Miracle-dz/UniFAR-FTUs huggingface dataset:
HELZ directly interacts with CCR4–NOT and causes decay of bound mRNAs

The putative UPF1-like SF1 helicase HELZ directly interacts with the CCR4–NOT deadenylase complex to induce translational repression and 5′-to-3′ decay of bound mRNAs. Eukaryotic superfamily (SF) 1 helicases have been implicated in various aspects of RNA metabolism, including transcription, processing, translation, and degradation. Nevertheless, until now, most human SF1 helicases remain poorly understood. Here, we have functionally and biochemically characterized the role of a putative SF1 helicase termed “helicase with zinc-finger,” or HELZ. We discovered that HELZ associates with various mRNA decay factors, including components of the carbon catabolite repressor 4-negative on TATA box (CCR4–NOT) deadenylase complex in human and Drosophila melanogaster cells. The interaction between HELZ and the CCR4–NOT complex is direct and mediated by extended low-complexity regions in the C-terminal part of the protein. We further reveal that HELZ requires the deadenylase complex to mediate translational repression and decapping-dependent mRNA decay. Finally, transcriptome-wide analysis of Helz-null cells suggests that HELZ has a role in the regulation of the expression of genes associated with the development of the nervous system.
Maternal smoking during pregnancy, semen characteristics and reproductive hormone levels in men consulting for couple infertility

The aim of our study was to evaluate the relationship between maternal tobacco consumption during pregnancy and sperm parameters and sexual hormonal levels of their sons in adulthood. We conducted a cross‐sectional study in four medical institutions in Argentina, between June 1999 and June 2015, among male partners of couples consulting for infertility. At inclusion, a structured interview was conducted to obtain information on the basic demographic, medical, surgical and reproductive history, personal tobacco consumption and that of their parents during pregnancy. Two semen analyses at an interval of 2–4 weeks and a blood hormone evaluation (FSH, LH, prolactin, total testosterone and oestradiol) were then ordered. Analyses using multivariate models adjusted for potential confounders were performed for 537 men. Maternal tobacco consumption during pregnancy was associated with a significantly higher risk of reduced sperm count and elevated total testosterone levels. We did not find any significant association between maternal smoking and other sperm parameters nor other hormone levels. Our study adds evidence concerning the association between maternal tobacco consumption during pregnancy and reduced sperm counts of their sons in adulthood. The results showing an association between elevated total testosterone levels and maternal tobacco consumption need to be replicated.
Extract from Aloysia polystachya Induces the Cell Death of Colorectal Cancer Stem Cells

Abstract Cancer stem cells (CSCs) are an important player in the resistance of cancers to therapy. In this work, we determined the flavonoids composition and biological action of Aloysia polystachya (AP) extracts in colorectal cancer. The chemical characterization of extracts was performed by HPLC. Assays of cytotoxicity, apoptosis, migration and invasion, metalloproteases activity, clonogenic growth, tumorspheres formation, Hoechts efflux, pluripotency marker expression and sensitization to chemotherapeutic drugs were performed in vitro in human HCT116 and murine CT26 colorectal cancer cells. The AP toxicity and effect in tumor growth administered alone or in combination with 5- Fluorouracile was analyzed in vivo, including histopathological studies. We found that AP extracts induced in vitro the apoptosis of colorectal cancer cell lines decreasing the CSC proportion. Moreover, they were capable to kill 5-Fluorouracile resistant side population cells. At not toxic doses in vivo, AP extracts inhibited tumor growth. Regarding the ability to reduce the CSC population, AP extracts deserves to be investigated as a useful therapy for colorectal cancer treatment.
Angiographic characteristics and in-hospital mortality among patients with ST-segment elevation myocardial infarction presenting without typical chest pain: an analysis of China Acute Myocardial Infarction registry

