Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Layered Control of the Conjugation Process of the Bacillus subtilis Plasmid pLS20

Bacterial conjugation is the main horizontal gene transfer route responsible for the spread of antibiotic resistance, virulence and toxin genes. During conjugation, DNA is transferred from a donor to a recipient cell via a sophisticated channel connecting the two cells. Conjugation not only affects many different aspects of the plasmid and the host, ranging from the properties of the membrane and the cell surface of the donor, to other developmental processes such as competence, it probably also poses a burden on the donor cell due to the expression of the large number of genes involved in the conjugation process. Therefore, expression of the conjugation genes must be strictly controlled. Over the past decade, the regulation of the conjugation genes present on the conjugative Bacillus subtilis plasmid pLS20 has been studied using a variety of methods including genetic, biochemical, biophysical and structural approaches. This review focuses on the interplay between RcopLS20, RappLS20 and Phr*pLS20, the proteins that control the activity of the main conjugation promoter P c located upstream of the conjugation operon. Proper expression of the conjugation genes requires the following two fundamental elements. First, conjugation is repressed by default and an intercellular quorum-signaling system is used to sense conditions favorable for conjugation. Second, different layers of regulation act together to repress the P c promoter in a strict manner but allowing rapid activation. During conjugation, ssDNA is exported from the cell by a membrane-embedded DNA translocation machine. Another membrane-embedded DNA translocation machine imports ssDNA in competent cells. Evidences are reviewed indicating that conjugation and competence are probably mutually exclusive processes. Some of the questions that remain unanswered are discussed.
Modeling and Bioinformatics Identify Responders to G-CSF in Patients With Amyotrophic Lateral Sclerosis

Objective: Developing an integrative approach to early treatment response classification using survival modeling and bioinformatics with various biomarkers for early assessment of filgrastim (granulocyte colony stimulating factor) treatment effects in amyotrophic lateral sclerosis (ALS) patients. Filgrastim, a hematopoietic growth factor with excellent safety, routinely applied in oncology and stem cell mobilization, had shown preliminary efficacy in ALS. Methods: We conducted individualized long-term filgrastim treatment in 36 ALS patients. The PRO-ACT database, with outcome data from 23 international clinical ALS trials, served as historical control and mathematical reference for survival modeling. Imaging data as well as cytokine and cellular data from stem cell analysis were processed as biomarkers in a non-linear principal component analysis (NLPCA) to identify individual response. Results: Cox proportional hazard and matched-pair analyses revealed a significant survival benefit for filgrastim-treated patients over PRO-ACT comparators. We generated a model for survival estimation based on patients in the PRO-ACT database and then applied the model to filgrastim-treated patients. Model-identified filgrastim responders displayed less functional decline and impressively longer survival than non-responders. Multimodal biomarkers were then analyzed by PCA in the context of model-defined treatment response, allowing identification of subsequent treatment response as early as within 3 months of therapy. Strong treatment response with a median survival of 3.8 years after start of therapy was associated with younger age, increased hematopoietic stem cell mobilization, less aggressive inflammatory cytokine plasma profiles, and preserved pattern of fractional anisotropy as determined by magnetic resonance diffusion tensor imaging (DTI-MRI). Conclusion: Long-term filgrastim is safe, is well-tolerated, and has significant positive effects on disease progression and survival in a small cohort of ALS patients. Developing and applying a model-based biomarker response classification allows use of multimodal biomarker patterns in full potential. This can identify strong individual treatment responders (here: filgrastim) at a very early stage of therapy and may pave the way to an effective individualized treatment option.
AWP1 Restrains the Aggressive Behavior of Breast Cancer Cells Induced by TNF-α

