Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach

Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current “management‐by‐phenotype” approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.
The effectiveness of cognitive behavioural therapy for patients with concurrent hand and psychological disorders

We investigated the effectiveness of cognitive behavioural therapy (CBT) for patients with psychological disorders thought to be influencing recovery from elective and traumatic hand conditions. Demographic data and psychological assessment scores (Primary Health Questionnaire 9 (PHQ9), General Anxiety Disorder Assessment (GAD7), Impact of Event Scale (IES)) were prospectively collected before and after CBT treatment. One hundred and fourteen patients underwent CBT with 81 completing treatment. Full data was available for 78 (68%) patients. Mean age was 43 (range 13–84) and 63% were women. Sixty-one per cent had sustained a traumatic hand injury. PHQ9, GAD7 and IES scores decreased significantly following treatment. Many patients with hand conditions have associated psychological problems that may influence outcome. CBT in a hand unit setting appears to be an effective treatment. Further research with a control group should investigate whether CBT improves psychological health or if this may occur as patients recover from their physical hand disorder regardless of CBT. Level of evidence: IV
Early glycaemic variability increases 28-day mortality and prolongs intensive care unit stay in critically ill patients with pneumonia

Abstract Objective This study aimed to evaluate the effect of early glycaemic variability (GV) on 28-day mortality in critically ill patients with pneumonia. Patients and methods This single-centre retrospective study included patients admitted to the intensive care unit (ICU) due to pneumonia between 2018 and 2019. A total of 282 patients (mean age, 68.6 years) with blood sugar test (BST) results measured more than three times within 48 h after hospitalization and haemoglobin A1c (HbA1c) levels recorded within 2 months were enrolled. Coefficient of variation (CV) was calculated using the BST values. The effects of GV on 28-day mortality and prolonged ICU stay (>14 days) were also assessed. Results The mean age was 60.6 years (male to female ratio, 2.5:1). The 28-day mortality rate was 31.6% (n = 89) and was not different according to the presence of diabetes (DM vs. non-DM) or HbA1c levels (≥7.5 vs. <7.5%; both p > .05). However, the mortality rate was significantly higher in patients with high GV (CV ≥ 36%) than in those with low GV (CV < 36%; 37.5 vs. 25.4%, p = .028). The risk of mortality in patients with high GV was prominent in the subgroups with DM or low HbA1c levels. Among the surviving patients (n = 193), 44 remained in the ICU for more than 14 days. Compared to low GV, high GV was associated with a higher rate of prolonged ICU stay, although not statistically significant (27.8 vs. 18.5%, p = .171). After adjusting for the severity of illness and treatment strategy, CV was an independent risk factor for 28-day mortality (hazard ratio [HR], 1.01, p = .04) and prolonged ICU stay (odds ratio, 1.02; p = .04). Conclusions High GV within 48 h of ICU admission was associated with an increased 28-day mortality risk and prolonged ICU stay. Early phase GV should be carefully managed in critically ill patients with pneumonia. KEY MESSAGES The presence of diabetes or HbA1c alone is insufficient to predict 28-day mortality and prolonged ICU stay in critically ill patients with pneumonia. High glycaemic variability (GV) within 48 h of ICU admission increases 28-day mortality and prolongs ICU stay, which is consistent after adjusting for severity of illness and treatment strategy. Patients with high GV, especially those with DM or low HbA1c levels (<7.5%) should be more carefully treated to reduce mortality.
Comprehensive bioinformatics analysis of ribonucleoside diphosphate reductase subunit M2(RRM2) gene correlates with prognosis and tumor immunotherapy in pan-cancer

