Miracle-dz/UniFAR-FTUs huggingface dataset:
Attribution analysis for runoff decline in Yellow River Basin during past fifty years based on Budyko hypothesis

Here 38 sub-catchments in Yellow River Basin have been selected to explore the driving factors for runoff decline in this region. Climate elasticity and landscape elasticity which indicate the sensitivity of runoff to climate and landscape change are calculated based on the catchment water-energy balance equation. Furthermore, we quantify the effect of climate and landscape change on mean annual water yield. Results show that the distribution of climate elasticity is consistent with landscape elasticity and regions with highest sensitivity is located in the Loess Plateau. The annual runoff had statistically negative trends in most study sub-catchments. Landscape change is the dominant forcing factor for runoff decline in most study sub-catchments, specially in the Loess Plateau. By the analysis of NDVI (Normalized Difference Vegetation Index) during recent thirty years, we find that the improvement of vegetation is the dominant changes in landscape. This research indicates that it is a effective and promising application approach to quantify the effect of climate and landscape change on annual water yield based on the catchment water-energy balance equation.
Characterization of the immunosuppressive environment induced by larval Echinococcus granulosus during chronic experimental infection

ABSTRACT The larval stage of Echinococcus granulosus causes the chronic infection known as cystic echinococcosis, deploying strong inhibitory mechanisms on host immune responses. Using experimental intraperitoneal infection in C57BL/6 mice, we carried out an in-depth analysis of the local changes in macrophage populations associated with chronic infection. In addition, we analyzed T cells and relevant soluble mediators. Infected animals showed an increase in local cell numbers, mostly accounted for by eosinophils, T cells, and macrophages. Within macrophage populations, the largest increases in cell numbers corresponded to resident large peritoneal macrophages (LPM). Monocyte recruitment appeared to be active, as judged by the increased number of monocytes and cells in the process of differentiation towards LPM, including small (SPM) and converting peritoneal macrophages (CPM). In contrast, we found no evidence of macrophage proliferation. Infection induced the expression of M2 markers in SPM, CPM, and LPM. It also enhanced the expression of the co-inhibitor PD-L1 in LPM, SPM, and CPM and induced the co-inhibitor PD-L2 in SPM and CPM. Therefore, local macrophages acquire M2-like phenotypes with probable suppressive capacities. Regarding T cells, infection induced an increase in the percentage of CD4+ cells that are PD-1+, which represent a potential target of suppression by PD-L1+/PD-L2+ macrophages. In possible agreement, CD4+ T cells from infected animals showed blunted proliferative responses to in vitro stimulation with anti-CD3. Further evidence of immune suppression in the parasite vicinity arose from the observation of an expansion in FoxP3+ CD4+ regulatory T cells and increases in the local concentrations of the anti-inflammatory cytokines TGF-β and IL-1Ra.
Antidiabetic properties of S-allyl cysteine, a garlic component on streptozotocin-induced diabetes in rats

Research and Development Centre, Bharathiyar University, Coimbatore, Tamil Nadu, India Department of Biochemistry, Centre for Biological Science, K.S. R. College of Arts and Science, Thokkavadi, Tiruchengode, Tamil Nadu, India Department of Biotechnology, K.S. R. College of Technology, Thokkavadi, Tiruchengode, Tamil Nadu, India Department of Biochemistry, School of Biotechnology, SASTRA University, Thanjavore, Tamil Nadu, India
Factors Associated With Intraocular Inflammation in Neovascular Age-Related Macular Degeneration Patients Treated With Brolucizumab