TNF-α plays a crucial role in cancer initiation and progression by enhancing cancer cell proliferation, survival, and migration. Even though the known functional role of AWP1 (zinc finger AN1 type-6, ZFAND6) is as a key mediator of TNF-α signaling, its potential role in the TNF-α-dependent responses of cancer cells remains unclear. In our current study, we found that an AWP1 knockdown using short hairpin RNAs increases the migratory potential of non-aggressive MCF-7 breast cancer cells with no significant alteration of their proliferation in response to TNF-α. A CRISPR/Cas9-mediated AWP1 knockout in MCF-7 cells led to mesenchymal cell type morphological changes and an accelerated motility. TNF-α administration further increased this migratory capacity of these AWP1-depleted cells through the activation of NF-κB accompanied by increased epithelial-mesenchymal transition-related gene expression. In particular, an AWP1 depletion augmented the expression of Nox1, reactive oxygen species (ROS) generating enzymes, and ROS levels and subsequently promoted the migratory potential of MCF-7 cells mediated by TNF-α. These TNF-α-mediated increases in the chemotactic migration of AWP1 knockout cells were completely abrogated by an NF-κB inhibitor and a ROS scavenger. Our results suggest that a loss-of-function of AWP1 alters the TNF-α response of non-aggressive breast cancer cells by potentiating ROS-dependent NF-κB activation.
Napabucasin Induces Mouse Bone Loss by Impairing Bone Formation via STAT3

The novel small molecule Napabucasin (also known as BBI608) was shown to inhibit gene transcription driven by Signal Transducer and Activator of Transcription 3 (STAT3), which is considered a promising anticancer target. Many preclinical studies have been conducted in cancer patients examining the selective targeting of cancer stem cells by Napabucasin, but few studies have examined side effects of Napabucasin in the skeleton system. In the present study, we found treating bone marrow mesenchymal stem cells (BMSCs) with Napabucasin in vitro impaired their osteogenic differentiation. In terms of mechanisms, Napabucasin disrupted differentiation of BMSCs by inhibiting the transcription of osteogenic gene osteocalcin (Ocn) through STAT3. Moreover, through micro-CT analysis we found 4 weeks of Napabucasin injections induced mouse bone loss. Histological analysis revealed that Napabucasin-induced bone loss in mice was the result of impaired osteogenesis. In conclusion, this study provided evidence for the effect of Napabucasin on mouse bone homeostasis and revealed its underlying mechanisms in vivo and in vitro.
An Exploratory Study of Police Officers’ Perceptions of Health Risk, Work Stress, and Psychological Distress During the COVID-19 Outbreak in China

Background How do the police officers perceive health risk, psychological distress, and work stress during the COVID-19 outbreak in China? This study explores the health risk perception, work stress, and psychological distress of police officers who worked at the front line to implement lockdown measures. Materials and Methods We conducted a large-scale field survey (N = 5,611) with police officers sample in the northwestern part of China from February 29 to March 7, 2020. Independent-sample T-test and ANOVA were used to analyze whether there are differences in health risk perception, work stress, and psychological distress between different groups. The regression analysis was employed to figure out the factors that influence police officers’ psychological distress. Results Results showed a gender difference in perceiving work stress among police officers. Also, police officers with chronic disease perceived higher health risks, more psychological distress, and higher work stress. Additionally, police officers above 45 years old significantly perceived higher health risks than young officers did. It also revealed that working hours contribute to police officers’ health risk perception, psychological distress, and work stress. Finally, our results highlight that age, working hours, chronic disease, health risk perception, and work stress significantly contribute to police officers’ psychological distress. Conclusion Our research verifies that there is a gender difference in perceiving work stress among police officers. Police officers with ongoing medical issues and above 45 years old suffer more during the COVID-19 outbreak in China. Our research suggests that the government should pay more attention to their physical health and mental health. The heavy workload containing the COVID-19 extends police officers’ working hours, causing higher health risks, work stress, and psychological distress. This study contributes to the psychological distress literature and provides a way forward to other countries struggling to contain the COVID-19.
Remote Ischemic Preconditioning to Prevent Acute Kidney Injury After Cardiac Surgery: A Meta-Analysis of Randomized Controlled Trials

