Miracle-dz/UniFAR-FTUs huggingface dataset:
Candidate resistance genes to foliar phylloxera identified at Rdv3 of hybrid grape

Abstract The foliage of the native grape species Vitis riparia and certain cold-hardy hybrid grapes are particularly susceptible to the insect pest phylloxera, Daktulosphaira vitifoliae Fitch. A previous study using a cold-hardy hybrid grape biparental F1 population (N ~ 125) detected the first quantitative trait locus (QTL) for foliar resistance on chromosome 14, designated as resistance to Daktulosphaira vitifoliae 3 (Rdv3). This locus spans a ~ 7-Mbp (10–20 cM) region and is too wide for effective marker-assisted selection or identification of candidate genes. Therefore, we fine mapped the QTL using a larger F1 population, GE1783 (N ~ 1023), and genome-wide rhAmpSeq haplotype markers. Through three selective phenotyping experiments replicated in the greenhouse, we screened 184 potential recombinants of GE1783 using a 0 to 7 severity rating scale among other phylloxera severity traits. A 500-kb fine mapped region at 4.8 Mbp on chromosome 14 was identified. The tightly linked rhAmpSeq marker 14_4 805 213 and flanking markers can be used for future marker-assisted breeding. This region contains 36 candidate genes with predicted functions in disease resistance (R genes and Bonzai genes) and gall formation (bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase). Disease resistance genes suggest a traditional R-gene-mediated resistance mechanism often accompanied by a hypersensitive response, which has been widely studied in the plant pathology field. A novel resistance mechanism, non-responsiveness to phylloxera gall formation is proposed as a function of the bifunctional dehydratase gene, which plays a role in gallic acid biosynthesis and is important in gall formation. This study has implications for improvement of foliar phylloxera resistance in cold-hardy hybrid germplasm and is a starting place to understand the mechanism of resistance in crops to gall-forming insects.
ALT-FISH quantifies alternative lengthening of telomeres activity by imaging of single-stranded repeats

Abstract Alternative lengthening of telomeres (ALT) occurs in ∼10% of cancer entities. However, little is known about the heterogeneity of ALT activity since robust ALT detection assays with high-throughput in situ readouts are lacking. Here, we introduce ALT-FISH, a method to quantitate ALT activity in single cells from the accumulation of single-stranded telomeric DNA and RNA. It involves a one-step fluorescent in situ hybridization approach followed by fluorescence microscopy imaging. Our method reliably identified ALT in cancer cell lines from different tumor entities and was validated in three established models of ALT induction and suppression. Furthermore, we successfully applied ALT-FISH to spatially resolve ALT activity in primary tissue sections from leiomyosarcoma and neuroblastoma tumors. Thus, our assay provides insights into the heterogeneity of ALT tumors and is suited for high-throughput applications, which will facilitate screening for ALT-specific drugs.
Process and Outcome Evaluations of Interventions to Promote Voluntary Exercise Training Among South Korean Firefighters

The main aim of the present study is to evaluate reach, dose, fidelity, and outcomes of the interventions for promoting voluntary exercise training among South Korean firefighters. Four interventions for promoting voluntary exercise training among firefighters (i.e., virtual reality exercise system intervention, poster intervention, monitor intervention, and wearable health device intervention) were performed in a fire station located in Seoul, South Korea. To evaluate reach and dose received related to each intervention, participants were asked to answer several simple questions. Three process evaluators completed a 20-item survey to share their impressions related to the quality of intervention delivery. Paired t test was used to examine mean changes in primary (i.e., mean minutes of exercise training per week) and secondary outcomes (i.e., beliefs and intention) between pre- and postinterventions. More than 60% of participants experienced monitor and wearable health device interventions. Process evaluators tend not to agree with a statement saying that the number of the virtual reality exercise equipment was appropriate. Among firefighters who participated in exercise training less than 150 min per week at 1-month follow-up, mean minutes of exercise training per week increased by 67.95 min after interventions. Future studies need to examine whether the monitor and wearable health device interventions effectively increase exercise training participation among firefighters in other fire stations located in Seoul, South Korea.
Multi-omics approaches identify a key gene, PpTST1, for organic acid accumulation in peach