Abstract Background: Patients with ST-segment elevation myocardial infarction (STEMI) who present without typical chest pain are associated with a poor outcome. However, whether angiographic characteristics are related to a higher risk of mortality in this population is unclear. This study aimed to investigate whether the higher mortality risk in patients with STEMI without chest pain could be explained by their “high-risk” angiographic characteristics. Methods: We used data of 12,145 patients with STEMI who was registered in China Acute Myocardial Infarction registry from January 2013 to September 2014. We compared the infarct-related artery (IRA), thrombolysis in myocardial infarction (TIMI) flow grade in the IRA, and other angiographic characteristics between patients without and those with chest pain. Multivariable logistic regression model was used to identify independent risk factor of in-hospital mortality. Results: The 2922 (24.1%) patients with STEMI presented without typical chest pain. These patients had a higher TIMI flow grade (mean TIMI flow grade: 1.00 vs. 0.94, P = 0.02) and a lower rate of IRA disease of the left anterior descending artery (44.6% vs. 51.2%, χ2 = 35.63, P < 0.01) than did those with typical chest pain. Patients without chest pain were older, more likely to have diabetes, longer time to hospital and higher Killip classification, and less likely to receive optimal medication treatment and primary percutaneous coronary intervention and higher In-hospital mortality (3.3% vs. 2.2%, χ2 = 10.57, P < 0.01). After adjusting for multi-variables, presentation without chest pain was still an independent predictor of in-hospital death among patients with STEMI (adjusted odds ratio: 1.36, 95% confidence interval: 1.02–1.83). Conclusions: Presentation without chest pain is common and associated with a higher in-hospital mortality risk in patients with acute myocardial infarction. Our results indicate that their poor prognosis is associated with baseline patient characteristics and delayed treatment, but not angiographic lesion characteristics. Clinical trial registration: NCT01874691, https://clinicaltrials.gov.
Factors Affecting Psychological Stress in Healthcare Workers with and without Chronic Pain: A Cross-Sectional Study Using Multiple Regression Analysis

Background and Objectives: Pain affects psychological stress and general health in the working population. However, the factors affecting psychological job stress related to chronic pain are unclear. This study aimed to clarify the structural differences among factors affecting psychological job stress in workers with chronic pain and those without pain. Materials and Methods: A stepwise multiple regression analysis revealed the differences in structure between the psychological stress of workers with chronic pain and those with no pain. Psychological job stress by the Brief Job Stress Questionnaire was used as the dependent variable, with psychological state (depression and anxiety), specifically that characteristic of chronic pain (pain catastrophizing); information on the nature of the pain (intensity and duration); and number of years of service as independent variables. Selected independent variables were evaluated for collinearity. Results: In the model with psychological stress as a dependent variable (chronic pain: r2 = 0.57, F = 41.7, p < 0.0001; no-pain: r2 = 0.63, F = 26.3, p < 0.0001), the difference between the experiences of workers with chronic pain and those with no pain was that chronic pain was associated with depression (Beta = 0.43, p < 0.0001) and no pain with anxiety (Beta = 0.34, p < 0.0001). In the model with chronic pain-related depression as a dependent variable (r2 = 0.62, F = 41.7, p < 0.0001), job-life satisfaction (Beta = −0.18, p = 0.0017) and magnification (a dimension of pain catastrophizing; Beta = 0.16, p < 0.0001) were significant. Conclusions: The results of this study suggest that the psychological characteristics of chronic pain, such as depression and magnification, should be considered when evaluating and intervening in the job stress of workers with chronic pain.
Comparison of the Utilities of Cryobiopsy and Forceps Biopsy for Peripheral Lung Cancer