Objective: Randomized controlled trials (RCTs) evaluating the influence of remote ischemic preconditioning (RIPC) on acute kidney injury (AKI) after cardiac surgery showed inconsistent results. We performed a meta-analysis to evaluate the efficacy of RIPC on AKI after cardiac surgery. Methods: Relevant studies were obtained by search of PubMed, Embase, and Cochrane's Library databases. A random-effect model was used to pool the results. Meta-regression and subgroup analyses were used to determine the source of heterogeneity. Results: Twenty-two RCTs with 5,389 patients who received cardiac surgery −2,702 patients in the RIPC group and 2,687 patients in the control group—were included. Moderate heterogeneity was detected (p for Cochrane's Q test = 0.03, I2 = 40%). Pooled results showed that RIPC significantly reduced the incidence of AKI compared with control [odds ratio (OR): 0.76, 95% confidence intervals (CI): 0.61–0.94, p = 0.01]. Results limited to on-pump surgery (OR: 0.78, 95% CI: 0.64–0.95, p = 0.01) or studies with acute RIPC (OR: 0.78, 95% CI: 0.63–0.97, p = 0.03) showed consistent results. Meta-regression and subgroup analyses indicated that study characteristics, including study design, country, age, gender, diabetic status, surgery type, use of propofol or volatile anesthetics, cross-clamp time, RIPC protocol, definition of AKI, and sample size did not significantly affect the outcome of AKI. Results of stratified analysis showed that RIPC significantly reduced the risk of mild-to-moderate AKI that did not require renal replacement therapy (RRT, OR: 0.76, 95% CI: 0.60–0.96, p = 0.02) but did not significantly reduce the risk of severe AKI that required RRT in patients after cardiac surgery (OR: 0.73, 95% CI: 0.50–1.07, p = 0.11). Conclusions: Current evidence supports RIPC as an effective strategy to prevent AKI after cardiac surgery, which seems to be mainly driven by the reduced mild-to-moderate AKI events that did not require RRT. Efforts are needed to determine the influences of patient characteristics, procedure, perioperative drugs, and RIPC protocol on the outcome.
Vaginal Epithelium Transiently Harbours HIV-1 Facilitating Transmission

Vaginal transmission accounts for majority of newly acquired HIV infections worldwide. Initial events that transpire post-viral binding to vaginal epithelium leading to productive infection in the female reproductive tract are not well elucidated. Here, we examined the interaction of HIV-1 with vaginal epithelial cells (VEC) using Vk2/E6E7, an established cell line exhibiting an HIV-binding receptor phenotype (CD4-CCR5-CD206+) similar to primary cells. We observed rapid viral sequestration, as a metabolically active process that was dose-dependent. Sequestered virus demonstrated monophasic decay after 6 hours with a half-life of 22.435 hours, though residual virus was detectable 48 hours’ post-exposure. Viral uptake was not followed by successful reverse transcription and thus productive infection in VEC unlike activated PBMCs. Intraepithelial virus was infectious as evidenced by infection in trans of PHA-p stimulated PBMCs on co-culture. Trans-infection efficiency, however, deteriorated with time, concordant with viral retention kinetics, as peak levels of sequestered virus coincided with maximum viral output of co-cultivated PBMCs. Further, blocking lymphocyte receptor function-associated antigen 1 (LFA-1) expressed on PBMCs significantly inhibited trans-infection suggesting that cell-to-cell spread of HIV from epithelium to target cells was LFA-1 mediated. In addition to stimulated PBMCs, we also demonstrated infection in trans of FACS sorted CD4+ T lymphocyte subsets expressing co-receptors CCR5 and CXCR4. These included, for the first time, potentially gut homing CD4+ T cell subsets co-expressing integrin α4β7 and CCR5. Our study thus delineates a hitherto unexplored role for the vaginal epithelium as a transient viral reservoir enabling infection of susceptible cell types.
Differences in Tumor Immune Microenvironment in Metastatic Sites of Breast Cancer

Introduction: Tumor immune microenvironment (TIME) promotes immune escape, allowing for tumor progression and metastasis. In spite of the current evidence of the complicated role of immune cells in promoting or suppressing cancer progression, the heterogeneity of TIME according to the tumor site has been scarcely investigated. Here, we analyzed transcriptomic profiles of metastatic breast cancer to understand how TIME varies according to tumor sites. Methods: Two gene expression datasets from metastatic breast cancer of various sites and a single-cell RNA sequencing dataset of primary breast cancer and metastatic lymph nodes were analyzed. The immune cell-type enrichment of each tumor was estimated. Immune cell types were identified by clustering analysis, and the proportions of cell types in TIME were assessed according to the tumor site. Results: Metastatic bone lesions showed more neutrophils than breast lesions. Tumors clustered according to immune cell type were significantly associated with tumor site. In single-cell analyses, the TIMEs of metastatic lymph nodes showed fewer macrophages than those of primary tumors. Differentially expressed gene signatures in the primary tumor and metastatic lymph nodes were associated with macrophage activation. Conclusion: We conclude that metastatic sites show variable enrichment patterns of immune cells, and that the TIME of metastatic lesions should be considered in precise immuno-oncology treatments.
Computed Tomography Features of Gastric Cancer Patients With DNA Mismatch Repair Deficiency

