Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Polymorphisms in a Pair of NSP2 Homoeologs Can Cause Loss of Nodulation in Peanut.

Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, which is important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3 ~ 1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings provided the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results provided implications and insights into the evolution of homoeologous genes in allopolyploid species.
Investigation of acidic free-glycans in urine and their alteration in cancer

Abstract Alterations to glycans in cancer patients have been used to identify novel tumor biomarkers. Most of these studies have focused on protein glycosylation but less attention has been paid to free-glycans. Here, we analyzed acidic free-glycans in the urine of cancer patients to identify novel tumor marker candidates. Specifically, urine samples were collected from patients with gastric cancer, pancreatic cancer and cholangiocarcinoma as well as normal controls. The free-glycans were extracted from creatinine-adjusted urine and fluorescently labeled with 2-aminopyridine. Initially, we performed profiling of urinary free-glycans by high-performance liquid chromatography and mass spectrometry with enzymatic and chemical degradation. More than 100 glycans, including novel structures, were identified. The chromatographic peaks suggested some of these glycans were present at elevated levels in cancer patients. To verify cancer-associated alterations, we compared the glycan levels between cancer patients and normal controls by selected reaction monitoring. Representative structures of glycans with elevated levels in cancer patients included the following: small glycans related to sialyllactose; sialyl Lewis X; lactose- and N-acetyllactosamine (LacNAc) type-II-core glycans with LacNAc (type-I or II)-extensions and modifications of α1,3/4-fucose and/or 6-sulfate on the Glc/GlcNAc; free-N-glycans containing sialylation or β1,6-branch of 6-sulfo Lewis X; novel NeuAcα2-3Galβ1-4(+/−Fucα1-3) Xylα1-3Glc glycans. Our results provide further insight into urinary free-glycans and suggest the potential utility of these compounds as tumor markers.
Novel approach to improving wastewater treatment and sewage sludge combustion using pulverized coal‐activated sludge

Sewage and sludge are usually treated separately. Considering improving sludge treatment while improving sewage treatment is beneficial to the synergetic effect of sewage treatment and sludge treatment. The efficiency of pulverized coal‐activated sludge (PAS) on contaminant removal, sludge calorific value, and combustion characteristic was investigated in contrast to conventional activated sludge (CAS) using the laboratory‐scale sequencing batch reactor (SBR). Results indicated that the average chemical oxygen demand, ammonium nitrogen, total nitrogen, and total phosphorus removal efficiency of PAS were highest under a dosage of 0.4 g/L, which were 98.56%, 94.22%, 68.60%, and 95.96%, respectively. The average effluent concentration satisfied the Level A discharge standard of pollutants for municipal wastewater treatment plants (GB18918‐2002). The calorific value and maximum weight loss of PAS gradually increased adjusting the dosage of pulverized coal. At the pulverized coal dosage of 0.2 g/L, the calorific value of PAS with 70% water content is 3,824.07 kJ/kg, which can satisfy the requirement of self‐maintained combustion. Overall, the pulverized coal can simultaneously improve the treatment of wastewater in SBR and promote the sludge combustion by increasing calorific value. Therefore, PAS system is an innovation based on improving the sewage treatment sludge combustion.
Effects of a nonviolent communication-based training program for inpatient alcoholics in South Korea.

PURPOSE This study aimed to evaluate a communication skills program based on nonviolent communication targeted on inpatient alcoholics at the alcoholics specialized ward. DESIGN AND METHODS The sample for this mixed methods quasi-experimental study comprised 47 patients who were hospitalized in the alcoholic wards of two psychiatric hospitals in South Korea. FINDINGS The program effectively improved participants' empathy, anger expression, communication competence, and alcohol abstinence self-efficacy (p < .001). PRACTICE IMPLICATIONS This program could be implemented in community-based alcoholic care with the aim of preventing relapse and serve as the basis for developing similar programs for family members.
Low dose velogenic viscerotropic Newcastle disease virus infection caused 30% mortalities in Anak broilers but none in Lohmann Brown layer chickens

