Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Explainable-AI to Find Geospatial Environmental and Sociodemographic Predictors of Suicide Attempts

Despite a global decrease in suicide rates in recent years, death by suicide has increased in the United States. It is therefore imperative to identify the risk factors associated with suicide attempts in order to combat this growing epidemic. In this study, we use an explainable artificial intelligence (X-AI) method, iterative Random Forest (iRF), to predict suicide attempts using data from the Million Veteran Program (MVP). Our predictive model incorporates multiple environmental variables (e.g., elevation, light wavelength absorbance, temperature, humidity, etc) at ZIP code-level geospatial resolution. We additionally consider demographic variables from the American Community Survey as well as the number of firearms and alcohol vendors per 10,000 people in order to assess the contributions of proximal environment, access to means, and restraint decreasement to suicide attempts. Our results show that geographic areas with higher concentrations of married males living with spouses are predictive of lower rates of suicide attempts, whereas geographic areas where males are more likely to live alone and to rent housing are predictive of higher rates of suicide attempts. We also identified climatic features that were associated with suicide attempt risk by age group. Additionally, we observed that firearms and alcohol vendors were associated with increased risk for suicide attempts irrespective of the age group examined, but that their effects were small in comparison to the top features. Taken together, our findings highlight the importance of social determinants and contextual factors in understanding suicide risk among veterans.
Identification of supraoptimal temperatures in juvenile blueback herring (Alosa aestivalis) using survival, growth rate and scaled energy reserves

We measured anadromous juvenile blueback herring survival, growth rate and energy reserves across temperatures 21–33°C when fed a constant ration. Growth was more sensitive to warm temperatures than energy reserves. Survival remained high, yet smaller size at high temperatures may detrimentally delay emigration, increase predation and lower physiological resilience.
Improved overall survival in dual compared to single immune checkpoint inhibitors in BRAF V600-negative advanced melanoma

Aim: To evaluate the efficacy of dual versus single immune checkpoint inhibitors (ICI) in BRAF wild-type advanced melanoma patients. Materials & methods: A retrospective study of all advanced BRAF wild-type melanoma patients on palliative-intent ICI between 2015 and 2020 (n = 67). Results: Dual ICI had better overall survival (OS) when compared with single ICI in BRAF wild-type patients (hazard ratio: 0.204; 95% CI: 0.064–0.649; p = 0.007), but lost its statistical significance (median OSl not reached vs 20.9 months; p = 0.213; adjusted hazard ratio: 0.475; 95% CI: 0.164–1.380; p = 0.171) when only including patients treated after 2018 when dual ICI was funded in our province. Dual ICI were significantly associated with more frequent (p = 0.005) and severe (p = 0.026) immune-related adverse events, and required more immune-related adverse events-indicated systemic corticosteroid use (p < 0.001) compared with single ICI. Conclusion: While limited by small sample size and retrospective nature, dual ICI may have non statistically significant trend toward better OS efficacy when compared with single ICI in BRAF V600 wild-type advanced melanoma patients.
Seroprevalence of anti-SARS-CoV-2 antibodies in Thai adults during the first three epidemic waves

This study determined the presence of anti-SARS-CoV-2 antibodies in 4964 individuals, comprising 300 coronavirus disease-19 (COVID-19) prepandemic serum samples, 142 COVID-19 patients, 2113 individuals at risk due to their occupations, 1856 individuals at risk due to sharing workplaces or communities with COVID-19 patients, and 553 Thai citizens returning after spending extended periods of time in countries with a high disease prevalence. We recruited participants between May 2020 and May 2021, which spanned the first two epidemic waves and part of the third wave of the COVID-19 outbreaks in Thailand. Their sera were tested in a microneutralization and a chemiluminescence immunoassay for IgG against the N protein. Furthermore, we performed an immunofluorescence assay to resolve discordant results between the two assays. None of the prepandemic sera contained anti-SARS-CoV-2 antibodies, while antibodies developed in 88% (15 of 17) of the COVID-19 patients at 8–14 days and in 94–100% of the patients between 15 and 60 days after disease onset. Neutralizing antibodies persisted for at least 8 months, longer than IgG antibodies. Of the 2113 individuals at risk due to their occupation, none of the health providers, airport officers, or public transport drivers were seropositive, while antibodies were present in 0.44% of entertainment workers. Among the 1856 individuals at risk due to sharing workplaces or communities with COVID-19 patients, seropositivity was present in 1.9, 1.5, and 7.5% of the Bangkok residents during the three epidemic waves, respectively, and in 1.3% of the Chiang Mai people during the first epidemic wave. The antibody prevalence varied between 6.5 and 47.0% in 553 Thai people returning from high-risk countries. This serosurveillance study found a low infection rate of SARS-CoV-2 in Thailand before the emergence of the Delta variant in late May 2021. The findings support the Ministry of Public Health’s data, which are based on numbers of patients and contact tracing.
Quantification of thermal impacts across freshwater life stages to improve temperature management for anadromous salmonids