Objective To explore the computed tomography (CT) features of gastric cancer (GC) patients with DNA mismatch repair deficiency (dMMR). Materials and Methods This study reviewed the clinical and CT features of GC patients with dMMR, confirmed by the postoperative results, between September 2017 and December 2019. The expression pattern of MMR major proteins (MLH1, MSH2, MSH6, and PMS2) in immunohistochemistry was used to confirm the MMR status in GC tissues. The correlation between pre-treatment CT features and MMR status was statistically analyzed. Results A total of 28 patients with GC were diagnosed as dMMR in our study, and 49 patients were MMR-proficient (pMMR). The tumor locations were significantly different between the dMMR and pMMR groups (p = 0.006). The CT tumor thickness, CT long and short diameters of the largest lymph node, and the number of lymph nodes on CT of the dMMR group were significantly different from the pMMR group. Conclusion The dMMR GC exhibited a lower stomach location, smaller tumor thickness and lymph node diameter, and fewer lymph nodes on CT imaging.
Australian carbon tetrachloride emissions in a global context

Environmental context Carbon tetrachloride in the background atmosphere is a significant environmental concern, responsible for ~10% of observed stratospheric ozone depletion. Atmospheric concentrations of CCl4 are higher than expected from currently identified emission sources: largely residual emissions from production, transport and use. Additional sources are required to balance the expected atmospheric destruction of CCl4 and may contribute to a slower-than-expected recovery of the Antarctic ozone ‘hole’. Abstract Global (1978–2012) and Australian (1996–2011) carbon tetrachloride emissions are estimated from atmospheric observations of CCl4 using data from the Advanced Global Atmospheric Gases Experiment (AGAGE) global network, in particular from Cape Grim, Tasmania. Global and Australian emissions are in decline in response to Montreal Protocol restrictions on CCl4 production and consumption for dispersive uses in the developed and developing world. However, atmospheric data-derived emissions are significantly larger than ‘bottom-up’ estimates from direct and indirect CCl4 production, CCl4 transportation and use. Australian CCl4 emissions are not a result of these sources, and the identification of the origin of Australian emissions may provide a clue to the origin of some of these ‘missing’ global sources.
Cultivation effects on the carbon and nitrogen dynamics at depth in oasis farmlands of the Southern Tarim Basin, China

Abstract The profile distribution of soil organic carbon (SOC) and total nitrogen (TN) are important indicators for predicting and simulating the effects of human activities on soil fertility and quality. However, most studies have focused on these changes in surface soil or the top 100 cm of short-term cultivated farmlands in arid regions. In the present study, farmlands cultivated for 0, 10, 15, 30, 80 and 100 years in the Cele oasis, at the southern margin of the Tarim Basin, were selected to examine cultivation effects on the vertical distribution of SOC and TN to 200 cm, and to try to find a rational approach to increase the SOC and TN stocks in cultivated farmland. The results showed that although SOC concentration and stock increased significantly at 0–20 cm along the chronosequence, the total SOC stock of the 0–200 cm layer was 13.8% lower in 30-year farmlands and 88.3% higher in 100-year farmlands than that in natural soil due to the corresponding decrease in 30-year farmlands and significant increase in 100-year farmlands at 40–200 cm depth. Cultivation also significantly increased TN concentration and stock at 0–20 cm, but the obvious increase of TN stock at 0–200 cm was only found in 100-year farmlands due to the slight change of TN stock at 40–200 cm except for 100-year farmlands. C and N stocks in the 40–200 cm layer of the cultivated farmlands contributed respectively 67.6 and 61.9% of the total SOC and TN stocks of 0–200 cm, further confirming the importance of C and N cycling in the deep layer. The continuous applications of N fertilizers combined with organic manures and irrigation with silt-laden river water contributed greatly to the increase of SOC and TN stocks. These results suggest that the oasis farmland has great potential capacity to accumulate SOC and TN only if long-term cultivation (> 30 years) and the enhancement of organic materials are implemented.
An Initial Study of Dynamic-Duplex Cellular System on 5G NR Downlink in High SHF Band