ABSTRACT The aim of this project was to find out the comparative susceptibilities of broilers and layer chickens to a low dose of velogenic viscerotropic Newcastle disease virus (vvNDV) infection using mortalities as the main indicator. Five weeks old Anak broilers and Lohmann Brown layer chicks were inoculated with vvNDV. The birds were monitored daily for clinical signs and disease evolution was evaluated. Clinical signs consisting of depression and diarrhea appeared at 3 days post-inoculation (DPI) in broilers and at 2 DPI in layer chickens resulting in total mortalities of 30% and 0% in broilers and layer chickens, respectively. Weight loss was statistically, significant in infected broilers on 3 to15 DPI (p < 0.05), while no such difference was observed in the weight of infected layer chicks (p > 0.05). Macroscopic lesions were similar but more severe in broilers compared to layer chickens and included proventricular haemorrhages, intestinal and caecal ulcers. But atrophy of the bursa, spleen and thymus and necrosis and depletion of lymphocytes in the three organs were severe in the infected broilers and pullets Antibody response was significantly (p < 0.05) higher in the layer chickens but virus isolation was more frequent in the broilers.
Systematic review and meta‐analysis of factors associated with re‐positive viral RNA after recovery from COVID‐19

Previous studies reported the positive viral RNA among coronavirus disease‐2019 (COVID‐19) recovered patients. This study aimed to summarize the current evidence of factors associated with the risk of disease recurrence. PubMed and Embase were searched until September 2020 to identify studies assessing characteristics of recurrence and nonrecurrence subjects after discharge. Random‐effect meta‐analysis was used to pool estimates of odds ratio (OR) or weighted mean difference (WMD) and their 95% confidence intervals (CIs) across studies. Meta‐analysis data were available for age, sex, hospital duration, disease severity, seven comorbidities, five symptoms, five indexes of blood routine, nine indexes of blood biochemistry, four treatment therapies, two antibodies, and history of high‐risk contact. Among them, hospital duration of recurrence cases was significantly shorter than nonrecurrence subjects (WMD, −1.55 days; 95% CI, −2.66 to −0.45). Fatigue, positive Immunoglobulin M (IgM), and positive IgG were associated with an increased risk of recurrence cases, with ORs and 95% CIs of 4.06 (1.14–14.4), 2.95 (1.15–7.61), and 3.45 (1.58–7.54), respectively. In contrast, the odds of recurrence cases were observed to significantly lower in subjects with elevated lactate dehydrogenase and C‐reactive protein, low lymphocyte count, steroid and arbidol use, with ORs (95% CIs) of 1.08 (0.27–4.37), 0.49 (0.27–0.97), 0.64 (0.42–0.97), 0.48 (0.25–0.96), and 0.48 (0.25–0.92), respectively. This study provided up‐to‐date evidence of several clinical and epidemiological characteristics in the association with COVID‐19 recurrence cases. Further in‐depth analyses for the causal effect of factors on re‐positive viral RNA are needed for the management of discharged patients with COVID‐19.
CD34 expression does not correlate with immunophenotypic stem cell or progenitor content in human cord blood products.

The CD34+ compartment of human cord blood contains a range of HSPC immunophenotypes, among which the Lin−CD34+CD38+CD127+ CLP is rare. There is no correlation between the frequencies of CD34+ cells and immunophenotypic HSC in umbilical cord blood products.
Characterization of antibody responses to SARS‐CoV‐2 in convalescent COVID‐19 patients

The coronavirus disease 2019 (COVID‐19) is a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). However, little is known about the durability of the antibody response during COVID‐19 convalescent phase. We investigated the prevalence of anti‐SARS‐CoV‐2 specific antibodies including immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies and the dynamic changes in antibody levels in convalescent COVID‐19 patients. A total of 159 blood samples were collected from 52 recovered COVID‐19 patients up to six months after symptom onset for longitudinal serological tests. The positive rate of IgG and IgM antibodies was 92.3% and 90.4% in the first month after symptom onset, and the seropositivity of IgG antibody remained high at all follow‐up time points, whereas the seropositivity of IgM antibody decreased to 22.73% by the sixth months after symptom onset. The level of IgG antibody was stable, the level of IgM antibody decreased slightly in the early convalescent phase and was detected in only five patients in the sixth month after symptom onset. The level of IgG antibody was higher in the severe and critical group than in the moderate group. The anti‐SARS‐CoV‐2 specific antibodies have a long‐term persistence in convalescent COVID‐19 patients, whether they have long‐term protection need to be further investigated.
RISK OF ADVERSE OUTCOMES IN HOSPITALIZED PATIENTS WITH AUTOIMMUNE DISEASE AND COVID-19: A MATCHED COHORT STUDY FROM NEW YORK CITY

