Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in root metabolites and soil microbial community structures in rhizospheres of sugarcanes under different propagation methods

Abstract Root metabolites and soil microbial community structure in the rhizosphere play critical roles in crop growth. Here, we assessed the efficiency of conventional and tissue culture propagation methods in modulating the soil health and microbiota in the rhizosphere of sugarcane (Saccharum officinarum L.) plants. The seeding canes were obtained using newly planted and two‐year ratooned canes propagated by conventional (CSN and CSR) or tissue culture (TCN and TCR) methods. Changes in soil fertility, root metabolites and soil microbial community structure in the rhizosphere of sugarcane plants obtained using these canes were assessed. The activities of soil β‐glucosidase and aminopeptidase, soil microbial biomass nitrogen, and abundances of soil beneficial microbes, both at phyla and genera levels, were significantly higher in the rhizosphere of sugarcane plants in TCN and TCR treatments than those in that of plants in CSN and CSR treatments. Furthermore, flavonoid and flavonol biosynthesis and alanine, aspartate and glutamate metabolism were significantly upregulated in the roots of TCR and TCN plants compared with those in the roots of CSN and CSR plants. These results suggest that the tissue culture propagation method is a sustainable method for sugarcane cultivation to improve soil fertility and health in sugarcane rhizosphere.
Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss

Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease. Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing. These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.
Optimising HIV care using information obtained from PROMs: protocol for an observational study

Introduction Successful antiviral therapy has transformed HIV infection into a chronic condition, where optimising quality of life (QoL) has become essential for successful lifelong treatment. Patient-reported outcome measures (PROMs) can signal potential physical and mental health problems related to QoL. This study aims to determine whether PROMs in routine clinical care improve quality of care as experienced by people with HIV (PWH). Methods and analysis We report the protocol of a multicentre longitudinal cohort studying PWH at Amsterdam University Medical Centres in the Netherlands. PROMs are offered annually to patients via the patient portal of the electronic health record. Domains include anxiety, depression, fatigue, sleep disturbances, social isolation, physical functioning, stigma, post-traumatic stress disorder, adherence, drug and alcohol use and screening questions for sexual health and issues related to finances, housing and migration status. Our intervention comprises (1) patients’ completion of PROMs, (2) discussion of PROMs scores during annual consultations and (3) documentation of follow-up actions in an individualised care plan, if indicated. The primary endpoint will be patient-experienced quality of care, measured by the Patient Assessment of Chronic Illness Care, Short Form (PACIC-S). Patients will provide measurements at baseline, year 1 and year 2. We will explore change over time in PACIC-S and PROMs scores and examine the sociodemographical and HIV-specific characteristics of subgroups of patients who participated in all or only part of the intervention to ascertain whether benefit has been achieved from our intervention in all subgroups. Ethics and dissemination Patients provide consent for the analysis of data collected as part of routine clinical care to the AIDS Therapy Evaluation in the Netherlands study (ATHENA) cohort through mechanisms described in Boender et al. Additional ethical approval for the analysis of these data is not required under the ATHENA cohort protocol. The results will be presented at national and international academic meetings and submitted to peer-reviewed journals for publication.
Critical Care Management of Patients After Cardiac Arrest: A Scientific Statement From the American Heart Association and Neurocritical Care Society

The critical care management of patients after cardiac arrest is burdened by a lack of high-quality clinical studies and the resultant lack of high-certainty evidence. This results in limited practice guideline recommendations, which may lead to uncertainty and variability in management. Critical care management is crucial in patients after cardiac arrest and affects outcome. Although guidelines address some relevant topics (including temperature control and neurological prognostication of comatose survivors, 2 topics for which there are more robust clinical studies), many important subject areas have limited or nonexistent clinical studies, leading to the absence of guidelines or low-certainty evidence. The American Heart Association Emergency Cardiovascular Care Committee and the Neurocritical Care Society collaborated to address this gap by organizing an expert consensus panel and conference. Twenty-four experienced practitioners (including physicians, nurses, pharmacists, and a respiratory therapist) from multiple medical specialties, levels, institutions, and countries made up the panel. Topics were identified and prioritized by the panel and arranged by organ system to facilitate discussion, debate, and consensus building. Statements related to postarrest management were generated, and 80% agreement was required to approve a statement. Voting was anonymous and web based. Topics addressed include neurological, cardiac, pulmonary, hematological, infectious, gastrointestinal, endocrine, and general critical care management. Areas of uncertainty, areas for which no consensus was reached, and future research directions are also included. Until high-quality studies that inform practice guidelines in these areas are available, the expert panel consensus statements that are provided can advise clinicians on the critical care management of patients after cardiac arrest.
In vitro activity of cefiderocol, a siderophore cephalosporin, against carbapenem-resistant hypervirulent Klebsiella pneumoniae in China