Background/Aim: This study aimed to compare the efficacies of cryobiopsy and forceps biopsy for peripheral lung cancer detection. Patients and Methods: A retrospective review of peripheral lung cancer cases between December 2017 and April 2019 was conducted. Forceps biopsy was performed followed by cryobiopsy using a guide sheath (GS). Diagnostic yields were compared between cryobiopsy and forceps biopsy. Results: A total of 53 lung cancer lesions were evaluated. The diagnostic yields of forceps biopsy and cryobiopsy were 86.8% and 81.1%, respectively. Univariate and multivariate analyses indicated that cryobiopsy with a GS was significantly associated with increased diagnostic yield (odds ratio(OR)=11.6; p=0.044). Among the four patients who tested positive on cryobiopsy and negative on forceps biopsy, one had diffused pulmonary metastases and the others showed intratumoural air bronchograms. Conclusion: Cryobiopsy using a GS can significantly increase diagnostic yield and help identify lesions with intratumoural air bronchograms and external wall lesions.
"There is something you must see": breaking down the remission concept in rheumatoid arthritis from a rheumatologist's perspective.

OBJECTIVES To explore the remission concept in rheumatoid arthritis (RA) and the implications of the existing definitions when applied to clinical practice among rheumatologists with different profiles. METHODS A qualitative study through focus groups was conducted. Three focus groups were organised from February to March 2016. Each group was composed of rheumatologists with extensive clinical experience with different profiles; experts in basic research (RBR), experts in imaging techniques research (RIR), and experts in clinical research (RCR). The data was collected with audio recording. Verbatim transcriptions of the audio files were made, and a subsequent reflexive thematic analysis assisted by ATLAS.ti (GmbH, Berlin, v. 7) software was performed. RESULTS From the reflexive thematic analysis, three main themes were generated: (1) remission limitations, (2) instruments or measures to assess remission, and (3) a new definition of remission. Rheumatologists mentioned frequently that the following variables should be considered when developing a new remission definition: inflammatory activity, calprotectin, psychological variables, sex, disease stage, and sociocultural factors. Contrary to what could be expected, all groups acknowledged that their research field could contribute with domains for a gold standard remission instrument, but not in a hierarchical arrangement of importance. The dissonance existing in the entire remission evaluation process was outlined: remission in clinical practice versus remission in clinical trials, remission following the American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) Boolean versus Musculoskeletal Ultrasound (US) remission, and remission from the rheumatologist's point of view versus the patient's point of view. CONCLUSIONS Currently, rheumatologists would not accept a domain as more important than others in remission. Our suggestion is, not to generate a universal definition of remission - one that could cover all aspects - but rather to develop definitions of remission for the different settings that could be pondered by the patient's perspective.
Transcriptome Sequencing and Metabolome Analysis Reveal Genes Involved in Pigmentation of Green-Colored Cotton Fibers

Green-colored fiber (GCF) is the unique raw material for naturally colored cotton textile but we know little about the pigmentation process in GCF. Here we compared transcriptomes and metabolomes of 12, 18 and 24 days post-anthesis (DPA) fibers from a green fiber cotton accession and its white-colored fiber (WCF) near-isogenic line. We found a total of 2047 non-redundant metabolites in GCF and WCF that were enriched in 80 pathways, including those of biosynthesis of phenylpropanoid, cutin, suberin, and wax. Most metabolites, particularly sinapaldehyde, of the phenylpropanoid pathway had a higher level in GCF than in WCF, consistent with the significant up-regulation of the genes responsible for biosynthesis of those metabolites. Weighted gene co-expression network analysis (WGCNA) of genes differentially expressed between GCF and WCF was used to uncover gene-modules co-expressed or associated with the accumulation of green pigments. Of the 16 gene-modules co-expressed with fiber color or time points, the blue module associated with G24 (i.e., GCF at 24 DPA) was of particular importance because a large proportion of its genes were significantly up-regulated at 24 DPA when fiber color was visually distinguishable between GCF and WCF. A total of 56 hub genes, including the two homoeologous Gh4CL4 that could act in green pigment biosynthesis, were identified among the genes of the blue module that are mainly involved in lipid metabolism, phenylpropanoid biosynthesis, RNA transcription, signaling, and transport. Our results provide novel insights into the mechanisms underlying pigmentation of green fibers and clues for developing cottons with stable green colored fibers.
A data-driven approach to predicting the attachment density of biofouling organisms