Ribonucleotide reductase (RNR) small subunit M2 (RRM2) levels are known to regulate the activity of RNR, a rate-limiting enzyme in the synthesis of deoxyribonucleotide triphosphates (dNTPs) and essential for both DNA replication and repair. The high expression of RRM2 enhances the proliferation of cancer cells, thereby implicating its role as an anti-cancer agent. However, little research has been performed on its role in the prognosis of different types of cancers. This pan-cancer study aimed to evaluate the effect of high expression of RRM2 the tumor prognosis based on clinical information collected from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) databases. We found RRM2 gene was highly expressed in 30 types of cancers. And we performed a pan-cancer analysis of the genetic alteration status and methylation of RRM2. Results indicated that RRM2 existed hypermethylation, associated with m6A, m1A, and m5C related genes. Subsequently, we explored the microRNAs (miRNA), long non-coding RNAs (lncRNA), and the transcription factors responsible for the high expression of RRM2 in cancer cells. Results indicated that has-miR-125b-5p and has-miR-30a-5p regulated the expression of RRM2 along with transcription factors, such as CBFB, E2F1, and FOXM. Besides, we established the competing endogenous RNA (ceRNA) diagram of lncRNAs-miRNAs-circular RNAs (circRNA) involved in the regulation of RRM2 expression. Meanwhile, our study demonstrated that high-RRM2 levels correlated with patients’ worse prognosis survival and immunotherapy effects through the consensus clustering and risk scores analysis. Finally, we found RRM2 regulated the resistance of immune checkpoint inhibitors through the PI3K-AKT single pathways. Collectively, our findings elucidated that high expression of RRM2 correlates with prognosis and tumor immunotherapy in pan-cancer. Moreover, these findings may provide insights for further investigation of the RRM2 gene as a biomarker in predicting immunotherapy’s response and therapeutic target.
Estimation of disease burden and clinical severity of COVID-19 caused by Omicron BA.2 in Shanghai, February-June 2022

ABSTRACT An outbreak of COVID-19 caused by the SARS-CoV-2 Omicron BA.2 sublineage occurred in Shanghai, China from February 26 to June 30, 2022. We use official reported data retrieved from Shanghai municipal Health Commissions to estimate the incidence of infections, severe/critical infections, and deaths to assess the disease burden. By adjusting for right censoring and RT-PCR sensitivity, we provide estimates of clinical severity, including the infection fatality ratio, symptomatic case fatality ratio, and risk of developing severe/critical disease upon infection. The overall infection rate, severe/critical infection rate, and mortality rate were 2.74 (95% CI: 2.73-2.74) per 100 individuals, 6.34 (95% CI: 6.02-6.66) per 100,000 individuals and 2.42 (95% CI: 2.23-2.62) per 100,000 individuals, respectively. The severe/critical infection rate and mortality rate increased with age, noted in individuals aged 80 years or older. The overall fatality ratio and risk of developing severe/critical disease upon infection were 0.09% (95% CI: 0.09-0.10%) and 0.27% (95% CI: 0.24-0.29%), respectively. Having received at least one vaccine dose led to a 10-fold reduction in the risk of death for infected individuals aged 80 years or older. Under the repeated population-based screenings and strict intervention policies implemented in Shanghai, our results found a lower disease burden and mortality of the outbreak compared to other settings and countries, showing the impact of the successful outbreak containment in Shanghai. The estimated low clinical severity of this Omicron BA.2 epidemic in Shanghai highlight the key contribution of vaccination and availability of hospital beds to reduce the risk of death.
Emerging immune checkpoint inhibitors for the treatment of non-small cell lung cancer

ABSTRACT Introduction Over the last decade, immune checkpoint inhibitors (ICIs) have impacted on the standard therapy for patients with non-small cell lung cancer (NSCLC). ICIs first showed efficacy in patients with advanced disease who had progressed after chemotherapy, later reaching the first-line therapy context alone, in combination with chemotherapy, and/or with dual-immunotherapy regimens. Areas covered Most of their benefit is, however, restricted to just 20% of patients due to primary or emergence of acquired resistance. In this review, we will describe the role of new emerging ICIs in the current panorama of NSCLC therapeutic approaches, not only in metastatic disease but also in locally advanced stage disease, with specific focus on those drugs under investigation in Phase 2/3 clinical trials. Expert opinion Several new ICIs are now under investigation to optimize NSCLC patient management; these are usually used in combination with other well-known agents, such as ‘traditional’ ICIs and chemotherapy, or with other newly developed drugs. Identification of better biomarkers will provide personalized treatment approaches to overcome patient-specific immune resistance.
A New Limit on the Distances of Nuclei UHECRs Sources