Abstract Water temperature is the major controlling factor that shapes the physiology, behaviour and, ultimately, survival of aquatic ectotherms. Here we examine temperature effects on the survival of Chinook salmon (Oncorhynchus tshawytscha), a species of high economic and conservation importance. We implement a framework to assess how incremental changes in temperature impact survival across populations that is based on thermal performance models for three freshwater life stages of Chinook salmon. These temperature-dependent models were combined with local spatial distribution and phenology data to translate spatial–temporal stream temperature data into maps of life stage-specific physiological performance in space and time. Specifically, we converted temperature-dependent performance (i.e. energy used by pre-spawned adults, mortality of incubating embryos and juvenile growth rate) into a common currency that measures survival in order to compare thermal effects across life stages. Based on temperature data from two abnormally warm and dry years for three managed rivers in the Central Valley, California, temperature-dependent mortality during pre-spawning holding was higher than embryonic mortality or juvenile mortality prior to smolting. However, we found that local phenology and spatial distribution helped to mitigate negative thermal impacts. In a theoretical application, we showed that high temperatures may inhibit successful reintroduction of threatened Central Valley spring-run Chinook salmon to two rivers where they have been extirpated. To increase Chinook salmon population sizes, especially for the threatened and declining spring-run, our results indicate that adults may need more cold-water holding habitat than currently available in order to reduce pre-spawning mortality stemming from high temperatures. To conclude, our framework is an effective way to calculate thermal impacts on multiple salmonid populations and life stages within a river over time, providing local managers the information to minimize negative thermal impacts on salmonid populations, particularly important during years when cold-water resources are scarce.
Prevalence and predictive factors of nocturia in patients with obstructive sleep apnea syndrome: A retrospective cross-sectional study

Objectives Many patients with obstructive sleep apnea syndrome (OSAS) have nocturia. However, the predictive index of nocturia in patients with OSAS is currently not well known. We aimed to investigate the prevalence of nocturia in patients with OSAS and determine the factors that could predict nocturia in these patients. Methods In this retrospective cross-sectional study, we enrolled 1,264 untreated patients with OSAS (Apnea-Hypopnea Index, AHI ≥5/h on polysomnography [PSG]) from January 2017 to January 2020. Participants completed the Beck Depression Inventory-II (BDI-II), Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), and Epworth Sleepiness Scale. Participants were divided by sex and then subdivided into nocturia and non-nocturia groups according to the following question, “Do you go to the bathroom two times or more during your sleep? ” Participants’ characteristics and underlying disease were investigated, and all information, including PSG data, was compared between the two groups using the t-test or chi-square test. Results Overall, 35.2% (337/958) of male participants with OSAS and 59.8% (183/306) of female participants with OSAS had nocturia. The nocturia group was older; scored higher on the BDI-II, PSQI, and ISI; and had more underlying disease in both sexes. There was no difference in the AHI between the two groups among both sexes, but the hypoxia-related PSG parameters and sleep quality parameters, such as higher 90% oxygen desaturation index (90% ODI), lesser N3 sleep, and higher wakefulness after sleep onset, were worse among male participants with OSAS in the nocturia group than in the non-nocturia group. In multivariate logistic analysis, 90% ODI was an independent risk factor associated with nocturia in male participants with OSAS. Conclusions Considerable number of patients with OSAS had nocturia and poor sleep quality. Nocturia should be evaluated in male OSAS patients with severe hypoxia observed during sleep.
Conventional amphotericin B elicits markers of immunogenic cell death on leukemic blasts, mediates immunostimulatory effects on phagocytic cells, and synergizes with PD-L1 blockade