Purpose To identify factors associated with intraocular inflammation (IOI) in patients with neovascular age-related macular degeneration (nAMD) treated with brolucizumab. Methods In this prospective observational study, we collected aqueous humor samples from 96 eyes of 96 patients receiving treatment with brolucizumab; IOI subsequently developed in 19 eyes of 19 patients. To identify cytokines upregulated in eyes with subsequent development of IOI, we compared the aqueous humor cytokine levels between the IOI and non-IOI groups. We also collected plasma from 20 patients who developed IOI and 20 age- and sex-matched controls to identify differences in plasma biomarkers and the subfraction of CD4+ cells. Using stepwise variable selection and multivariate binary regression analysis, we developed an algorithm that accurately assessed the likelihood of IOI occurrence. Results The IOI group showed elevated aqueous humor levels of P-selectin (584 vs. 324 pg/mL, P = 0.013), TNF-α (0.89 vs. 0.60 pg/mL, P = 0.018), and IL-1α (2.0 vs. 1.4 pg/mL, P = 0.035) compared with the non-IOI group. Serum MMP-9 concentrations were higher in the IOI group than the non-IOI group (18,310 vs. 13,450 pg/mL, P = 0.029). Furthermore, the percentage of Th2 cells was significantly decreased in the IOI compared with the non-IOI group (3.1% vs. 4.2%, P = 0.013). The receiver operating characteristic curves for the optimal models showed an area under the curve ranging from 0.71 to 0.89, indicating good performance. Conclusions The combination of elevated concentrations of multiple aqueous humor cytokines and of serum MMP-9 and a lower number of plasma Th2 cells is associated with brolucizumab-related IOI in patients with nAMD.
CRESCIMENTO INICIAL E TOLERÂNCIA DE CULTIVARES DE PEPINO SOB ESTRESSE SALINO

O pepino e uma hortalica de grande importância economica e alimentar, devido a sua apreciacao como componente de saladas. No entanto, o seu cultivo no semiarido apresenta risco, devido aos problemas de salinidade, sendo necessaria a identificacao de cultivares tolerantes, que se desenvolvam melhor em ambientes com problemas de salinidade. Com isso, Objetivou-se avaliar a emergencia, o crescimento e a tolerância de cultivares de pepino ao estresse salino. O experimento foi desenvolvido em ambiente protegido (casa de vegetacao) localizado no municipio de Pombal, Paraiba, PB. O estudo foi arranjado em esquema fatorial 2 x 5 um delineamento experimental inteiramente casualizado, constituido de duas cultivares de pepino (C1 – Aopdai e C2- Wisconsin SEM-58) e cinco niveis de salinidade da agua de irrigacao (0,6 (controle); 1,2; 1,8, 2,4 e 3,0 dS m -1 ) com quatro repeticoes e dez plantas por parcela. As plantas de pepino foram conduzidas por 20 dias, nos quais se avaliou a emergencias de plântulas, o crescimento inicial, o acumulo de biomassa e o indice de tolerâncias das cultivares com relacao ao rendimento de biomassa. A salinidade da agua de irrigacao afeta a emergencia, o crescimento e o acumulo de massa seca das plantas de pepino. A cultivar Aopdai apresenta os maiores indices de emergencia, o crescimento e o acumulo de massa seca em relacao a cultivar Wisconsin SEM-58. A cultura do pepino pode ser irrigada com agua salina de ate 1,8 dS m -1 durante a sua fase de crescimento inicial.
Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host

Abstract In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However, transmission analysis cannot rely solely on a phylogeny of the genomes but must account for the within-host evolution of the pathogen, which blurs the relationship between phylogenetic and transmission trees. When only a single genome is sampled for each host, the uncertainty about who infected whom can be quite high. Consequently, transmission analysis based on multiple genomes of the same pathogen per host has a clear potential for delivering more precise results, even though it is more laborious to achieve. Here, we present a new methodology that can use any number of genomes sampled from a set of individuals to reconstruct their transmission network. Furthermore, we remove the need for the assumption of a complete transmission bottleneck. We use simulated data to show that our method becomes more accurate as more genomes per host are provided, and that it can infer key infectious disease parameters such as the size of the transmission bottleneck, within-host growth rate, basic reproduction number, and sampling fraction. We demonstrate the usefulness of our method in applications to real datasets from an outbreak of Pseudomonas aeruginosa amongst cystic fibrosis patients and a nosocomial outbreak of Klebsiella pneumoniae.
Lower limb muscle MRI fat fraction is a responsive outcome measure in CMT X1, 1B and 2A