Abstract Organic acid content in fruit is an important determinant of peach organoleptic quality, and undergoes considerable variations during development and maturation. However, its molecular mechanism remains largely unclear. In this study, an integrative approach of genome-wide association studies and comparative transcriptome analysis was applied to identify candidate genes involved in organic acid accumulation in peach. A key gene, PpTST1, encoding tonoplast sugar transporter, was identified and the genotype of PpTST1 with a single-base transversion (G1584T) in the third exon that leads to a single amino acid substitution (Q528H) was associated with a low level of organic acid content in peach. Overexpression of PpTST1His resulted in reduced organic acid content along with increased sugar content both in peach and tomato fruits, suggesting its dual function in sugar accumulation and organic acid content reduction. Two V-type proton ATPases interacted with PpTST1 in a yeast two-hybrid assay. In addition, the G1584T transversion appeared and gradually accumulated during domestication and improvement, which indicated that PpTST1 was under selection. The identification and characterization of PpTST1 would facilitate the improvement of peach fruit quality.
Functional tests in patients with ischemic heart disease

Lately, easier and shorter tests have been used in the functional evaluation of cardiac patients. Among these, walking speed (WS) and Timed Up and Go (TUG) tests are associated with all-cause mortality, mainly cardiovascular and the rate of re-hospitalization, especially in the elderly population. We prospectively analyzed a group of 38 patients admitted to the Cardiology Clinic from Elias Hospital, Romania, with chronic coronary syndrome (CCS) (n=22) and STEMI (n=16). We assessed the patients immediately after admission and before discharge with G-WALK between the 1st and 30th of September 2019. Our study group had a mean age of 62.7±12.1 years. Patients with a low WS were older (69.90±12.84 vs. 59.90±10.32 years, p=0.02) and had a lower serum hemoglobin (12.38±1.20 vs. 13.72±2.07 g/dl, p=0.02). The WS significantly improved during hospitalization (p=0.03) after optimal treatment. The TUG test performed at the time of admission had a longer duration in patients with heart failure (14.05 vs. 10.80 sec, p=0.02) and was influenced by patients’ age (r=0.567, p=0.02), serum creatinine (r=0.409, p=0.03) and dilation of right heart chambers (r=0.399, p=0.03). WS and TUG tests can be used in patients with CCS and STEMI, and are mainly influenced by age, thus having a greater value among the elderly.
Single‐cell RNA sequencing reveals the multi‐cellular ecosystem in different radiological components of pulmonary part‐solid nodules

Abstract Background Early‐stage lung adenocarcinoma that radiologically manifests as part‐solid nodules, consisting of both ground‐glass and solid components, has distinctive growth patterns and prognosis. The characteristics of the tumour microenvironment and transcriptional features of the malignant cells of different radiological phenotypes remain poorly understood. Methods Twelve treatment‐naive patients with radiological part‐solid nodules were enrolled. After frozen pathology was confirmed as lung adenocarcinoma, two regions (ground‐glass and solid) from each of the 12 part‐solid nodules and 5 normal lung tissues from 5 of the12 patients were subjected to single‐cell sequencing by 10x Genomics. We used Seurat v3.1. 5 for data integration and analysis. Results We comprehensively dissected the multicellular ecosystem of the ground‐glass and solid components of part‐solid nodules at the single‐cell resolution. In tumours, these components had comparable proportions of malignant cells. However, the angiogenesis, epithelial‐to‐mesenchymal transition, KRAS, p53, and cell‐cycle signalling pathways were significantly up‐regulated in malignant cells within solid components compared to those within ground‐glass components. For the tumour microenvironment, the relative abundance of myeloid and NK cells tended to be higher in solid components than in ground‐glass components. Slight subtype composition differences existed between the ground‐glass and solid components. The T/NK cell subsets’ cytotoxic function and the macrophages’ pro‐inflammation function were suppressed in solid components. Moreover, pericytes in solid components had a stronger communication related to angiogenesis promotion with endothelial cells and tumour cells. Conclusion The cellular landscape of ground‐glass components is significantly different from that of normal tissue and similar to that of solid components. However, transcriptional differences exist in the vital signalling pathways of malignant and immune cells within these components.
Hypothermic machine perfusion for liver graft preservation