ABSTRACT Immunostimulatory regimens are a game changer in the fight against cancer, but still only a minority of patients achieve clinical benefit. Combination with immunomodulatory drugs and agents converting otherwise non-immunogenic forms of cell death into bona fide “immunogenic cell death” (ICD) could improve the efficacy of these novel therapies. The aim of our study was to investigate conventional Amphotericin B (AmB) as an enhancer of antitumor immune responses. In tumor cell line models, AmB induced ICD with its typical hallmarks of calreticulin (CALR) expression and release of high mobility group box 1 (HMGB1) as well as Adenosine 5’-triphosphate (ATP). Interestingly, in contrast to non-ICD inducing treatments, ICD induction led to up-regulation of PD-L1-expression by ICD experiencing cells, resulting in decreased maturation of dendritic cells (DCs). Blocking this PD-L1 expression on tumor cells could unleash full ICD effects on antigen presenting cells. Even at sub-toxic concentrations, AmB was able to enhance CALR on leukemic blasts, particularly on phagocytic monoblastic THP-1 cells, which also showed features of “M1-like” differentiation after AmB exposure. The ability of AmB to increase the immunogenicity of tumor cells was confirmed in vivo in a mouse vaccination experiment. In conclusion, we demonstrate that AmB can promote antitumor immune responses in a dose-dependent manner by ICD induction, surface translocation of CALR on leukemic blasts even at sub-toxic concentrations, and “M1-like” polarization of phagocytic cells, making it noteworthy as potential booster for cancer immunotherapy. We additionally report for the first time that PD-L1 expression may be a feature of ICD, possibly as a negative feedback mechanism regulating the maturation status of DCs and thus indirectly affecting T-cell priming.
Frontal plane biomechanics during single-leg squat and hip strength in patients with isolated patellofemoral osteoarthritis compared to matched controls: A cross-sectional study

The patellofemoral compartment of the knee is the most frequently affected by osteoarthritis. However, there is a lack of biomechanics studies on patellofemoral osteoarthritis (PFOA). This study’s purpose was to compare the frontal plane biomechanics of the trunk and lower limb during the single-leg squat and isometric hip abductor torque in individuals with isolated PFOA and controls. Frontal plane kinematics during the single-leg squat were evaluated using a three-dimensional (3-D) motion analysis system. Isometric hip abductor torque was determined using a handheld dynamometer. Twenty individuals participated in the study (10 with PFOA and 10 controls). No significant differences between groups were found regarding age (mean ± SD, PFOA group = 51.8 ± 6.9 versus control group = 47.8 ± 5.5; mean difference = 4, 95% confidence interval [CI] = -1.9 to 9.9, p = 0.20) or body mass index (PFOA group = 27.6 ± 2.2 versus control group = 25.5 ± 2.5; mean difference = 2.1, 95% confidence interval [CI] = -0.1 to 4.3, p = 0.06). Compared to control, the PFOA group presented greater hip adduction in the descending and ascending phases of the single-leg squat at 45° (mean difference [95% CI] = 6.44° [0.39–12.48°], p = 0.04; mean difference [95% CI] = 5.33° [0.24–10.42°], p = 0.045, respectively) and 60° (mean difference [95% CI] = 8.44° [2.15–14.73°], p = 0.01; mean difference [95% CI] = 7.58° [2.1–13.06°], p = 0.009, respectively) of knee flexion. No significant differences between groups were found for the frontal plane kinematics of the trunk, pelvis or knee (p > 0.05). The PFOA group exhibited lower isometric hip abductor torque (mean difference [95% CI] = -0.34 Nm/kg [-0.67 to -0.01 Nm/kg], p = 0.04). The individuals with PFOA presented greater hip adduction than the control group, which could increase lateral patellofemoral joint stress at 45° and 60° of knee flexion in the descending and ascending phases of the single-leg squat. These individuals also exhibited hip abductor weakness in comparison to healthy controls.
Complication and cost analysis of transbronchial lung cryobiopsy and awake video-assisted thoracic surgery in diagnosis of interstitial lung disease