Recent evidence from the Pierre Auger Observatory suggests a transition, at 5 EeV-10EeV in the composition of Ultra High Energy Cosmic Rays (UHECRs), from protons to heavier nuclei such as iron. I consider here the implications of the heavier composition on the sources of UHECRs. The smaller magnetic rigidity implies that nuclei UHECRs are: (i) More easily accelerated (ii) Local, as they can diffuse only a few Mpc from their sources before disintegrating (iii) Isotropic, because large deflections in the extra galactic and the galactic magnetic fields erase the directional information. Uncertainties in the strength and structure of the the extra galactic magnetic field (EGMF) makes it difficult to estimate the overall effects. However, with typical reasonable parameters of a few nG and a coherence distance of a Mpc the distance a nuclei UHECR above the GZK energy traverses before photodisintegrating is only a few Mpc. In spite of the significantly weaker limits on the luminosity, Cen A is the only currently active potential source of nuclei UHECRs within this distance. The large deflections erases the directional anisotropy expected from a single source. If indeed the composition of above-GZK-UHECRs is iron and if the EGMF is not too small then Cen A is the dominant source of observed nuclei UHECRs above the GZK limit.
The optical counterpart to the Be/X-ray binary SAX J2239.3+6116

The main goal of this work is to perform a detailed study of the optical variability of the Be/X-ray binary SAX J2239.3+6116. We obtained multi-colour BVRI photometry and polarimetry and 4000-7000 A spectroscopy. The optical counterpart to SAX J2239.3+6116 is a V=14.8 B0Ve star located at a distance of ~4.9 kpc. The interstellar reddening in the direction of the source is E(B-V)=1.70 mag. The monitoring of the Halpha line reveals a slow long-term decline of its equivalent width since 2001. The line profile is characterized by a stable double-peak profile with no indication of large-scale distortions. Although somewhat higher than predicted by the models, the optical polarization is consistent with electron scattering in the circumstellar disk. We attribute the long-term decrease in the intensity of the Halpha line to the dissipation of the circumstellar disk of the Be star. The longer variability timescales observed in SAX J2239.3+6116 compared to other Be/X-ray binaries may be explained by the wide orbit of the system.
Health Care Professionals' Perspectives on Implementation, Adoption, and Maintenance of a Community Health Worker–Led Advance Care Planning and Cancer Symptom Screening Intervention: A Qualitative Study

PURPOSE: Advance care planning (ACP) and symptom screening are nationally recommended for all patients with advanced stages of cancer. Yet, routine delivery of such care remains challenging because of multilevel barriers. We hired and trained community health workers (CHWs) to assist with delivery of these services across the United States. The aim of this study was to explore health care professionals' perspectives on barriers and facilitators to these team-based approaches. METHODS: We conducted semistructured interviews with 44 health care professionals in 21 cancer clinics in seven US cities using the Reach, Effectiveness, Adoption, Implementation, and Maintenance framework. We recorded, transcribed, and analyzed interviews using the framework analysis approach. RESULTS: Participants noted barriers and facilitators to implementation, adoption, and maintenance of CHW-led ACP and symptom management approaches. Participants were initially skeptical; however, they noted a positive shift in their views over time because of personal experiences and effectiveness in their clinics. There was significant variation in adoption with some using a prescriptive top-down approach and others a bottom-up approach. Most agreed that the combination of top-down and bottom-up approaches would be most efficient and effective for promoting team-based care. All participants discussed implementation and provided suggestions for maintenance including organizational support, leadership, and CHW retention. CONCLUSION: CHW-led ACP and proactive symptom management interventions are effective and accepted by cancer care professionals at scale. Tailoring on the basis of organization and local contexts is required to ensure successful adoption, implementation, and maintenance of these effective team-based care delivery approaches.
No hydrogen exosphere detected around the super-Earth HD 97658 b

The exoplanet HD 97658 b provides a rare opportunity to probe the atmospheric composition and evolution of moderately irradiated super-Earths. It transits a bright K star at a moderate orbital distance of 0.08 au. Its low density is compatible with a massive steam envelope that could photodissociate at high altitudes and become observable as escaping neutral hydrogen. Our analysis of three transits with HST/STIS at Lyman-α reveals no such signature, suggesting that the thermosphere of HD 97658 b is not hydrodynamically expanding and is subjected to a low escape of neutral hydrogen (<108 g s-1 at 3σ). Using HST/STIS Lyman-α observations and Chandra/ACIS-S and XMM-Newton/EPIC X-ray observations at different epochs, we find that HD 97658 is in fact a weak and soft X-ray source with signs of chromospheric variability in the Lyman-α line core. We determine an average reference for the intrinsic Lyman-α line and X-EUV (XUV) spectrum of the star, and show that HD 97658 b is in mild conditions of irradiation compared to other known evaporating exoplanets with an XUV irradiation about three times lower than the evaporating warm Neptune GJ436 b. This could be the reason why the thermosphere of HD 97658 b is not expanding: the low XUV irradiation prevents an efficient photodissociation of any putative steam envelope. Alternatively, it could be linked to a low hydrogen content or inefficient conversion of the stellar energy input. The HD 97658 system provides clues for understanding the stability of low-mass planet atmospheres in terms of composition, planetary density, and irradiation. Our study of HD 97658 b can be seen as a control experiment of our methodology, confirming that it does not bias detections of atmospheric escape and underlining its strength and reliability. Our results show that stellar activity can be efficiently discriminated from absorption signatures by a transiting exospheric cloud. They also highlight the potential of observing the upper atmosphere of small transiting planets to probe their physical and chemical properties.
Effect of a new phacoemulsification and aspiration handpiece on anterior chamber stability

