Miracle-dz/UniFAR-FTUs huggingface dataset:
The deep-water rose shrimp in the Ionian Sea: a spatio-temporal analysis of zero-inflated abundance data

In the ecological field, the sampling of abundance data is often characterized by the zero inflation of population distributions. Constrained zero-inflated GAM’s (COZIGAM) are obtained assuming that the probability of non-zero inflation and the mean non-zero-inflated population abundance are linearly related. Models of this class have been applied to a spatio-temporal case study concerning the deep-water rose shrimp, Parapenaeus longirostris (Lucas, 1846). Abundance data were collected during 16 experimental trawl surveys conducted from 1995 to 2010 in the Ionian Sea. The sampling design adopted was random-stratified by depth, with proportional allocation of hauls to the area of each depth range and geographical sector. Density index (N/km2) and length (mm) were considered for each haul identified by time, depth, geographic coordinates and geographical sector.
OCT4 regulates WNT/β‐catenin signaling and prevents mesoendoderm differentiation by repressing EOMES in porcine pluripotent stem cells

The regulatory network between signaling pathways and transcription factors (TFs) is crucial for the maintenance of pluripotent stem cells. However, little is known about how the key TF OCT4 coordinates signaling pathways to regulate self‐renewal and lineage differentiation of porcine pluripotent stem cells (pPSCs). Here, we explored the function of OCT4 in pPSCs by transcriptome and chromatin accessibility analysis. The TFs motif enrichment analysis revealed that, following OCT4 knockdown, the regions of increased chromatin accessibility were enriched with EOMES, GATA6, and FOXA1, indicating that pPSCs differentiated toward the mesoendoderm (ME) lineage. Besides, pPSCs rapidly differentiated into ME when the WNT/β‐catenin inhibitor XAV939 was removed. However, the ME differentiation of pPSCs caused by OCT4 knockdown did not rely on the activation of WNT/β‐catenin signaling because the target gene of WNT/β‐catenin signaling, AXIN2 was not upregulated after OCT4 knockdown, despite significant upregulation of WLS and some WNT ligands. Importantly, OCT4 is directly bound to the promoter and enhancers of EOMES and repressed its transcription. Overexpression of EOMES was sufficient to induce ME differentiation in the presence of XAV939. These results demonstrate that OCT4 can regulate WNT/β‐catenin signaling and prevent ME differentiation of pPSCs by repressing EOMES transcription.
XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes

Co-transcriptional RNA-DNA hybrids can not only cause DNA damage threatening genome integrity but also regulate gene activity in a mechanism that remains unclear. Here, we show that the nucleotide excision repair factor XPF interacts with the insulator binding protein CTCF and the cohesin subunits SMC1A and SMC3, leading to R-loop–dependent DNA looping upon transcription activation. To facilitate R-loop processing, XPF interacts and recruits with TOP2B on active gene promoters, leading to double-strand break accumulation and the activation of a DNA damage response. Abrogation of TOP2B leads to the diminished recruitment of XPF, CTCF, and the cohesin subunits to promoters of actively transcribed genes and R-loops and the concurrent impairment of CTCF-mediated DNA looping. Together, our findings disclose an essential role for XPF with TOP2B and the CTCF/cohesin complex in R-loop processing for transcription activation with important ramifications for DNA repair–deficient syndromes associated with transcription-associated DNA damage.
Rationale and design of a randomized trial of the dapagliflozin evaluation on atrial fibrillation patients followed Cox-Maze IV: the DETAIL-CMIV study

Abstract Aims Dapagliflozin has been widely used for the treatment of type 2 diabetes mellitus (T2DM) and heart failure (HF). However, data concerning the association between dapagliflozin and the recurrence of atrial fibrillation (AF), especially in patients following Cox-Maze IV (CMIV), are rare. We aim to explore the effect of dapagliflozin on the recurrence of AF after CMIV with and without T2DM or HF. Methods and results The study of dapagliflozin evaluation in AF patients followed by CMIV (DETAIL-CMIV) is a prospective, double-blind, randomized, placebo-controlled trial. A total of 240 AF patients who have received the CMIV procedure will be randomized into the dapagliflozin group (10 mg/day, n = 120) and the placebo group (10 mg/day, n = 120) and treated for 3 months. The primary endpoint is any documented atrial tachyarrhythmia (AF, atrial flutter or atrial tachycardia) lasting 30 s following a blanking period of 3 months after CMIV. Conclusion DETAIL-CMIV will determine whether the sodium-glucose cotransporter-2 inhibitor dapagliflozin, added to guideline-recommended post-operative AF therapies, safely reduces the recurrence rate of AF in patients with and without T2DM or HF.
Immediate post performance judgements about cognitive performance in schizophrenia and bipolar disorder: associations with test performance and subjective overall judgments regarding abilities