Purpose of review Ex-vivo machine perfusion has emerged as a promising alternative to static cold storage (SCS) for preservation of liver grafts over the last decade. This review describes the mechanistic benefits associated with hypothermic machine perfusion (HMP) for preservation of liver grafts and highlights clinical outcomes of liver transplantation using HMP technology. Recent findings Over the last decade, several single-centre studies have shown decreased biliary complications, decreased early allograft dysfunction (EAD) rates and improved patient survival in liver transplant recipients after application of HMP for liver graft preservation. This has led to initiation of prospective, multicentre, randomized controlled trials (RCTs) in both Europe and North America focused on clinical outcomes in liver transplant recipients using HMP-preserved liver grafts. In addition, recent single-centre studies have shown the utility of perfusate biomarker analysis during HMP in predicting EAD after liver transplantation. Summary HMP technology has potential to increase the available donor liver organ pool for liver transplant recipients and improve clinical outcomes after liver transplantation. Broader clinical application of HMP in resuscitation and preservation of liver grafts is anticipated over the next decade once regulatory, logistical and financial challenges are overcome.
Evidence for two domestication lineages supporting a middle-eastern origin for Brassica oleracea crops from diversified kale populations

Abstract Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as “species”) using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the “leafy head” lineage (LHL) and the “arrested inflorescence” lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.
Hospital factors that predict intention of health care workers to leave their job during the COVID‐19 pandemic

Abstract Purpose To identify factors responsible for hospital health care workers' intention to leave their job during the COVID‐19 pandemic. Design A cross‐sectional study was performed. Methods A self‐administered questionnaire was delivered to solicit hospital health care workers' demographics, intention to leave, workplace environment, and changes related to COVID‐19 from July to November 2020 in Taiwan. Principal component analysis was performed to compare group‐related factors. Multiple logistic regression was used to determine the risk factors for the intention of health care workers to leave their job. Findings Among the 1209 health care workers (mean age, 36.3 years) who participated in the study, intention to leave the job was found to be related to factors relating to COVID‐19, including perceived risk, affected social relationships, and increased workload and job stress, after adjustment for demographic and work factors. Supportive administration/management were protective factors against leaving the job. These results were supported by sensitivity analyses. Conclusions Our findings suggest that the intention of health care workers to leave their job during a pandemic is related to potentially modifiable factors relating to the infection itself and work environment. Clinical relevance High perceived risk of COVID‐19, affected social relationaops, and increased workload and job stress were positively associated with the intention of health care workers to leave their job, whereas supportive administration and management were protective factors against leaving the job. Development of workplace strategies is important to help mitigate these above factors, improve psychological wellbeing, and promote workforce stability.
Husband’s income, wife’s income, and number of biological children in the U.S.

ABSTRACT Previous studies have found that the positive relationship between personal income and fertility for men in the United States is primarily due to childlessness among low-income men. Yet because of the opposite effects of income on fertility for men and women, it is important to examine the effects of income net of spouse’s income. An analysis of income from all sources and biological fertility data for husbands and wives from the Survey of Income and Program Participation (2014) shows that for men their own income is positively associated with the number of their biological children, while their spouse’s income is negatively associated with total children ever fathered. The reverse is true for women. These results are not because of childlessness among low-income men and high-income women, but also hold true among all those with children. For men and women aged 45–65, who likely have completed fertility, these results hold regardless of whether or not education is controlled. These findings suggest that if status is measured as personal income for men and husband’s income for women, the positive relationship between status and fertility persists in a postdemographic transition society.
Emergency Room Nurses’ Attitudes toward Family Presence during Resuscitation: A Cross-Sectional Study

Abstract Introduction Although there are guidelines that encourage the family presence during cardiopulmonary resuscitation, literature that reported on the healthcare team’s attitudes suggested that this practice is often discouraged, and it remains a debatable topic. Aim To assess the Emergency Room Nurses’ Attitudes toward family presence during cardiopulmonary resuscitation procedures. Research design A cross-sectional descriptive correlation research design was used for this study. Participants and research context A non-probability convenience sample for this study comprised 222 registered nurses who have worked in emergency departments. The study used Family Presence During Resuscitation scale to collect the data related to nurses’ attitude toward family presence during CPR. Ethical considerations This study was approved by the ethics committee at Al-Zaytoonah University of Jordan. Results Jordanian nurses had a positive attitude toward the health beliefs with a mean score of (3.71 ± 0.81), followed by cues and triggers (3.60 ± 0.82). The least attitude endorsed by nurses was perceived self-efficacy with a mean score of (2.87 ± 0.80). Point-biserial correlation yielded a positive correlation between marital status and cues or triggers (r = 0.055; p = 0.043). Moreover, person correlation showed a positive relationship between age and health beliefs (r = 00.134; p = 0.040) and a negative correlation between experience and self-efficacy (r=-0.141; p = 0.043). Conclusion Enhancing nurses’ confidence based on evidence-based practice would prepare nurses to handle family presence during resuscitation.
A case of ganglioglioma grade 3 with H3 K27M mutation arising in the medial temporal lobe in an elderly patient