Abstract The attachment efficiency of biofouling organisms on solid surfaces depends on a variety of factors, including fouler species, nutrition abundance, flow rate, surface morphology and the stiffness of the solid to which attachment is to be made. So far, extensive research has been carried out to investigate the effects of these factors on the attachment of various fouling species. However, the results obtained are species-dependent and scattered. There is no universal rule that can be applied to predict the attachment efficiency of different species. To solve this problem, the authors carried out meta-analysis of the effects of ten selected factors on attachment efficiency, resulting in a universal correlation between the attachment density and the selected factors, which was validated by attachment tests of tubeworms on PDMS surfaces. The results provide a practical approach to predicting the attachment efficiency of fouling organisms and should be of great value in the design of anti-biofouling materials.
One-Hour Esophageal String Test: A Nonendoscopic Minimally Invasive Test That Accurately Detects Disease Activity in Eosinophilic Esophagitis

OBJECTIVES: Eosinophilic esophagitis (EoE), a chronic food allergic disease, lacks sensitive and specific peripheral biomarkers. We hypothesized that levels of EoE-related biomarkers captured using a 1-hour minimally invasive Esophageal String Test (EST) would correlate with mucosal eosinophil counts and tissue concentrations of these same biomarkers. We aimed to determine whether a 1-hour EST accurately distinguishes active from inactive EoE or a normal esophagus. METHODS: In a prospective, multisite study, children and adults (ages 7–55 years) undergoing a clinically indicated esophagogastroduodenoscopy performed an EST with an esophageal dwell time of 1 hour. Subjects were divided into 3 groups: active EoE, inactive EoE, and normal esophageal mucosa. Eosinophil-associated protein levels were compared between EST effluents and esophageal biopsy extracts. Statistical modeling was performed to select biomarkers that best correlated with and predicted eosinophilic inflammation. RESULTS: One hundred thirty-four subjects (74 children, 60 adults) with active EoE (n = 62), inactive EoE (n = 37), and patient controls with a normal esophagus (n = 35) completed the study. EST-captured eosinophil-associated biomarkers correlated significantly with peak eosinophils/high-power field, endoscopic visual scoring, and the same proteins extracted from mucosal biopsies. Statistical modeling, using combined eotaxin-3 and major basic protein-1 concentrations, led to the development of EoE scores that distinguished subjects with active EoE from inactive EoE or normal esophagi. Eighty-seven percent of children, 95% of parents, and 92% of adults preferred the EST over endoscopy if it provided similar information. DISCUSSION: The 1-hour EST accurately distinguishes active from inactive EoE in children and adults and may facilitate monitoring of disease activity in a safe and minimally invasive fashion.
Homicide Profiles Based on Crime Scene and Victim Characteristics

One of the current trends in homicide research includes developing works based on scientific study and empirical evidence, which offer conclusions that can be used in an operational manner during police investigations. The objective of this study was to identify homicide characteristics from behaviors carried out on the crime scene and victim characteristics associated with those of the perpetrators of these crimes in Spain. The sample consisted of 448 homicide cases from the database of the Homicide Revision Project led by the Office of Coordination and Studies of the Secretary of State and Security. After creating six classification tree models, it was found that the modus operandi of the aggressor and the victim characteristics may permit hypothesizing about the demographic characteristics of the perpetrator (gender, age, and country of origin), his/her criminal record, and the type of relationship with the victim. Furthermore, the importance of the study of victimology during a criminal investigation is highlighted, as it may indirectly offer information about the potential perpetrator. The findings of this study suggest that criminal profiling contributes notably to the decision-making process to establish more rigorous suspect prioritization, improve the management of human resources and materials, and increase the efficiency of criminal investigations.
Contribution of GO System Glycosylases to Mutation Prevention in Caulobacter crescentus