ABSTRACT Introduction: The study explored associations between the accuracy of post assessment judgements of cognitive performance with global self-assessments of psychosocial functioning compared to evaluations generated by observers in schizophrenia and bipolar disorder. Methods: An abbreviated cognitive assessment based on the MATRICS Consensus Cognitive Battery was administered to 122 individuals with schizophrenia and 113 with bipolar disorder. They provided self-estimates of their performance after each subtest. In addition, self-reports on cognition, social cognition, and everyday functioning were collected and compared to observer ratings. Results: Both groups overestimated their cognitive function, but in bipolar disorder, there was 30% shared variance between task performance and self-rated task performance (vs. 5% in schizophrenia). Significant correlations were found between self-reported everyday outcomes and both actual and self-assessed performance. In schizophrenia, immediate judgements were only related to self-rated functioning, not to observer rated functioning. In bipolar disorder, impairments in self-assessment of performance correlated with observer ratings of cognitive ability, which was not observed in schizophrenia. Conclusions: While both groups showed correlations between cognitive performance and introspective accuracy, individuals with bipolar disorder showed higher accuracy in assessing their cognitive performance and other outcomes. Notably, impairments in introspective accuracy were associated with observer-rated functioning exclusively in bipolar disorder.
Association of thoracic epidural analgesia with risk of atrial arrhythmias after pulmonary resection : a retrospective cohort study

ryukomatsu80@gmail.com. Conflict of interest No conflicts of interest. HHS Public Access Author manuscript J Anesth. Author manuscript; available in PMC 2016 March 14. Published in final edited form as: J Anesth. 2015 February ; 29(1): 47–55. doi:10.1007/s00540-014-1865-z. A uhor M anscript
High-fidelity large-diversity monoclonal mammalian cell libraries by cell cycle arrested recombinase-mediated cassette exchange

Abstract Mammalian cells carrying defined genetic variations have shown great potentials in both fundamental research and therapeutic development. However, their full use was limited by lack of a robust method to construct large monoclonal high-quality combinatorial libraries. This study developed cell cycle arrested recombinase-mediated cassette exchange (aRMCE), able to provide monoclonality, precise genomic integration and uniform transgene expression. Via optimized nocodazole-mediated mitotic arrest, 20% target gene replacement efficiency was achieved without antibiotic selection, and the improved aRMCE efficiency was applicable to a variety of tested cell clones, transgene targets and transfection methods. As a demonstration of this versatile method, we performed directed evolution of fragment crystallizable (Fc), for which error-prone libraries of over 107 variants were constructed and displayed as IgG on surface of CHO cells. Diversities of constructed libraries were validated by deep sequencing, and panels of novel Fc mutants were identified showing improved binding towards specific Fc gamma receptors and enhanced effector functions. Due to its large cargo capacity and compatibility with different mutagenesis approaches, we expect this mammalian cell platform technology has broad applications for directed evolution, multiplex genetic assays, cell line development and stem cell engineering.
Comparison of Two Contact Detection Methods for Ground Reaction Forces and Moment Estimation During Sidestep Cuts, Runs and Walks.