Objective. To examine the effect of autoimmune (AI) disease on the composite outcome of intensive care unit (ICU) admission, intubation, or death from COVID-19 in hospitalized patients. Methods. Retrospective cohort study of 186 patients hospitalized with COVID-19 between March 1, 2020, and April 15, 2020 at NewYork-Presbyterian Hospital/Columbia University Irving Medical Center. The cohort included 62 patients with AI disease and 124 age- and sex-matched controls. The primary outcome was a composite of ICU admission, intubation, and death, with secondary outcome as time to in-hospital death. Baseline demographics, comorbidities, medications, vital signs, and laboratory values were collected. Conditional logistic regression and Cox proportional hazards regression were used to assess the association between AI disease and clinical outcomes. Results. Patients with AI disease were more likely to have at least one comorbidity (87.1% vs 74.2%, P = 0.04), take chronic immunosuppressive medications (66.1% vs 4.0%, P < 0.01), and have had a solid organ transplant (16.1% vs 1.6%, P < 0.01). There were no significant differences in ICU admission (13.7% vs 19.4%, P = 0.32), intubation (13.7% vs 17.7%, P = 0.47), or death (16.1% vs 14.5%, P = 0.78). On multivariable analysis, patients with AI disease were not at an increased risk for a composite outcome of ICU admission, intubation, or death (ORadj 0.79, 95% CI 0.37–1.67). On Cox regression, AI disease was not associated with in-hospital mortality (HRadj 0.73, 95% CI 0.33–1.63). Conclusion. Among patients hospitalized with COVID-19, individuals with AI disease did not have an increased risk of a composite outcome of ICU admission, intubation, or death.
Spirituality, religiosity and the mental health consequences of social isolation during Covid-19 pandemic

Background: Evidence shows that religiosity and spirituality (R/S) are highly used in critical moments of life and that these beliefs are associated with clinical outcomes. However, further studies are needed to assess these beliefs during the COVID-19 pandemic. Aims: To evaluate the use of R/S during the COVID-19 pandemic in Brazil and to investigate the association between R/S and the mental health consequences of social isolation. Methods: Cross-sectional study conducted in May 2020. Online surveys were carried out assessing sociodemographics, R/S measures, and social isolation characteristics and mental health consequences (hopefulness, fear, worrying and sadness). Adjusted regression models were used. Results: A total of 485 participants were included from all regions of Brazil. There was a high use of religious and spiritual beliefs during the pandemic and this use was associated with better mental health outcomes. Lower levels of worrying were associated with greater private religious activities (OR = 0.466, CI 95%: 0.307–0.706), religious attendance (OR = 0.587, CI 95%: 0.395–0.871), spiritual growth (OR = 0.667, CI 95%: 0.448–0.993) and with an increase in religious activities (OR = 0.660, CI 95%: 0.442–0.986); lower levels of fear were associated with greater private religious activities (OR = 0.632, CI 95%: 0.422–0.949) and spiritual growth (OR = 0.588, CI 95%: 0.392–0.882) and, lower levels of sadness (OR = 0.646, CI 95%: 0.418–0.997) were associated with spiritual growth. Finally, hope was associated with all R/S variables in different degrees (ranging from OR = 1.706 to 3.615). Conclusions: R/S seem to have an important role on the relief of suffering, having an influence on health outcomes and minimizing the consequences of social isolation. These results highlight the importance of public health measures that ensure the continuity of R/S activities during the pandemic and the training of healthcare professionals to address these issues.
Effect of the Molecularly Imprinted Polymer Component Ratio on Analytical Performance.