ABSTRACT Cefiderocol is a siderophore cephalosporin that binds ferric iron and utilizes iron transporters to cross the cell membrane. Hypervirulent Klebsiella pneumoniae (hvKp) is known to produce more siderophores; in this case, the uptake of cefiderocol may be decreased. Therefore, the objective of this study was to evaluate the in vitro activity of cefiderocol against hvKp isolates. A total of 320 carbapenem-resistant K. pneumoniae (CRKp) isolates were collected in China between 2014 and 2022, including 171 carbapenem-resistant hvKp (CR-hvKp) and 149 carbapenem-resistant classical K. pneumoniae (CR-cKp). Quantitative detection of siderophores showed that the average siderophore production of CR-hvKp (234.6 mg/L) was significantly higher than that of CR-cKp (68.9 mg/L, P < 0.001). The overall cefiderocol resistance rate of CR-hvKp and CR-cKp was 5.8% (10/171) and 2.7% (4/149), respectively. The non-susceptible rates of both cefiderocol and siderophore production of CR-hvKp isolates were higher than those of CR-cKp in either NDM-1- or KPC-2-producing groups. The MIC90 and MIC50 for CR-hvKp and CR-cKp were 8 mg/L and 2 mg/L and 4 mg/L and 1 mg/L, respectively. The cumulative cefiderocol MIC distribution for CR-hvKp was significantly lower than that of CR-cKp isolates (P = 0.003). KL64 and KL47 consisted of 53.9% (83/154) and 75.7% (53/70) of the ST11 CR-hvKp and CR-cKp, respectively, and the former had significantly higher siderophore production. In summary, cefiderocol might be less effective against CR-hvKp compared with CR-cKp isolates, highlighting the need for caution regarding the prevalence of cefiderocol-resistant K. pneumoniae strains, particularly in CR-hvKp isolates.
What Can Customers See? Exposed Information on E-Cigarette Online Retail Website

Abstract Background The internet is the main channel for electronic nicotine delivery systems sales that the media uses to publicize electronic cigarettes (e-cigarettes). Once e-cigarettes entered the market, they quickly became widely available online and in retail stores in many countries and regions around the world. This systematic review aims to explore the online marketing strategies for e-cigarette retail websites including the design of e-cigarette retail websites and how the information of retail websites was exposed to the public. Method Studies were searched in five databases: Cumulative Index to Nursing and Allied Health Literature, EMBASE, Web of Science, Communication & Mass Media Complete, and PubMed. Included studies were published between 2007 and 2019. Results Eight studies were included in this review. Topics covered included smoking cessation claims, nicotine content claims, health or harmful substance exposure claims, age restriction/verification, membership and discounts, and media and celebrity effect. Most of the claims included information about the benefits of e-cigarettes, such as helping to quit smoking, being more environmentally friendly than traditional paper cigarettes, and not containing nicotine. Common marketing techniques included celebrity endorsements, showing discounts or membership offers, or getting a link to buy from the media. Conclusions The marketing of e-cigarettes is complex, and the authenticity of the information presented on the websites needs to be thoroughly understood. Such information will undoubtedly increase the interest and desire of potential buyers for e-cigarettes. Therefore, it is critical to establish necessary regulations regarding e-cigarette product information.
Meta‐Analysis Global Group in Chronic Heart Failure score for the prediction of mortality in valvular heart disease

