates their differentiation into dermal papilla (DP) and dermal sheath (DS). In mice carrying hfDSC-specific activated allele of β-catenin, hfDSCs accelerated their differentiation into DP cells. Results: Notably, with β-catenin stabilization in CD34-expressing cells and potential activation of canonical Wnt signaling, the mutant mice showed a brief increase of hair density in the short term, but over time leads to a senescence phenotype developing premature canities and thinning [hair follicle (HF) miniaturization]. Conclusion: β-catenin signaling drove HF senescence by accelerating differentiation of CD34+ hfDSCs, resulting in phenotypes attributable to the differentiation of the hfDSCs into DP cells and the loss of their stem cell potential. Therefore, our study reveals that the regulation of β-catenin signaling in hfDSCs may potentially become an important subject for future exploration in development of clinically effective therapies for hair loss treatment and an excellent model for revealing new therapeutic approaches to reverse aging or retarding the development of alopecia.
The Influence of Form-Focused Instruction on the L2 Chinese Oral Production of Korean Native Speakers

Form-focused instruction (FFI) can help second language (L2) learners notice the forms of language, which is conducive to the acquisition of linguistic forms. Two types of FFIs had been proposed, including focus-on-formS (FonFs) and focus-on-form (FonF). Previously, studies on FFI in L2 classroom teaching have focused mainly on the influence of two types of FFIs on the L2 acquisition of grammar and vocabulary. The influence of FonFs and FonF on L2 oral production, however, has been addressed less often. The advantages and disadvantages of different teaching methods in FonFs and FonF have not been well investigated. On the basis of Schmidt’s noticing hypothesis, VanPatten’s input processing hypothesis, and Long’s interactive hypothesis, we investigated the effects of teaching goals, teaching steps, and interactive activities in FonFs and FonF on the complexity, accuracy, and fluency of 32 native Korean speakers’ L2 Chinese oral production. We found that FFI significantly improved the performance of L2 Chinese oral production, although different FFIs had different effects on complexity, accuracy, and fluency. FonF and FonFs could improve both complexity and accuracy, whereas FonF also significantly improved fluency, which was not observed in FonFs. Furthermore, we found that the level of L2 proficiency could modulate the interaction between instruction methods and learning outcomes. For low-proficiency learners, FonF was more helpful for the improvement of fluency. For high-proficiency learners, FonFs was more helpful for the improvement of accuracy. These results demonstrated that teachers should pay attention to the interaction between specific teaching conditions with different L2 proficiency and learning outcomes when implementing FFI. The findings of this study have important implications for the design of procedures and interactive activities of L2 spoken Chinese teaching.
Clinical Use of Hydrogen Sulfide to Protect Against Intimal Hyperplasia

Arterial occlusive disease is the narrowing of the arteries via atherosclerotic plaque buildup. The major risk factors for arterial occlusive disease are age, high levels of cholesterol and triglycerides, diabetes, high blood pressure, and smoking. Arterial occlusive disease is the leading cause of death in Western countries. Patients who suffer from arterial occlusive disease develop peripheral arterial disease (PAD) when the narrowing affects limbs, stroke when the narrowing affects carotid arteries, and heart disease when the narrowing affects coronary arteries. When lifestyle interventions (exercise, diet…) fail, the only solution remains surgical endovascular and open revascularization. Unfortunately, these surgeries still suffer from high failure rates due to re-occlusive vascular wall adaptations, which is largely due to intimal hyperplasia (IH). IH develops in response to vessel injury, leading to inflammation, vascular smooth muscle cells dedifferentiation, migration, proliferation and secretion of extra-cellular matrix into the vessel’s innermost layer or intima. Re-occlusive IH lesions result in costly and complex recurrent end-organ ischemia, and often lead to loss of limb, brain function, or life. Despite decades of IH research, limited therapies are currently available. Hydrogen sulfide (H2S) is an endogenous gasotransmitter derived from cysteine metabolism. Although environmental exposure to exogenous high H2S is toxic, endogenous H2S has important vasorelaxant, cytoprotective and anti-inflammatory properties. Its vasculo-protective properties have attracted a remarkable amount of attention, especially its ability to inhibit IH. This review summarizes IH pathophysiology and treatment, and provides an overview of the potential clinical role of H2S to prevent IH and restenosis.
An Aminobutyric Acid Transaminase in Zea mays Interacts With Rhizoctonia solani Cellulase to Participate in Disease Resistance

Corn sheath blight, caused by AG1-IA, a fusion group of Rhizoctonia solani, which acts as a kind of necrotrophic fungal pathogen, poses a global threat to the production of Zea mays. Although cellulase plays a crucial role in R. solani infections, how plants respond to it is still poorly understood. In this study, we identified a gamma-aminobutyric acid transaminase (GABA-T), ZmGABA-T, in Z. mays that interacts with a cell wall–degrading enzyme (CWDE), EG1, in the cell membrane, using yeast two-hybrid assay, co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation assays. We found that the combination of EG1 and ZmGABA-T suppressed the allergic necrosis induced by EG1. We also found that the substrate of GABA-T–GABA, can inhibit the transcription of EG1. Transient expression of ZmGABA-T inhibited R. solani infection in Nicotiana benthamiana. The homolog in Oryza sativa, OsGABA-T, could also interact with EG1 to suppress the allergic necrosis induced by EG1. The OsGABA-T knocked out plants displayed enhanced susceptibility to R. solani and showed larger lesions. In conclusion, our results suggest that ZmGABA-T inhibits allergic necrosis induced by EG1 based on the combination with EG1, producing resistance to R. solani infection.
A Whole Leaf Comparative Study of Stomatal Conductance Models