Molecular imprinting technology is a new analytical method that is highly selective and specific for certain analytes in artificial receptor design. The renewal possibilities of this technology make it an ideal material for sundry application fields. Molecularly imprinted polymers (MIPs) are polymeric matrices that have molecules printed on their surfaces; these surfaces can chemically interact with molecules or follow the pattern of the available template cavities obtained using imprinting technology. A MIP is useful for separating and analysing complex samples, such as biological fluids and environmental samples, because it is a strong analytical recognition element that can mimick natural recognition entities like biological receptors and antibodies. The MIP components consist of the target template, functional monomer, crosslinker, polymerisation initiator, and porogen. The effectiveness and selectivity of a MIP are greatly influenced by variations in the components. This review will provide an overview of the effect of MIP component ratio on analytical performance to each target analyte; it will also provide a strategy to obtain the best MIP performance. For every MIP, each template : monomer : crosslinker ratio shows a distinct performance for a specific analyte. The effects of the template : monomer : crosslinker ratio on a MIP's analytical performances-measured by the imprinting factor, sorbent binding capacity, and sorbent selectivity-are briefly outlined.
Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana.

Alternative splicing (AS) is a major gene regulatory mechanism in plants. Recent evidence supports co-transcriptional splicing in plants, hence the chromatin state can impact AS. However, how dynamic changes in the chromatin state such as nucleosome occupancy influence the cold-induced AS remains poorly understood. Here, we generated transcriptome (RNA-Seq) and nucleosome positioning (MNase-Seq) data for Arabidopsis thaliana to understand how nucleosome positioning modulates cold-induced AS. Our results show that characteristic nucleosome occupancy levels are strongly associated with the type and abundance of various AS events under normal and cold temperature conditions in Arabidopsis. Intriguingly, exitrons, alternatively spliced internal regions of protein-coding exons, exhibit distinctive nucleosome positioning pattern compared to other alternatively spliced regions. Likewise, nucleosome patterns differ between exitrons and retained introns pointing to their distinct regulation. Collectively, our data show that characteristic changes in nucleosome positioning modulate AS in plants in response to cold.
Structural basis for activation of Dot1L methyltransferase on the nucleosome by histone H2BK120 ubiquitylation

Histone H3 lysine 79 (H3K79) methylation is enriched on actively transcribed genes, and its misregulation is a hallmark of leukemia. Methylation of H3K79, which resides on the structured disk face of the nucleosome, is mediated by the Dot1L methyltransferase. Dot1L activity is part of a trans-histone crosstalk pathway, requiring prior histone H2B ubiquitylation of lysine 120 (H2BK120ub) for optimal activity. However, the molecular details describing both how Dot1L binds to the nucleosome and why Dot1L is activated by H2BK120 ubiquitylation are unknown. Here we present the cryo-EM structure of Dot1L bound to a nucleosome reconstituted with a site-specifically ubiquitylated H2BK120. The structure reveals that Dot1L engages the nucleosome acidic patch using an arginine anchor and occupies a conformation poised for methylation. Ubiquitin directly interacts with Dot1L and is positioned as a clamp on the nucleosome interacting region of Dot1L. Using our structure, we identify point mutations that disrupt the nucleosome-specific and ubiquitin-dependent activities of Dot1L. This study establishes a path to better understand Dot1L function in normal and leukemia cells.
Non‐apoptotic caspase activation preserves Drosophila intestinal progenitor cells in quiescence

Caspase malfunction in stem cells often precedes the appearance and progression of multiple types of cancer, including human colorectal cancer. However, the caspase‐dependent regulation of intestinal stem cell properties remains poorly understood. Here, we demonstrate that Dronc, the Drosophila ortholog of caspase‐9/2 in mammals, limits the number of intestinal progenitor cells and their entry into the enterocyte differentiation programme. Strikingly, these unexpected roles for Dronc are non‐apoptotic and have been uncovered under experimental conditions without epithelial replenishment. Supporting the non‐apoptotic nature of these functions, we show that they require the enzymatic activity of Dronc, but are largely independent of the apoptotic pathway. Alternatively, our genetic and functional data suggest that they are linked to the caspase‐mediated regulation of Notch signalling. Our findings provide novel insights into the non‐apoptotic, caspase‐dependent modulation of stem cell properties that could improve our understanding of the origin of intestinal malignancies.
Identification of a Metabolic, Transcriptomic, and Molecular Signature of Patatin‐Like Phospholipase Domain Containing 3–Mediated Acceleration of Steatohepatitis