Abstract Aims Valvular heart disease (VHD) is one of the leading causes of heart failure. Clinically significant VHD can induce different patterns of cardiac remodelling, and risk stratification is challenging in patients with various degrees of cardiac dysfunction. The study aimed to investigate the prognostic implications of Meta‐Analysis Global Group in Chronic Heart Failure (MAGGIC) score in patients with VHD. Methods and results This study used data from the China Valvular Heart Disease (China‐VHD) registry, which was a multicentre, prospective, observational cohort study for patients with significant (at least moderate) VHD. In total, 10 446 patients with moderate or greater VHD from the China‐VHD study were included in the present analysis. The primary outcome of interest was all‐cause mortality within 2 years. Among 10 446 patients with VHD, the mean age was 61.98 ± 13.47 years, and 5819 (55.7%) were male. During 2 years of follow‐up, 895 (8.6%) patients died. The MAGGIC score was monotonically and independently associated with mortality in both total cohort [adjusted hazard ratio: 1.095, 95% confidence interval (CI): 1.084–1.107, P < 0.001] and most types of VHD (aortic regurgitation, mitral stenosis, mitral regurgitation, tricuspid regurgitation, mixed aortic stenosis and aortic regurgitation, and multiple VHD). The score was also an independent prognostic factor in patients with or without symptoms or preserved left ventricular ejection fraction (LVEF) and exhibited both satisfactory discrimination and calibration properties in predicting mortality. The prognostic value of MAGGIC score was robust in most quartiles of N‐terminal pro‐brain natriuretic peptide level, with no significant interaction observed (P interaction = 0.498). Compared with the EuroSCORE II, the MAGGIC score achieved significantly better predictive performance in overall population [C index: 0.769 vs. 0.727; net reclassification improvement index (95% CI): 0.354 (0.313–0.396), P < 0.001; integrated discrimination improvement index (95% CI): 0.069 (0.052–0.085), P < 0.001] and in subgroups of patients divided by therapeutic strategy, LVEF, symptomatic status, stage of VHD, and aetiology of VHD. Conclusions The MAGGIC score is a reliable prognostic factor across the range of cardiac dysfunction in VHD and may assist in risk stratification and guide clinical decision‐making.
Draft genomes of two rhizosphere associated bacterial isolates from Tims Branch, a heavy metal contaminated wetland

ABSTRACT Two bacterial isolates were recovered from wetland sediments from Tims Branch, a heavy metal contaminated wetland located at the Savannah River Site. Draft genomes of the two recovered isolates, Rhodoblastus strain 17X3 and Comamonas strain 17RB, were generated from Illumina MiSeq sequencing data.
New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data

International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity – so‐called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome‐wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern‐most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long‐term viability of these populations. Inbreeding (FROH) spans 10%–30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.
Situational features of smartphone betting are linked to sports betting harm: An ecological momentary assessment study

Abstract Background and aims Smartphones extend the situational characteristics of sports betting beyond those available with land-based and computer platforms. This study examined 1) the role of situational features and betting platforms in harmful betting behaviours and short-term betting harm, and 2) whether people with more gambling problems have preferred situational features, engage more in harmful betting behaviours, and experience more severe short-term betting harm. Methods An ecological momentary assessment analysed 1,378 betting sessions on sports, esports or daily fantasy sports, reported by 267 respondents (18–29 years; 50.9% male) over 10 weeks. Results Factor analysis revealed five situational features of betting sessions: 1) quick, easy access from home, 2) ability to bet anywhere anytime, 3) privacy while betting, 4) greater access to promotions and betting options, and 5) ability to use electronic financial transactions. Regression models underpinned the analyses. Greater short-term betting harm was significantly associated with the ability to bet anywhere anytime, privacy when betting, and greater access to promotions and betting options. Betting sessions when these features were prioritised were more likely to involve impulsive betting, use of betting inducements, and betting with more operators. Respondents with more gambling problems were more likely to prioritise privacy and the ability to bet anywhere anytime; and to bet on in-game events, use promotional inducements, bet with more operators, and report greater betting harm. Discussion and conclusions Certain situational features of sports betting are empirically associated with engagement and subsequent harm. Only smartphone betting combines all three features associated with betting harm.
Perception of illusory clusters: the role of native timing