The use of force platforms limits the study of human movement in the laboratory. Promising methods for estimating ground reaction forces and moments minimise a cost function, constrained by the subject's dynamic equilibrium, to distribute the overall force over the contact surfaces. The detection of the contact surfaces is dependent on parameter settings. The aim of this study was to evaluate two contact surface detection methods: one based on foot kinematics and the other based on pressure insoles data. Optimal parameters were identified for both methods on sidestep cuts, runs and walks. Contact can be detected on the basis of a position threshold or of a velocity threshold. Using pressure insoles data to detect contact gives a better estimate of the position of the centre of pressure. The two contact detection methods demonstrated comparable accuracy in terms of estimating the external forces.
Dietary Isoflavone Intake and Breast Cancer Prognosis: A Prospective Analysis and Meta-Analysis

Abstract We aimed to examine the association between dietary isoflavone intake and the risk of breast cancer recurrence and summarize evidence on the role of dietary isoflavone intake in breast cancer prognosis. This prospective study included 592 breast cancer survivors who completed a dietary assessment. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards models. Of the studies published until May 31, 2023, that were searched in PUBMED and EMBASE databases, 14 studies were selected. Adjusted HRs were combined using fixed- or random-effects models. During the median follow-up of 4.3 years, 47 recurrences were identified. The HR (95% CI) for recurrence comparing the highest versus the lowest tertile of isoflavones intake was 1.29 (0.60–2.78). In a meta-analysis of previously published data and ours, dietary isoflavone intake was associated with a better breast cancer prognosis. The combined HRs (95% CIs) comparing the extreme categories were 0.81 (0.67–0.98) for recurrence and 0.85 (0.76–0.96) for all-cause mortality. A nonlinear inverse association was observed between isoflavone intake and the risk of recurrence and all-cause mortality. Our study suggests that dietary isoflavone intake is associated with a favorable prognosis in breast cancer survivors and warrants further investigation.
MODELING CURRENT AND FUTURE WATER USE IN UTAH WITH NASA'S TERRESTRIAL OBSERVATION AND PREDICTION SYSTEM

Cache County is one of the biggest agricultural producers in Utah and over 70% of the county’s water is used for irrigation. In this project, we use NASA’s Terrestrial Observation and Prediction System (TOPS) and Moderate Resolution Imaging Spectroradiometer (MODIS) data to gain an understanding of the water cycle in Cache County by comparing the precipitation, snowpack, and runoff amounts to the crop evapotranspiration (ET) requirements. By modeling ET, we evaluated the true demand for water and compare it to the amount of water supplied, determining the water efficiency. We found that the current irrigation practices have an efficiency of approximately 30%. Furthermore, we employed a climate change scenario to study the effects of temperature increase on Cache County’s water cycle and agricultural production. As climate changes, snow cover will significantly decrease and crop evapotranspiration will increase, altering the current water supply.
Interactive effects of mindfulness and negative urgency on intimate partner aggression perpetration.

Intimate partner aggression (IPA) is a costly and incompletely understood phenomenon. Negative urgency, the tendency to act impulsively in response to negative affect, is predictive of IPA perpetration. Mindfulness, by virtue of its emphasis on nonreactivity to negative affect, is an opposing force to urgent tendencies that may mitigate the negative urgency-IPA link. Yet, no research to date investigates the interactive effects of negative urgency and mindfulness on IPA perpetration. Two studies were conducted that measured and manipulated multiple facets of mindfulness alongside measures of negative urgency and tendencies of IPA perpetration (combined N = 508 undergraduate students in monogamous intimate relationships). Counter to our preregistered predictions, we found that negative urgency's association with greater IPA perpetration increased at higher levels of mindfulness. These findings suggest that mindfulness may not be a protective factor against IPA perpetration for individuals higher in negative urgency, but rather may serve as a risk factor.
Mono-(2-ethylhexyl) phthalate reversibly disrupts the blood-testis barrier in pubertal rats

Abstract The blood-testis barrier (BTB) is constituted by tight junctions between adjacent Sertoli cells (SCs) that create a specialized adluminal microenvironment to foster the development of spermatocytes and spermatids. The BTB is a well-studied target of numerous environmental toxicants, including di-(2-ethylhexyl) phthalate (DEHP), a compound widely used in various consumer products. Mono-(2-ethylhexyl) phthalate (MEHP) is the active toxic metabolite of DEHP that has long been recognized in postnatal rodents to disrupt SC function. This study evaluates the impact of MEHP on the integrity of the BTB in both pubertal and adult rats and the signal transduction pathways known to be involved in the disruption of the BTB. Treatment of prepubertal rats with 700 mg/kg MEHP for 24 h functionally disrupted the BTB integrity. A similar treatment of adult rats with MEHP did not disrupt the integrity of the BTB. The observed disruption of the BTB integrity in the MEHP-treated prepubertal rats occurred concomitantly with a decreased expression and mislocalization of both the ZO1 and occludin tight junction-associated proteins, as well as sloughing of spermatocytes and spermatids. At this same time, MEHP treatment induced a transient surge of p44/42 mitogen-activated protein kinase (MAPK) pathway. Interestingly, after a recovery period of 5 weeks, the BTB recovered and was functionally intact. This is the first report to indicate that acute MEHP exposure of prepubertal rats, but not adult rats, disrupts the functional integrity of the BTB and that this effect on the BTB is reversible.
Development and validation of a multimorbidity risk prediction nomogram among Chinese middle-aged and older adults: a retrospective cohort study