The mechanisms by which the I148M mutant variant of the patatin‐like phospholipase domain‐containing 3 (PNPLA3I148M) drives development of nonalcoholic steatohepatitis (NASH) are not known. The aim of this study was to obtain insights on mechanisms underlying PNPLA3I148M‐induced acceleration of NASH.
Prevalence and Risk Factors for Women’s Reports of Past-Year Intimate Partner Violence: A Comparative Analysis of Six East African National Surveys

Violence against women, in all its forms, has been acknowledged as a violation of basic human rights and research evidence shows that it could lead to adverse health consequences. In this study we aimed to determine the prevalence and coexistence of different forms of IPV as well as examine individual-level factors associated with ever experiencing any form of IPV in the 12 months preceding the survey using the most recent Demographic Health Survey data from six East African countries. Results show that the prevalence ranged between 16.5% (Burundi) and 29.3% (Uganda) for emotional, 16.8% (Ethiopia) and 26.6% (Tanzania) for physical, and 8.3% (Rwanda and Ethiopia) and 18.4% (Burundi) for sexual IPV. The prevalence of any IPV ranged from 26.7% to 39.3%. In terms of coexistence, 15.6% to 19.0% of women reported experiencing all the three forms of IPV, with higher proportions reporting experiencing two of the three forms of IPV. The prevalence of both physical and emotional IPV was highest in Tanzania (49.1%), both emotional and sexual IPV in Uganda (28.0%), and both physical and sexual IPV in Burundi (26.2%). A partner’s use of alcohol and a woman’s justification of wife beating were both statistically significant common risk factors for IPV across the six countries. Women whose partners got drunk often were found to be up to nine times more likely to experience IPV compared to those whose partners did not drink. Younger women and those with larger families were at an increased risk of experiencing IPV, while other significant factors were country specific. In conclusion, our findings highlight the need for integrated and context-specific approaches that deconstruct gendered norms related to power dynamics and patriarchal nuances at household and community level in order to holistically address different forms of IPV.
Association of demographic, career, and lifestyle factors with resilience and association of resilience with mental health outcomes in veterinarians in Canada.

OBJECTIVE To investigate the association of demographic, career, and lifestyle factors with resilience and the association of resilience with mental health outcomes in Canadian veterinarians. SAMPLE 1,130 veterinarians in clinical practice across Canada. PROCEDURES An online questionnaire was used to collect participant data and included 5 validated psychometric scales to evaluate resilience (through the Connor-Davidson Resilience Scale [CD-RISC]), perceived stress (through the Perceived Stress Scale), emotional distress (through the Hospital Anxiety and Depression Scale), burnout (through the Maslach Burnout Inventory), and secondary traumatic stress (through the Professional Quality of Life Scale). A multivariable linear regression model was used to investigate associations between CD-RISC scores and demographic, career, and lifestyle characteristics. Univariable linear regression models were used to assess the relationship between resilience scores and other mental health outcomes. RESULTS The strongest positive association was between CD-RISC score and overall health. The level of satisfaction with support from friends and workplace resources had positive associations with the CD-RISC score. The presence of mental illness had the strongest negative association with the CD-RISC score. Being married, working in a small animal practice, or having an associate role were negatively associated with the CD-RISC score. The CD-RISC score had negative associations with scores for perceived stress, anxiety, depression, burnout, and secondary traumatic stress. CONCLUSIONS AND CLINICAL RELEVANCE Models provided evidence for the role of resilience in protecting against negative mental health outcomes in veterinarians. Both personal and workplace factors were associated with resilience, presenting opportunities for intervention at each of these levels.