Abstract Objective With potential therapies for many forms of Charcot‐Marie‐Tooth disease (CMT), responsive outcome measures are urgently needed for clinical trials. Quantitative lower limb MRI demonstrated progressive calf intramuscular fat accumulation in the commonest form, CMT1A with large responsiveness. In this study, we evaluated the responsiveness and validity in the three other common forms, due to variants in GJB1 (CMTX1), MPZ (CMT1B) and MFN2 (CMT2A). Methods 22 CMTX1, 21 CMT1B and 21 CMT2A patients and matched controls were assessed at a 1‐year interval. Intramuscular fat fraction (FF) was evaluated using three‐point Dixon MRI at thigh and calf level along with clinical measures including CMT examination score, clinical strength assessment, CMT‐HI and plasma neurofilament light chain. Results All patient groups had elevated muscle fat fraction at thigh and calf levels, with highest thigh FF and atrophy in CMT2A. There was moderate correlation between calf muscle FF and clinical measures (CMTESv2 rho = 0.405; p = 0.001, ankle MRC strength rho = −0.481; p < 0.001). Significant annualised progression in calf muscle FF was seen in all patient groups (CMTX1 2.0 ± 2.0%, p < 0.001, CMT1B 1.6 ± 2.1% p = 0.004 and CMT2A 1.6 ± 2.1% p = 0.002). Greatest increase was seen in patients with 10–70% FF at baseline (calf 2.7 ± 2.3%, p < 0.0001 and thigh 1.7 ± 2.1%, p = 0.01). Interpretation Our results confirm that calf muscle FF is highly responsive over 12 months in three additional common forms of CMT which together with CMT1A account for 90% of genetically confirmed cases. Calf muscle MRI FF should be a valuable outcome measure in upcoming CMT clinical trials.
How well does vaccine literacy predict intention to vaccinate and vaccination status? A systematic review and meta-analysis

ABSTRACT This review quantified the association of vaccine literacy (VL) and vaccination intention and status. PubMed, Scopus, and Web of Science were searched. Any study, published until December 2022, that investigated the associations of interest were eligible. For each outcome, articles were grouped according to the vaccine administrated and results were narratively synthesized. Inverse-variance random-effect models were used to compare standardized mean values in VL domain(s) between the two groups: individuals willing vs. unwilling to get vaccinated, and individuals vaccinated vs. unvaccinated. This review of 18 studies shows that VL strongly predicts the vaccination intention while its association with vaccination status is attenuated and barely significant, suggesting that other factors influence the actual vaccination uptake. However, given the scarce evidence available, the heterogeneity in the methods applied and some limitations of the studies included, further research should be conducted to confirm the role of VL in the vaccination decision-making process.
Association of Muscle Mass Loss with Diabetes Development in Liver Transplantation Recipients

Background Post-transplant diabetes mellitus (PTDM) is one of the most significant complications after transplantation. Patients with end-stage liver diseases requiring transplantation are prone to sarcopenia, but the association between sarcopenia and PTDM remains to be elucidated. We aimed to investigate the effect of postoperative muscle mass loss on PTDM development. Methods A total of 500 patients who underwent liver transplantation at a tertiary care hospital between 2005 and 2020 were included. Skeletal muscle area at the level of the L3–L5 vertebrae was measured using computed tomography scans performed before and 1 year after the transplantation. The associations between the change in the muscle area after the transplantation and the incidence of PTDM was investigated using a Cox proportional hazard model. Results During the follow-up period (median, 4.9 years), PTDM occurred in 165 patients (33%). The muscle mass loss was greater in patients who developed PTDM than in those without PTDM. Muscle depletion significantly increased risk of developing PTDM after adjustment for other confounding factors (hazard ratio, 1.50; 95% confidence interval, 1.23 to 1.84; P=0.001). Of the 357 subjects who had muscle mass loss, 124 (34.7%) developed PTDM, whereas of the 143 patients in the muscle mass maintenance group, 41 (28.7%) developed PTDM. The cumulative incidence of PTDM was significantly higher in patients with muscle loss than in patients without muscle loss (P=0.034). Conclusion Muscle depletion after liver transplantation is associated with increased risk of PTDM development.
A giant stem-group chaetognath