Objectives The aim of this study is to establish a self-simple-to-use nomogram to predict the risk of multimorbidity among middle-aged and older adults. Design A retrospective cohort study. Participants We used data from the Chinese Longitudinal Healthy Longevity Survey, including 7735 samples. Main outcome measures Samples’ demographic characteristics, modifiable lifestyles and depression were collected. Cox proportional hazard models and nomogram model were used to estimate the risk factors of multimorbidity. Results A total of 3576 (46.2%) participants have multimorbidity. The result showed that age, female (HR 0.80, 95% CI 0.72 to 0.89), chronic disease (HR 2.59, 95% CI 2.38 to 2.82), sleep time (HR 0.78, 95% CI 0.72 to 0.85), regular physical activity (HR 0.88, 95% CI 0.81 to 0.95), drinking (HR 1.27 95% CI 1.16 to 1.39), smoking (HR 1.40, 95% CI 1.26 to 1.53), body mass index (HR 1.04, 95% CI 1.03 to 1.05) and depression (HR 1.02, 95% CI 1.01 to 1.03) were associated with multimorbidity. The C-index of nomogram models for derivation and validation sets were 0.70 (95% CI 0.69 to 0.71, p=0.006) and 0.71 (95% CI 0.70 to 0.73, p=0.008), respectively. Conclusions We have crafted a user-friendly nomogram model for predicting multimorbidity risk among middle-aged and older adults. This model integrates readily available and routinely assessed risk factors, enabling the early identification of high-risk individuals and offering tailored preventive and intervention strategies.
Public Health Response Measures for COVID-19 in Kazakhstan

Abstract The article describes measures developed to counter the spread of coronavirus infection in the Republic of Kazakhstan. The first cases of coronavirus disease 2019 (COVID-19) in Kazakhstan were detected on March 13, 2020, among people who arrived from Germany. After declaring the state of emergency in the country, the Ministry of Healthcare of the Republic of Kazakhstan began to formulate and implement a comprehensive package of measures aimed at slowing down and stopping the transmission of infection, preventing outbreaks, ensuring optimal care for all patients, especially the seriously ill, minimizing the negative impact of the pandemic on health systems, social services, and economic activities. Developed set of restrictive measures was approved by the Country Office of Word Health Organization (WHO) in Kazakhstan, being later adapted by the European Union (EU) countries and applied in Kyrgyzstan. In addition, article identifies Kazakhstan’s experience in creating epidemiological surveillance systems, studying virus mutations, and the clinical aspects of dealing with it to combat the infection. It also indicates the impact of the epidemic on health-care workers and the development of measures to protect them, strengthening infection prevention, and control in medical organizations.
The 1997-98 drought in Papua New Guinea: failure of policy or triumph of citizenry?

The 1997 drought — natural disaster or national disaster At first glance, the 1997–98 drought in Papua New Guinea was a natural disaster. Between December 1996 and March 1997 the Southern Oscillation Index (SOI), which is the standardized difference in surface air pressure between Darwin and Tahiti and is the oldest and simplest measure of the El Niño-Southern Oscillation (ENSO) phenomenon in the Pacific, fell from +12 to –25. This is the most spectacular fall in the SOI in the post-1950 history of ENSO events. In Papua New Guinea, usually one of the wettest and cloudiest places on the globe, rainfall declined across much of the country. Crops withered and died, local sources of drinking water dried up, and bushfires burned from the coast to the crests of the main mountain ranges, destroying economic trees, sago stands and dwellings. Above 2000 metres altitude, night time temperatures repeatedly fell below zero.
Identification of virulence factors and antibiotic resistance in Salmonella enterica subsp. enterica serovar Javiana (FARPER-220) isolated from broiler chickens