We employed a detailed whole leaf hydraulic model to study the local operation of three stomatal conductance models distributed on the scale of a whole leaf. We quantified the behavior of these models by examining the leaf-area distributions of photosynthesis, transpiration, stomatal conductance, and guard cell turgor pressure. We gauged the models' local responses to changes in environmental conditions of carbon dioxide concentration, relative humidity, and light irradiance. We found that a stomatal conductance model that includes mechanical processes dependent on local variables predicts a spatial variation of physiological activity across the leaf: the leaf functions of photosynthesis and transpiration are not uniformly operative even when external conditions are uniform. The gradient pattern of hydraulic pressure which is needed to produce transpiration from the whole leaf is derived from the gradient patterns of turgor pressures of guard cells and epidermal cells and consequently leads to nonuniform spatial distribution patterns of transpiration and photosynthesis via the mechanical stomatal model. Our simulation experiments, comparing the predictions of two versions of a mechanical stomatal conductance model, suggest that leaves exhibit a more complex spatial distribution pattern of both photosynthesis and transpiration rate and more complex dependencies on environmental conditions when a non-linear relationship between the stomatal aperture and guard cell and epidermal cell turgor pressures is implemented. Our model studies offer a deeper understanding of the mechanism of stomatal conductance and point to possible future experimental measurements seeking to quantify the spatial distributions of several physiological activities taking place over a whole leaf.
Impact of COVID-19 Outbreak on the Gynecological Outpatients HPV Infection Rate in Wuhan, China: A Retrospective Observational Study

Background The recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak has caused millions of deaths and greatly influenced the timely diagnosis and treatment of other diseases. Throughout the pandemic, there was a dramatic reduction in the prevalence of several sexually transmitted infections. However, the impact of the ongoing pandemic on human papillomavirus (HPV) infection rates has not been investigated thus far. Materials and Methods We retrospectively collected data regarding HPV and cervical cancer screening results of outpatients from gynecological clinics of a tertiary hospital from 1 December 2018 to 31 December 2020 in Wuhan. Based on the timeline of the SARS-CoV-2 pandemic in Wuhan, we divided this period into four relatively independent stages to compare the HPV screening visit numbers and infection rates. Results There was a 50% drop in HPV screening visits and a 10% drop in HPV infection rates throughout the pandemic when compared with the numbers collected before the pandemic. Strict lockdown measures greatly decreased the HPV infection rate (17.03 vs. 8.29, P = 0.003). During the pandemic, the most prevalent HPV genotypes were HPV 16, 52, 58, and 53. After the pandemic, the HPV infection rate recovered quickly, but it was still slightly lower than the infection rate found before the outbreak (23.3 vs. 21.2%). Conclusion During coronavirus disease 2019 (COVID-19) pandemic, cervical cancer screening visits and HPV infection rates have decreased dramatically. The HPV transmission has also decreased after strict lockdown. Effective HPV and cervical cancer screening programs should be strengthened immediately to reduce the transmission of HPV during and after the pandemic.
Effects of Early Physical Therapy and Follow-Up in Acute Severe Coronavirus Disease 2019 Pneumonia: A Retrospective Observational Study

Background Rehabilitation in subjects with severe coronavirus disease 2019 (COVID-19) pneumonia has been widely recommended. However, data regarding the starting time of rehabilitation, subjects and healthcare workers’ safety, as well as rehabilitation program features are limited. We aimed to assess the safety and characterize the effect of early and non-early physiotherapy on severe COVID-19 pneumonia subjects. Methods A retrospective cohort study, including a consecutive sample of surviving subjects admitted to an acute care hospital due to severe COVID-19 pneumonia from March 13th to May 15th of 2020, is made. Subjects were separated into three groups: non-physical therapy, early physiotherapy (onset <7 days of admission), and non-early physiotherapy. Subject and therapist safety and length of hospital stay were the main evaluated outcomes. Results A total of 159 subjects were included (72% men; median age 62 years). Rehabilitation was performed on 108 subjects (32 early and 76 non-early physiotherapies). The length of hospital stay was 19 [interquartile range (IQR) 36.25] and 34 days (IQR 27.25) (p = 0.001) for early and non-early physiotherapy groups, respectively. No physiotherapist was infected and no subject adverse effect was identified. Multivariate analysis of subjects receiving physiotherapy during admission identified obesity [odds ratio (OR) 3.21; p-value 0.028], invasive mechanical ventilation (OR 6.25; p-value <0.001), and non-early physiotherapy (OR 3.54; p-value 0.017) as independent factors associated with a higher risk of prolonged hospital stay. Survivors’ follow-up after hospital discharge at 8 weeks was completed by 54% of subjects. Conclusion Rehabilitation in acute severe COVID-19 pneumonia is safe for subjects and healthcare workers and could reduce the length of hospitalization stay, especially in those that may start early.
Modeling the Potential of Treg-Based Therapies for Transplant Rejection: Effect of Dose, Timing, and Accumulation Site