Chaetognaths, with their characteristic grasping spines, are the oldest known pelagic predators, found in the lowest Cambrian (Terreneuvian). Here, we describe a large stem chaetognath, Timorebestia koprii gen. et sp. nov., from the lower Cambrian Sirius Passet Lagerstätte, which exhibits lateral and caudal fins, a distinct head region with long antennae and a jaw apparatus similar to Amiskwia sagittiformis. Amiskwia has previously been interpreted as a total-group chaetognathiferan, as either a stem-chaetognath or gnathostomulid. We show that T. koprii shares a ventral ganglion with chaetognaths to the exclusion of other animal groups, firmly placing these fossils on the chaetognath stem. The large size (up to 30 cm) and gut contents in T. koprii suggest that early chaetognaths occupied a higher trophic position in pelagic food chains than today.
International Systematic Review of Utility Values Associated with Cardiovascular Disease and Reflections on Selecting Evidence for a UK Decision-Analytic Model

Purpose Evaluating interventions for cardiovascular disease (CVD) requires estimates of its effect on utility. We aimed to 1) systematically review utility estimates for CVDs published since 2013 and 2) critically appraise UK-relevant estimates and calculate corresponding baseline utility multipliers. Methods We searched MEDLINE and Embase (April 22, 2021) using CVD and utility terms. We screened results for primary studies reporting utility distributions for people with experience of heart failure, myocardial infarction, peripheral arterial disease, stable angina, stroke, transient ischemic attack, or unstable angina. We extracted characteristics from studies included. For UK estimates based on the EuroQoL 5-dimension (EQ-5D) measure, we assessed risk of bias and applicability to a decision-analytic model, pooled arms/time points as appropriate, and estimated baseline utility multipliers using predicted utility for age- and sex- matched populations without CVD. We sought utility sources from directly applicable studies with low risk of bias, prioritizing plausibility of severity ordering in our base-case model and highest population ascertainment in a sensitivity analysis. Results Most of the 403 studies identified used EQ-5D (n = 217) and most assessed Organisation for Economic Co-operation and Development populations (n = 262), although measures and countries varied widely. UK studies using EQ-5D (n = 29) produced very heterogeneous baseline utility multipliers for each type of CVD, precluding meta-analysis and implying different possible severity orderings. We could find sources that provided a plausible ordering of utilities while adequately representing health states. Conclusions We cataloged international CVD utility estimates and calculated UK-relevant baseline utility multipliers. Modelers should consider unreported sources of heterogeneity, such as population differences, when selecting utility evidence from reviews. Highlights Published systematic reviews have summarized estimates of utility associated with cardiovascular disease published up to 2013. We 1) reviewed utility estimates for 7 types of cardiovascular disease published since 2013, 2) critically appraised UK-relevant studies, and 3) estimated the effect of each cardiovascular disease on baseline utility. Our review 1) recommends a consistent and reliable set of baseline utility multipliers for 7 types of cardiovascular disease and 2) provides systematically identified reference information for researchers seeking utility evidence for their own context.
Preliminary evidence for the importance of therapeutic alliance in MDMA-assisted psychotherapy for posttraumatic stress disorder

ABSTRACT Background: MDMA-assisted psychotherapy (MDMA-AP) is a combined psychotherapeutic and pharmacologic intervention that shows promise in the treatment of posttraumatic stress disorder (PTSD). Although therapeutic alliance has been established as a key predictor across psychotherapies and is emphasised within MDMA-AP treatment manuals, research has not yet examined the relationship between therapeutic alliance and MDMA-AP treatment outcomes. Objective: Examine whether therapeutic alliance predicts changes in PTSD symptoms following MDMA-AP. Method: Twenty-three individuals with chronic PTSD participated in a MDMA-AP clinical trial that included a randomised (MDMA vs. placebo) and open-label phase. The present analyses focused on participants who were administered MDMA over the course of the randomised and open-label phases (n = 22). Therapeutic alliance was assessed using the Working Alliance Inventory at sessions baseline (pre-session 3) and sessions 4 and 9. PTSD symptoms were assessed using the Clinician Administered PTSD Scale and the Impact of Events Scale-Revised. Results: Controlling for baseline clinician-assessed PTSD severity, therapeutic alliance at sessions 4 and 9 (but not baseline) significantly predicted post-MDMA-AP clinician-assessed PTSD severity. Controlling for baseline self-reported PTSD severity, therapeutic alliance at baseline (although this did not survive correction for multiple comparisons) and sessions 4 and 9 predicted post-MDMA-AP self-reported PTSD severity. Conclusions: The present results provide the first preliminary evidence for the relationship between the therapeutic alliance and treatment outcomes within MDMA-AP for PTSD. These findings highlight the important role of psychotherapy, and common psychotherapeutic factors, within MDMA-AP. Replication in studies with larger and more diverse clinical samples remain necessary. Trial registration: ClinicalTrials.gov identifier: NCT00090064.
Utility of Cerebrospinal Fluid Protein Levels as a Potential Predictive Biomarker of Disease Severity in HIV-Associated Cryptococcal Meningitis