Aim and introduction: Diagnosing of interstitial lung disease (ILD) is difficult and expensive. The standard diagnostical approaches to ILD are bronchoalveolar lavage, transbronchial lung biopsy, transbronchial lung cryobiopsy (TBLC) and surgical lung biopsy (SLB). SLB is gold standard for the confident diagnosis of ILD but because of the poor performance of the patients it’s use is limited. We conducted a retrospective study to point out that TBLC plays an important role in diagnosis of ILD and has fewer complications and lower cost than awake video-assisted thoracic surgery (AVATS). Material and methods: 132 patients who underwent TBLC and AVATS with a pre-diagnosis of ILD in our hospital between 2015 and 2020 were evaluated retrospectively. Diagnosis rates, complications and costs were recorded. Results: There were no non-diagnostic materials in 44 patients in AVATS arm. Prolonged air leak was observed in 11(25.0%) of the patients, and six of them (13.6%) were discharged with Heimlich Valve (HV). Median length of stay in the hospital was 8 days, while average patient cost was $515.9 (415.2-2662.9) in the AVATS arm. Non-diagnostic material was obtained from 10 (11.3%) of 88 patients in TBLC arm. Six (6.8%) of them had pneumothorax, only one of them required a chest tube. No patient was discharged with HV (p=0.001). Median cost for each patient with a median hospital stay of 2.0 (1.0-21.0) (p<0.001) days was $171.9 (80.8-1493.3) (p<0.001). Discussion: Although TBLC is behind AVATS in terms of diagnostic accuracy, it may be an alternative diagnostic tool in the diagnosis of interstitial lung disease due to its acceptable safety profile and cost-effectiveness.
Detection of blaKPC and blaNDM carbapenemase genes among Klebsiella pneumoniae isolates in Addis Ababa, Ethiopia: Dominance of blaNDM

Background Infections caused by Klebsiella pneumoniae have been difficult to control because of the worldwide emergence of carbapenem-resistant isolates mainly due to carbapenemase production. Information regarding carbapenemase-producing K. pneumoniae is still scarce in Ethiopia. Therefore, the current study aimed to determine the prevalence of carbapenemase-producing K. pneumoniae and to assess the occurrence of blaNDM and blaKPC carbapenemase genes. Methods A cross-sectional study was conducted from September 2018 to February 2019 at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia. A total of 132 non-duplicate K. pneumoniae isolates were studied. Phenotypic confirmation of carbapenemase production was done by modified Carbapenem Inactivation Method (mCIM). Multiplex PCR was performed for the detection of carbapenemase-encoding genes blaKPC, and blaNDM. Results Out of the total 132 K. pneumoniae isolates, 39 (29.6%) were non-susceptible to one or more carbapenems. The prevalence of carbapenemase-producing isolates from the total was 28 (21.2%) with mCIM of which the most dominant gene was blaNDM 26 (92.9%) and one isolate carried blaKPC concomitantly. Carbapenemase-producing K. pneumoniae isolates were 100% non-susceptible to half of the antimicrobials used in the study, including meropenem and ertapenem. Previous use of carbapenems was associated with carbapenemase production (P = 0.004). Conclusions The prevalence of carbapenemase-producing K. pneumoniae isolates was worrying in the study area. To our knowledge, the study described the emergence of blaNDM and blaKPC gene carrying K. pneumoniae in Ethiopia for the first time. Further large-scale molecular-based studies, including other carbapenemase genes and sequencing of K. pneumoniae, are warranted to have a clear awareness about the presence of antimicrobial resistance high-risk clones in Ethiopia.
Consumer acceptance of fungus-resistant grape wines: Evidence from Italy, the UK, and the USA