Abstract We explore the influence of native timing patterns on nonnative speech perception, by asking whether a nonnative CVCV sequence can be perceived as CCV when the temporal organization of nonnative CVCV is similar to native CCV. To explore this question, Georgian listeners are tested on a CCa-CVCá discrimination in French. Georgian has a rich word-onset cluster inventory, with component consonants loosely timed. The loose timing often, though not always, results in a schwa-like CC transition. French, the stimulus language, exhibits tighter timing in biconsonantal clusters, no vocalic transitions, and a reduced non-prominent first vowel in CVCá sequences. We hypothesize that the cross-language difference in inter-consonantal timing can facilitate the perception of an illusory cluster when Georgian listeners hear French CVCá. The findings reveal such perceptual confusion, particularly in the CCa-CøCá contrast in which the nonnative /ø/ is phonetically similar to the CC transition in Georgian, both in terms of temporal organizations and tongue shape. This confirms the possibility of illusory clusters, which is consistent with the interpretation that Georgian listeners utilize their knowledge of how word-onset CC clusters are temporally implemented in their native language when responding to the task. We propose that the timing pattern may constitute language-specific knowledge and that it can influence the perceptual assimilation patterns in nonnative speech perception.
Machine learning facilitates the prediction of long-term mortality in patients with tricuspid regurgitation

Objective Tricuspid regurgitation (TR) is a prevalent valve disease associated with significant morbidity and mortality. We aimed to apply machine learning (ML) to assess risk stratification in patients with ≥moderate TR. Methods Patients with ≥moderate TR on echocardiogram between January 2005 and December 2016 were retrospectively included. We used 70% of data to train ML-based survival models including 27 clinical and echocardiographic features to predict mortality over a 3-year period on an independent test set (30%). To account for differences in baseline comorbidities, prediction was performed in groups stratified by increasing Charlson Comorbidity Index (CCI). Permutation feature importance was calculated using the best-performing model separately in these groups. Results Of 13 312 patients, mean age 72 ± 13 years and 7406 (55%) women, 7409 (56%) had moderate, 2646 (20%) had moderate–severe and 3257 (24%) had severe TR. The overall performance for 1-year mortality by 3 ML models was good, c-statistic 0.74–0.75. Interestingly, performance varied between CCI groups, (c-statistic = 0.774 in lowest CCI group and 0.661 in highest CCI group). The performance decreased over 3-year follow-up (average c-index 0.78). Furthermore, the top 10 features contributing to these predictions varied slightly with the CCI group, the top features included heart rate, right ventricular systolic pressure, blood pressure, diuretic use and age. Conclusions Machine learning of common clinical and echocardiographic features can evaluate mortality risk in patients with TR. Further refinement of models and validation in prospective studies are needed before incorporation into the clinical practice.
Treating posttraumatic stress disorder and alcohol use disorder comorbidity: Current pharmacological therapies and the future of MDMA-integrated psychotherapy

Posttraumatic stress disorder (PTSD) and alcohol use disorder (AUD) frequently co-occur in patients who have experienced trauma. This comorbidity leads to a vicious cycle where PTSD symptoms beget heavy drinking and vice versa. There are no FDA-approved medications to treat PTSD-AUD; therefore, individuals suffering from this comorbidity are treated with medication approved to treat the disorders separately or with off-label pharmacological interventions. However, these medications are limited in their efficacy for treating PTSD-AUD comorbidity. Emerging research on the nonclassical psychedelic drug 3,4-methylenedioxymethamphetamine (MDMA) suggests that it may be an effective drug used in conjunction with psychotherapy. The following reviews the current research for clinical pharmacotherapies, as well as MDMA-integrative psychotherapy as they pertain to PTSD and AUD in isolation and co-occurrence. Future directions for the role of psychedelic-integrative therapy for the treatment of this comorbidity are discussed.
Large Language Models Suffer From Their Own Output: An Analysis of the Self-Consuming Training Loop

Large language models (LLM) have become state of the art in many benchmarks and conversational LLM applications like ChatGPT are now widely used by the public. Those LLMs can be used to generate large amounts of content which is posted on the internet to various platforms. As LLMs are trained on datasets usually collected from the internet, this LLM-generated content might be used to train the next generation of LLMs. Therefore, a self-consuming training loop emerges in which new LLM generations are trained on the output from the previous generations. We empirically study this self-consuming training loop using a novel dataset to analytically and accurately measure quality and diversity of generated outputs. We find that this self-consuming training loop initially improves both quality and diversity. However, after a few generations the output inevitably degenerates in diversity. We find that the rate of degeneration depends on the proportion of real and generated data.