The mutation p.K27M in H3F3A (H3 K27M mutation) is mainly detected in diffuse midline glioma. However, recent studies have demonstrated that H3 K27M mutation could also be observed in a subset of gangliogliomas. Importantly, most H3 K27‐mutated ganglioglioma cases also harbor BRAF V600E mutation. Herein, we report a rare case of H3 K27M‐mutated ganglioglioma grade 3 without BRAF mutation arising in the medial temporal lobe in an elderly man. A small biopsy specimen was sampled. The pathological diagnosis was diffuse astrocytoma. The tumor progressed gradually during an 18‐month follow‐up period. Gadolinium enhancement on magnetic resonance imaging was noted 36 months after the biopsy. The patient was referred to a hospital for tumor resection. Histological analysis of resected specimens led to a diagnosis of ganglioglioma grade 3 with H3 K27M mutation. The patient underwent concurrent temozolomide chemotherapy with radiotherapy. Although the patient's condition deteriorated after chemotherapy due to disease progression, he survived for more than 23 months after tumor resection. We present this rare case and discuss the involvement of H3 K27M mutation in ganglioglioma grade 3.
Follicle‐stimulating hormone modestly predicts improvement in semen parameters in men with infertility treated with clomiphene citrate

Clomiphene citrate is a commonly prescribed empiric medical therapy for male infertility, but outcomes data and response rates remain incompletely understood. We retrospectively reviewed our single‐institutional experience of infertile men prescribed clomiphene. Clomiphene treatment in the final cohort of 140 men was associated with a modest increase in median sperm concentration from 2.2 to 2.5 million/ml (p < 0.001). A total of 46/140 (33%) of men upgraded according to World Health Organization concentration categories. Clomiphene treatment in 26/113 (23%) of previously ineligible men became eligible for intrauterine insemination. Using both univariate and multivariable regression, pre‐treatment follicle‐stimulating hormone was inversely associated with change in semen concentration with clomiphene treatment. On binary logistic regression, follicle‐stimulating hormone level was inversely related to World Health Organization concentration category upgrade (p = 0.01). Unfortunately, 17/140 (12%) of men paradoxically worsened on clomiphene, but no predictors for this could be identified. In summary, clomiphene citrate confers a clinically relevant but modest benefit in a subset (1/3rd) of infertile men, particularly those with lower pre‐treatment follicle‐stimulating hormone levels. Men with elevated follicle‐stimulating hormone over 15 IU/ml are less likely to benefit from treatment and should be counselled on other relevant treatment alternatives.
Invasive Exploitation and the Multiplicative Hypothesis: Polyvictimization and Adolescent Depression Symptoms in Nepal

Adverse effects of childhood maltreatment experience and adolescent depression symptoms are theorized to be more profound for adolescents who have suffered multiple maltreatments (polyvictimization). New theoretical insights into the study of polyvictimization suggest that it must be studied using a multiplicative logic, particularly when maltreatment is characterized by invasive exploitation. This study, for the first time, examined the concept of invasive exploitation in the context of polyvictimization and its association with adolescent depression symptoms. The study used a random, three stage probability proportional to size (PPS) cluster sample of 565 mother-adolescent dyads in Kathmandu, Nepal, and also examined the protective effects of maternal empathy. We hypothesized that (a) singly, the empirical categories of maltreatment (neglect, physical abuse, and child sexual abuse) would associate positively with adolescent depressive symptoms and (b) main effects held constant, the interaction effects of a child sexual abuse X neglect and a child sexual abuse X physical abuse would be positive. Regression with clustering corrections found that neglect (B = 3.17, p < .01) and sexual abuse (B = 3.48, p < .05) positively associated with adolescent depression symptoms. Results support the multiplicative invasive exploitation polyvictimization hypothesis (child sexual abuse X neglect interaction; B = 6.14, p < .05). The positive neglect X sexual abuse interaction is consistent with the theory that sexual abuse is distinct as invasive exploitation, and demonstrates that the multiplicative hypothesis can be fruitfully applied to the study of polyvictimization. Interventions targeting polyvictims with experience of invasive exploitation and studies aiming to provide deeper insights into sexual abuse as invasive exploitation are needed.