Background. Cerebrospinal fluid (CSF) protein levels exhibit high variability in HIV-associated cryptococcal meningitis from being normal to markedly elevated. However, the clinical implications of CSF protein levels in cryptococcal meningitis remain unclear. Methods. We analysed data from 890 adults with HIV-associated cryptococcal meningitis randomized into two clinical trials in Uganda between 2015 and 2021. CSF protein was grouped into ≥100 mg/dL (n=249) and <100 mg/dL (n=641). We described baseline clinical variables and mortality by CSF protein levels. Results. Approximately one-third of individuals had a baseline CSF protein ≥100 mg/dL. Those with CSF protein ≥100 mg/dL were more likely to present with Glasgow coma scale scores <15 (P<0.01), self-reported seizures at baseline (P=0.02), higher CD4 T-cells (p<0.001), and higher CSF white cells (p<0.001). Moreover, those with a baseline CSF protein ≥100 mg/dL also had a lower baseline CSF fungal burden (p<0.001) and a higher percentage of sterile CSF cultures at day 14 (p=0.02). Individuals with CSF protein ≥100 mg/dL demonstrated a more pronounced immune response consisting of upregulation of immune effector molecules pro-inflammatory cytokines, type-1 T-helper cell cytokines, type-3 chemokines, and immune-exhaustion marker (p<0.05). 18-week mortality risk in individuals with a CSF protein <100 mg/dL was 34% higher, (unadjusted Hazard Ratio 1.34; 95% CI, 1.05 to 1.70; p=0.02) than those with ≥100 mg/dL. Conclusion. In cryptococcal meningitis, individuals with CSF protein ≥100 mg/dL more frequently presented with seizures, altered mental status, immune activation, and favourable fungal outcomes. Baseline CSF protein levels may serve as a surrogate marker of immune activation and prognosis.
Stakeholders’ perspectives on clinical trial acceptability and approach to consent within a limited timeframe: a mixed methods study

Objectives The Bronchiolitis Endotracheal Surfactant Study (BESS) is a randomised controlled trial to determine the efficacy of endo-tracheal surfactant therapy for critically ill infants with bronchiolitis. To explore acceptability of BESS, including approach to consent within a limited time frame, we explored parent and staff experiences of trial involvement in the first two bronchiolitis seasons to inform subsequent trial conduct. Design A mixed-method embedded study involving a site staff survey, questionnaires and interviews with parents approached about BESS. Setting Fourteen UK paediatric intensive care units. Participants Of the 179 parents of children approached to take part in BESS, 75 parents (of 69 children) took part in the embedded study. Of these, 55/69 (78%) completed a questionnaire, and 15/69 (21%) were interviewed. Thirty-eight staff completed a questionnaire. Results Parents and staff found the trial acceptable. All constructs of the Adapted Theoretical Framework of Acceptability were met. Parents viewed surfactant as being low risk and hoped their child’s participation would help others in the future. Although parents supported research without prior consent in studies of time critical interventions, they believed there was sufficient time to consider this trial. Parents recommended that prospective informed consent should continue to be sought for BESS. Many felt that the time between the consent process and intervention being administered took too long and should be ‘streamlined’ to avoid delays in administration of trial interventions. Staff described how the training and trial processes worked well, yet patients were missed due to lack of staff to deliver the intervention, particularly at weekends. Conclusion Parents and staff supported BESS trial and highlighted aspects of the protocol, which should be refined, including a streamlined informed consent process. Findings will be useful to inform proportionate approaches to consent in future paediatric trials where there is a short timeframe for consent discussions. Trial registration number ISRCTN11746266.