Active Sentry, a new fluid dynamics mechanism, greatly contributes to anterior chamber stability even when occlusion occurs, suggesting its usefulness in cataract surgery with a low intraocular pressure. Purpose: To evaluate the responsiveness of 3 phacoemulsification and aspiration (PEA) systems and a new handpiece to occlusion break by measuring anterior chamber depth (ACD) and intraocular pressure (IOP). Setting: Zengyo Suzuki Eye Clinic, Kanagawa, Japan. Design: Experimental study. Methods: ACD change during intentional occlusion breaks was observed and evaluated using the slit side view (SSV) method and IOP measurement with the Centurion Vision System (Group 1), Centurion Vision System with Active Sentry (Group 2), Infiniti Vision System (Group 3), and Constellation Vision System (Group 4). 5 eyes were included per group. Occlusion breaks were triggered at IOP of 30 mm Hg, vacuum limits of 550 mm Hg, and aspiration rate of 40 mL/min. ACD change ratio, surge duration, and surge volume were analyzed from videos of SSV and IOP measurement. Results: The smallest ACD change was observed in Group 2 with SSV. ACD change ratios in Groups 1 to 4 were 17.5% ± 3.9%, 7.3% ± 1.2%, 35.7% ± 9.5%, and 74.1 ± 7.7%, respectively. Surge duration and surge volume were calculated only for Groups 1 and 2 and were significantly lower in Group 2 than in Group 1 (0.32 ± 0.03 vs 1.17 ± 0.07 seconds; 18.91 ± 4.70 vs 45.70 ± 0.83 μL). In these 2 groups, ACD change ratio correlated with surge volume. Conclusions: This study evaluated the responsiveness of 3 PEA systems and a new handpiece to occlusion breaks by measuring IOP and ACD. The Active Sentry system was useful for maintaining the ACD even during occlusion breaks.
Mixed Tree Nuts, Cognition, and Gut Microbiota: A 4-Week, Placebo-Controlled, Randomized Crossover Trial in Healthy Nonelderly Adults

ABSTRACT Background Beneficial effects of nut supplementation on cognitive function have previously been demonstrated in young and older adults. Alterations to gut microbiota have also been shown following tree nut consumption. However, no data exists on the effects of nuts on cognition and intestinal microbial communities assessed within the same study. Objectives The study aimed to examine the effects of daily consumption of tree nuts for 4 wk on cognitive function (primary outcome), mood, metabolomics, and gut microbial species (secondary outcomes) in healthy, nonelderly adults. Methods This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30 g/d mixed tree nuts versus placebo on cognition and mood in 79 healthy adults aged 18–49 y. Metabolic responses, gut bacterial community structure, and the potential for these to impact cognition were explored using a multi-omic approach. Bacterial community analysis was conducted in Quantitative Insights Into Microbial Ecology 2 (QIIME2). Results Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M = 92.2% compared with NUTS M = 94.5%; P = 0.019) and speed of response (placebo M = 788 ms compared with NUTS M = 757 ms; P = 0.004) on a picture recognition task. No significant changes to bacterial community α or β diversity were observed when comparing nut consumption to the placebo arm. However, an unclassified Lachnospiraceae amplicon sequence variant (ASV) was significantly enriched in participants when supplemented with nuts (P = 0.015). No correlations were observed between the changes to picture recognition and the changes to the unclassified Lachnospiraceae ASV. There were no significant changes to the urinary metabolome. Conclusions These findings indicate a positive effect of nut on cognition following only 4 wk of consumption in a healthy nonelderly sample, as well as upregulation of a microbial taxa associated with gut health. The effects appear to be independent of one another, but further exploration is required in those experiencing cognitive decline and/or gut dysbiosis.