Currently, in-band full-duplex (IBFD) has attracted much attention and has been researched for the beyond 5G systems. IBFD enables simultaneous operation of downlink (DL) and uplink (UL) communications at the same frequency and ideally doubles spectrum efficiency compared with the conventional half-duplex. In recent years, the dynamic-duplex cellular (DDC) system has been proposed to flexibly expand the system capacity with IBFD. However, previous studies of the DDC system were based on the LTE (Long-Term Evolution) system in the sub-6 GHz band. In this paper, we propose a 5G new radio-based DDC system to add UL communications to the DL subframes by considering the antenna directivity in the super high frequency (SHF) band.
Ergodic Capacity of Multiuser Hybrid Satellite-Terrestrial Cooperative Networks with SNR-Threshold Based Feedback

In this paper, we investigate the performance of a multiuser hybrid satellite-terrestrial cooperative network (HSTCN) with amplify-and-forward protocol. Different from the existing works, we propose an opportunistic user scheduling (OUS) scheme based on SNR-threshold feedback. By assuming that the satellite link and the terrestrial links undergo Shadowing-Rician fading and Rayleigh fading, respectively, we first obtain probability density function of the output signal-to-noise ratio (SNR) with the proposed scheduling scheme. Then, we derive analytical expression for the ergodic capacity (EC) of the considered system. Finally, numerical results prove that the OUS scheme with SNR-threshold based feedback can reduce the amount of feedback greatly, and the system with proposed scheme can achieve the same capacity as that without feedback threshold.
Chemical and Physical Properties of Cotton Modified by N-Methylol Agents

A study of the influence of cotton cellulose on reaction paths and rates involving intermediate oxonium-carbonium ions has been expanded to include a similar study of immonium-carbonium ions. A study of these mechanisms suggests that for acetal- or aldehyde-type reactions, cellulose can have an influence on reaction paths and rates, but for N-methylol-type reactions, cellulose would only be expected to have an influence on the rate. These generalizations depend on a number of factors and limitations which are discussed here for both the forward (cure) and reverse (recure or hydrolysis) reactions. Monomeric grafts or crosslinks to cellulose in the presence of formaldehyde crosslinks were found to be readily accessible to the hydrolytic medium. Considerations based on comparisons of the resistance to acid hydrolysis of cellulose ethers prepared from N-methylol methyl carbamate, its isopropoxy and acetoxy derivatives, and from N-methylolpyrrolidone suggest that these pure car bamates do not produce a pure finish. The finish from N-methylolpyrrolidone is considered to be pure and its formation in the presence of organic solvents and its resistance to hydrolysis were examined. Based on these studies the conclusion was that in comparisons of derivatives of cotton cellulose, chemical effects appear to determine completely the resistance to hydrolysis of a specific or pure finish. Further, leaving group effects from 2-, 3-, or 6-positions of cellulose play only a partial role, and cellulose appears also to influence the rates of reaction in a manner similar to the solvent in homogeneous reactions. Stronger or longer reaction conditions are needed for an agent to complete reaction because of a slower rate in certain portions of cotton cellulose during the cure. Links to cellulose formed in this manner produce a more durable finish. Generalizations made in this paper apply to conventional finishing and stripping conditions.
Terahertz pulsed imaging of dehydrated human breast cancer samples

In this work, we examine the validation and the test-retest reliability of the terahertz (THz) image contrasts between healthy and cancerous regions in dehydrated human breast cancer samples mounted on Teflon plates. We used a newly acquired THz time-domain spectrometer to record THz reflection impulse responses of these samples during two sessions, one week apart. The validation was carried out using histopathological images. The test-retest reliability was assessed by comparing the contrasts obtained from both sessions. The results show that the THz image contrasts (1) are highly correlated with the associated histopathological results in samples having a good adhesion to Teflon plates, and (2) can be reliably obtained in a controlled environment.