ABSTRACT Genome sequencing of highly virulent Salmonella enterica subsp. enterica serovar Javiana strain FARPER-220 (ST-1674) isolated from broiler chickens in Peru revealed multiple virulence factors, antibiotic resistance genes, and invasion-related subcategories. The results provide insights into the potential importance of this strain in causing infections in various animals.
Talking about falls: a qualitative exploration of spoken communication of patients’ fall risks in hospitals and implications for multifactorial approaches to fall prevention

Background Inpatient falls are the most common safety incident reported by hospitals worldwide. Traditionally, responses have been guided by categorising patients’ levels of fall risk, but multifactorial approaches are now recommended. These target individual, modifiable fall risk factors, requiring clear communication between multidisciplinary team members. Spoken communication is an important channel, but little is known about its form in this context. We aim to address this by exploring spoken communication between hospital staff about fall prevention and how this supports multifactorial fall prevention practice. Methods Data were collected through semistructured qualitative interviews with 50 staff and ethnographic observations of fall prevention practices (251.25 hours) on orthopaedic and older person wards in four English hospitals. Findings were analysed using a framework approach. Findings We observed staff engaging in ‘multifactorial talk’ to address patients’ modifiable risk factors, especially during multidisciplinary meetings which were patient focused rather than risk type focused. Such communication coexisted with ‘categorisation talk’, which focused on patients’ levels of fall risk and allocating nursing supervision to ‘high risk’ patients. Staff negotiated tensions between these different approaches through frequent ‘hybrid talk’, where, as well as categorising risks, they also discussed how to modify them. Conclusion To support hospitals in implementing multifactorial, multidisciplinary fall prevention, we recommend: (1) focusing on patients’ individual risk factors and actions to address them (a ‘why? ’ rather than a ‘who’ approach); (2) where not possible to avoid ‘high risk’ categorisations, employing ‘hybrid’ communication which emphasises actions to modify individual risk factors, as well as risk level; (3) challenging assumptions about generic interventions to identify what individual patients need; and (4) timing meetings to enable staff from different disciplines to participate.
Bosentan Does Not Affect Renal Resistive Index in Scleroderma/Systemic Sclerosis Patients

Introduction: If properly evaluated, chronic kidney disease can be found in up to 50% of patients with systemic sclerosis (SSc). The renal resistive index (RRI) is a marker of intrarenal vascular resistance and can predict SSc-associated vasculopathy. This study aimed to determine the impact of bosentan, a nonselective endothelin-1 receptor antagonist, on RRI and kidney function in SSc patients with recurrent digital ulcers. Methods: Twenty-one patients (age 57 ± 9 years, 19 females) were recruited in a 16-week prospective open-label uncontrolled study. Standardized procedures were used to measure general clinical and laboratory characteristics, systolic, diastolic, and mean arterial pressure (MAP), pulse pressure (PP), diastolic to systolic blood pressure (D/S) ratio, and urinary endothelin-1 levels. The Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation was used to calculate kidney function as an estimated glomerular filtration rate (eGFR). RRI was measured by Doppler ultrasound as the average of three samplings of intrarenal blood flow in different kidney regions of both kidneys. Patients with secondary causes of kidney disease or kidney diseases associated with albuminuria were excluded. Results: Bosentan treatment for 16 weeks did not change RRI (0.731 ± 0.049–0.730 ± 0.054, p = 0.925), but increased urine endothelin-1 to creatinine ratio (0.27 ± 0.15–0.49 ± 0.57 pg/mg, p = 0.032) and reduced MAP (123 ± 10–101 ± 11 mm Hg, p < 0.001), PP (76 ± 11–68 ± 10 mm Hg, p = 0.003), D/S ratio (0.563 ± 0.044–0.538 ± 0.031, p = 0.006), and eGFR (92 ± 20–84 ± 24 mL/min/1.73 m2, p = 0.003). Discussion/Conclusion: In conclusion, in patients with SSc complicated by digital ulcers and normal to mildly diminished kidney function, bosentan had no effect on intrarenal hemodynamics, but reduced blood pressure levels and kidney function.