Introduction: The adoptive transfer of regulatory T cells (Tregs) has emerged as a method to promote graft tolerance. Clinical trials have demonstrated the safety of adoptive transfer and are now assessing their therapeutic efficacy. Strategies that generate large numbers of antigen specific Tregs are even more efficacious. However, the combinations of factors that influence the outcome of adoptive transfer are too numerous to be tested experimentally. Here, mathematical modeling is used to predict the most impactful treatment scenarios. Methods: We adapted our mathematical model of murine heart transplant rejection to simulate Treg adoptive transfer and to correlate therapeutic efficacy with Treg dose and timing, frequency of administration, and distribution of injected cells. Results: The model predicts that Tregs directly accumulating to the graft are more protective than Tregs localizing to draining lymph nodes. Inhibiting antigen-presenting cell maturation and effector functions at the graft site was more effective at modulating rejection than inhibition of T cell activation in lymphoid tissues. These complex dynamics define non-intuitive relationships between graft survival and timing and frequency of adoptive transfer. Conclusion: This work provides the framework for better understanding the impact of Treg adoptive transfer and will guide experimental design to improve interventions. Graphical Abstract
U-RISC: An Annotated Ultra-High-Resolution Electron Microscopy Dataset Challenging the Existing Deep Learning Algorithms

Connectomics is a developing field aiming at reconstructing the connection of the neural system at the nanometer scale. Computer vision technology, especially deep learning methods used in image processing, has promoted connectomic data analysis to a new era. However, the performance of the state-of-the-art (SOTA) methods still falls behind the demand of scientific research. Inspired by the success of ImageNet, we present an annotated ultra-high resolution image segmentation dataset for cell membrane (U-RISC), which is the largest cell membrane-annotated electron microscopy (EM) dataset with a resolution of 2.18 nm/pixel. Multiple iterative annotations ensured the quality of the dataset. Through an open competition, we reveal that the performance of current deep learning methods still has a considerable gap from the human level, different from ISBI 2012, on which the performance of deep learning is closer to the human level. To explore the causes of this discrepancy, we analyze the neural networks with a visualization method, which is an attribution analysis. We find that the U-RISC requires a larger area around a pixel to predict whether the pixel belongs to the cell membrane or not. Finally, we integrate the currently available methods to provide a new benchmark (0.67, 10% higher than the leader of the competition, 0.61) for cell membrane segmentation on the U-RISC and propose some suggestions in developing deep learning algorithms. The U-RISC dataset and the deep learning codes used in this study are publicly available.
Effect of Different Fertilizations on the Plant-Available Nitrogen in Soil Profile (0–100 cm): A Study on Chinese Cabbage

The aim of this study is to analyze the variations in the plant-available nitrogen (PAN) concentrations in the soil profile. Different fertilizers were applied for Chinese cabbage plantation (CCP) in the experimental fields of the Shunyi region. The treatments used for the comparative analysis are (i) no fertilizer and plantation (NVP), (ii) no fertilizer with CCP (CTP), (iii) fertilization as urea (URP), and (iv) potassium nitrate (KNP) and chicken manure (CMP) with CCP. It was concluded that the yield was significantly high in URP, CMP, and KNP as compared to CTP. In URP, maximum PAN in soil layers 0–60 cm was recorded during crop production and in 60–100 cm after harvesting as compared to other treatments. Significant variations in soil pH and electrical conductivity (EC) for the soil profile (0–100 cm) from the initial values with respect to time and treatments were observed. CMP showed maximum ammonium in the upper layers of 0–60 cm throughout the season, whereas minimum PAN was observed in NVP but increased in lower layers of 60–100 cm. In general, all fertilizers raised the PAN below the soil 60–100 cm which indicates their potential for nitrate leaching (NL).
Virtualness : a new organisational dimension

In current literature a new organisational form is presented, the virtual organisation (VO). ms organisational form is a co-operation between a number of companies who combine their strengths to develop a new service or product. The current VO literature is ambiguous about the definition and characteristics of VOs. Furthermore, few empirical studies have been performed about the organisational structure, the internal communication and the consequences of virtual settings to knowledge and learning. In the literature it is assumed that knowledge is developed and transferred between the involved parties. However, little is mentioned how this knowledge is transferred and to who it is transferred. In this research the VO is not defined as a new organisation structure, but virtualness is an organisational dimension. The main research question is to investigate the relationshp between virtualness and knowledge development and transfer. Several dimensions are important in this respect: (a) the degree of virtualness; @) the context dependent indicators that indirectly influence virtualness; (c) knowledge development and transfer and (d) the consequences of different degrees of virtualness (and context dependent indicators) for knowledge development and transfer. It is assumed that knowledge development and transfer are affected by a high degree of virtualness. These questions are investigated with help of three case studies.