While there is evidence of consumers’ interest in wine sustainability, acceptance of innovations in wine production is not guaranteed. The current study addresses this issue by analyzing consumers’ acceptance of fungus-resistant grape (FRG) wines, a sustainable innovation that can substantially reduce the need for chemical inputs in viticulture. To do so, by means of an online survey including large samples of regular wine drinkers in Italy (N = 752), the UK (N = 858) and the USA (N = 856), the study compares individuals’ preferences for conventional wines with preferences for FRG wines. The study also explores whether FRG wine acceptance is influenced by informal or formal purchase occasion, by different types of information regarding the product, and by individual attitudinal characteristics. The findings show a general acceptance of FRG wines among consumers. In particular, consumers’ preferences for FRG wines on formal occasions are not significantly different from their preferences for conventional wine, whereas on informal occasions, consumers prefer FRG wines over conventional wines. Regarding the impact of information on participant choice, participants informed about the potential effects of FRG on sensory wine characteristics had lower preferences for FRG wines than those who read an information script regarding crop biodiversity. Last, individuals’ sustainability concerns and food technology neophobia had positive and negative influences on FRG acceptance, respectively. Overall, this research provides wineries, nurseries and policy-makers with important insights concerning the market potential of FRG wines in three key markets.
Relationship of interferon regulator factor 5 and interferon-γ with missed abortion

The aim of the present study was to reveal the association of missed abortion, a process integrated with the immune system, with interferon regulatory factor 5 (IRF5) and interferon-γ (IFN-γ), and to demonstrate the function of these molecules by examining their levels in decidual tissue. This prospective cohort study included 13 patients with no additional systemic disease, between 6 and 10 weeks of gestation with negative fetal heartbeat, and 11 patients between 6 and 10 weeks of gestation with positive heartbeat who presented for voluntary termination of pregnancy. In the fresh decidual tissue materials recovered after therapeutic curettage, IFN-γ and IRF5 protein levels were determined by ELISA method and IFN-γ and IRF5 gene expression levels by qPCR method. The mean IFN-γ (86.5 vs. 27.3 pg/mg protein; P<0.001) and IRF5 (2.0 vs. 1.5 ng/mg protein; P<0.001) levels were significantly higher in pregnant women who had missed abortion compared to the voluntary abortion group. The increases in the mean IFN-γ/GAPDH (3.5 vs. 1.5-fold increase; P<0.001) and IRF5/GAPDH (3.9 vs. 1.4-fold increase; P<0.001) gene expression levels were significantly higher in the tissues of pregnant women with missed abortion than in the voluntary abortion group. A threshold value of 45.2 pg/mg protein for IFN-γ had a sensitivity of 100% and specificity of 100% in determination of missed abortion. The findings of present study revealed, to the best of our knowledge for the first time in the literature, that IFN-γ and IRF5 may be associated with missed abortion, and that IFN-γ and IRF5 protein levels and gene expression levels were significantly increased in the case of missed abortion. According to our findings, IFN-γ and IRF5 play an important role in placental invasion and pregnancy and can be used as markers for endometrial implantation.
Phyllachora species infecting maize and other grass species in the Americas represents a complex of closely related species

Abstract The genus Phyllachora contains numerous obligate fungal parasites that produce raised, melanized structures called stromata on their plant hosts referred to as tar spot. Members of this genus are known to infect many grass species but generally do not cause significant damage or defoliation, with the exception of P. maydis which has emerged as an important pathogen of maize throughout the Americas, but the origin of this pathogen remains unknown. To date, species designations for Phyllachora have been based on host associations and morphology, and most species are assumed to be host specific. We assessed the sequence diversity of 186 single stroma isolates collected from 16 hosts representing 15 countries. Samples included both herbarium and contemporary strains that covered a temporal range from 1905 to 2019. These 186 isolates were grouped into five distinct species with strong bootstrap support. We found three closely related, but genetically distinct groups of Phyllachora are capable of infecting maize in the United States, we refer to these as the P. maydis species complex. Based on herbarium specimens, we hypothesize that these three groups in the P. maydis species complex originated from Central America, Mexico, and the Caribbean. Although two of these groups were only found on maize, the third and largest group contained contemporary strains found on maize and other grass hosts, as well as herbarium specimens from maize and other grasses that include 10 species of Phyllachora. The herbarium specimens were previously identified based on morphology and host association. This work represents the first attempt at molecular characterization of Phyllachora species infecting grass hosts and indicates some Phyllachora species can infect a broad range of host species and there may be significant synonymy in the Phyllachora genus.