8‐oxo‐7,8‐dihydroguanine, commonly referred to as 8‐oxoG, is considered one of the most predominant oxidative lesions formed in DNA. Due to its ability to pair with adenines in its syn configuration, this lesion has a strong mutagenic potential in both eukaryotes and prokaryotes. Escherichia coli cells are endowed with the GO system, which protects them from the mutagenic properties of this lesion when formed both in cellular DNA and the nucleotide pool. MutY and MutM (Fpg) DNA glycosylases are crucial components of the GO system. A strong mutator phenotype of the Escherichia coli mutM mutY double mutant underscores the importance of 8‐oxoG repair for genomic stability. Here, we report that in Caulobacter crescentus, a widely studied alpha‐proteobacterium with a GC‐rich genome, the combined lack of MutM and MutY glycosylases produces a more modest mutator phenotype when compared to E. coli. Genetic analysis indicates that other glycosylases and other repair pathways do not act synergistically with the GO system for spontaneous mutation prevention. We also show that there is not a statistically significant difference in the spontaneous levels 8‐oxodGuo in E. coli and C. crescentus, suggesting that other yet to be identified differences in repair or replication probably account for the differential importance of the GO system between these two species. Environ. Mol. Mutagen. 61:246–255, 2020. © 2019 Wiley Periodicals, Inc.
Emergency bedside ultrasound-benefits as well as caution: Part 2: Echocardiography.

PURPOSE OF REVIEW Critical care echocardiography (CCE) has become an important component of general critical care ultrasonography, and a current review of its performance is presented. RECENT FINDINGS Basic CCE should be performed as a goal-directed examination to better identify specific signs and to answer important clinical questions concerning acute hemodynamic concerns. It has evolved in the ICU and also in the emergency department not only for improved diagnostic capability but also as an effective part of the triage process. It remains an efficacious procedure even in patients with respiratory failure when combined with lung ultrasonography. Numerous acronyms were proposed, but in all cases, CCE responds to the same rules as fundamental echocardiography. Basic CCE requires accessible and comprehensive training for physicians and is mandatory for all intensivists. Development of pocket echo devices may increase the use of basic CCE as has miniaturization of other medical technologies. Performance should be managed by guidelines, and the CCE training program should be standardized worldwide. More trials are welcome to evaluate its impact on patient outcomes. SUMMARY Thanks to its ability to quickly obtain a diagnostic orientation at the bedside and to implement targeted therapy, basic CCE over the past decade has become an essential tool for hemodynamic assessment of the cardiopulmonary unstable patient. Its more recent incorporation into the education of trainees in medical school and residencies/fellowships has reinforced its perceived importance in critical care management, despite the relative paucity as yet of rigorous scientific evidence demonstrating positive outcome modification from its use.
Genome‐resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep‐sea hydrothermal vents

Summary The structure and function of microbial communities inhabiting the subseafloor near hydrothermal systems are influenced by fluid geochemistry, geologic setting and fluid flux between vent sites, as well as biological interactions. Here, we used genome‐resolved metagenomics and metatranscriptomics to examine patterns of gene abundance and expression and assess potential niche differentiation in microbial communities in venting fluids from hydrothermal vent sites at the Mid‐Cayman Rise. We observed similar patterns in gene and transcript abundance between two geochemically distinct vent fields at the community level but found that each vent site harbours a distinct microbial community with differing transcript abundances for individual microbial populations. Through an analysis of metabolic pathways in 64 metagenome‐assembled genomes (MAGs), we show that MAG transcript abundance can be tied to differences in metabolic pathways and to potential metabolic interactions between microbial populations, allowing for niche‐partitioning and divergence in both population distribution and activity. Our results illustrate that most microbial populations have a restricted distribution within the seafloor, and that the activity of those microbial populations is tied to both genome content and abiotic factors.