Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical outcomes among adolescents living with HIV in Kenya following initiation on antiretroviral treatment

In Kenya, HIV/AIDS remains a leading cause of morbidity and mortality among adolescents living with HIV (ALHIV). Our study evaluated associations between demographic and healthcare factors and HIV treatment outcomes among ALHIV in care in Kenya. This retrospective cohort study evaluated the clinical outcomes of newly diagnosed ALHIV enrolled in HIV care during January 2017-June 2018 at 32 healthcare facilities in Homabay and Kakamega Counties. Demographic and clinical data were abstracted from patient clinical records and registers during the follow up study period January 2017-through May 2019. ALHIV were stratified by age (10–14 versus 15–19 years). Categorical variables were summarized using descriptive statistics; continuous variables were analyzed using mean values. The latest available treatment and virological outcomes for ALHIV were assessed. 330 ALHIV were included in the study (mean age 15.9 years; 81.8% female, 63.0% receiving HIV care at lower-level healthcare facilities). Most (93.2%) were initiated on ART within 14 days of diagnosis; 91.4% initiated EFV-based regimens. Of those on ART, only 44.6% were active on care at the end of the study period. Of those eligible for viral load testing, 83.9% were tested with 84.4% viral suppression rate. Retention in care was higher at higher-level facilities (67.5%) compared to lower-level facilities (28.6%). Factors associated with higher retention in care were school attendance (aRR = 1.453), receipt of disclosure support (aRR = 13.315), and receiving care at a high-level health facility (aRR = 0.751). Factors associated with viral suppression included older age (15–19 years) (aRR = 1.249) and pre-ART clinical WHO stage I/II (RR = .668). Viral suppression was higher among older ALHIV. Studies are needed to evaluate effective interventions to improve outcomes among ALHIV in Kenya.
DOSIMETRIC VERIFICATION OF INTENSITY MODULATED RADIOTHERAPY (IMRT) TREATMENT PLANS FOR PROSTATE CANCER PATIENTS

Intensity modulated radiotherapy (IMRT) has become widely used as a standard radiation therapy technique for the treatment of localized prostate cancer. The transition from conformal radiotherapy (3D CRT) to a more complex IMRT technique triggered the need for more thorough verification of the accuracy in the dose delivery. In this work we present the clinical workflow and the results of patient specific quality assurance (PSQA) procedures for 40 prostate cancer patients who have been treated with step and shot IMRT ever since its implementation in our routine clinical practice. PSQA procedures include dosimetric verification of each treatment plan with dedicated rotational phantom and high-resolution matrix detector system Octavius 4D (PTW Freiburg) that allows three-dimensional comparison of the calculated and delivered radiation dose distribution. Our results proved the compliance with the universal tolerance limits recommended for those procedures (1), assuring the safety of the treatment and providing the possibility for the adoption of more stringent constraints in the future.
Group theoretical basis of some identities for the generalized hypergeometric series

It is shown that Thomae’s identity between two 3F2 hypergeometric series of unit argument together with the trivial invariance under separate permutations of numerator and denominator parameters implies that the symmetric group S5 is an invariance group of this series. A similar result is proved for the terminating Saalschutzian 4F3 series, where S6 is shown to be the invariance group of this series (or S5 if one parameter is eliminated by using the Saalschutz condition). Here Bailey’s identity is realized as a permutation of appropriately defined parameters. Finally, the set of three‐term relations between 3F2 series of unit argument discovered by Thomae [J. Thomae, J. Reine Angew. Math. 87, 26 (1879)] and systematized by Whipple [F. J. Whipple, Proc. London Math. Soc. 23, 104 (1925)] is shown to be transformed into itself under the action of the group S6×Λ, where Λ is a two‐element group. The 12 left cosets of S6×Λ with respect to the invariance group S5 are the structural elements underlying the three‐.
Association of CTNND2 gene polymorphism with schizophrenia: Two-sample case-control study in Chinese Han population

Objectives Genetic factors play an important role in the etiology of schizophrenia (SZ). Catenin Delta 2 (CTNND2) is one of the genes regulating neuronal development in the brain. It is unclear whether CTNND2 is involved in SZ. With the hypothesis that CTNND2 may be a risk gene for SZ, we performed a case-control association analysis to investigate if CTNND2 gene single nucleotide polymorphisms (SNPs) are implicated in SZ in a Han Chinese population. Materials and Methods We recruited subjects from 2010 to 2022 from the Han population of northern Henan and divided them into two case-control samples, including a discovery sample (SZ = 528 and controls = 528) and replication sample (SZ = 2458 and controls = 6914). Twenty-one SNPs were genotyped on the Illumina BeadStation 500G platform using GoldenGate technology and analyzed by PLINK. The Positive and Negative Syndrome Scale (PANSS) was used to assess clinical symptoms. Results Rs16901943, rs7733427, and rs2168878 SNPs were associated with SZ (Chi2 = 7.484, 11.576, and 5.391, respectively, df = 1; p = 0.006, 0.00067, and 0.02, respectively) in the two samples. Rs10058868 was associated with SZ in male patients in the discovery sample (Chi2 = 6.264, df = 1, p = .044). Only the relationship with rs7733427 survived Bonferroni correction. Linkage disequilibrium block three haplotypes were associated with SZ in the discovery and total sample. PANSS analysis of the four SNPs implicated rs10058868 and rs2168878 in symptoms of depression and excitement, respectively, in the patients with SZ. Conclusion Four SNPs of the CTNND2 gene were identified as being correlated with SZ. This gene may be involved in susceptibility to SZ.
Risk Factors for Post-ERCP Pancreatitis in Pediatric and Young Adult Patients

Objectives: Post-ERCP pancreatitis (PEP) is the most common complication of endoscopic retrograde cholangiopancreatography (ERCP). Limited existing data suggest that prophylactic pancreatic duct (PD) stenting in pediatric patients may increase the risk of PEP. The aim of this study is to identify factors associated with PEP in pediatric patients. Methods: Patients at a single institution who underwent ERCP between 2012 and 2020 were retrospectively reviewed. Patient and procedure-related factors were collected. Data were analyzed using Chi-square or Fisher exact tests as appropriate and Mann-Whitney-Wilcoxon tests. Results: Seven hundred thirty-six ERCPs were performed for 402 unique patients. Ninety-four cases were complicated by PEP (12.8%), of which 91 were mild and 3 were moderately severe. Pancreatic indication, native major papilla, PD cannulation and injection, and higher American Society for Gastrointestinal Endoscopy (ASGE) complexity were associated with PEP. A higher proportion of patients who received rectal indomethacin (65% vs 47%, P = 0.002), or who had placement of a prophylactic (31% vs 20%, P = 0.01) or therapeutic PD stent (37% vs 27%, P = 0.04) developed PEP; however, in a subgroup analysis of high-risk patients, this association was not persistent. A smaller proportion of PEP patients had PRSS1 mutation compared to non-PEP patients (22% vs 40%, P = 0.04). Conclusions: This study evaluates factors associated with developing PEP in a large pediatric cohort. A high rate of PEP was observed, likely secondary to higher rates of pancreatic indication and higher ASGE complexity scores compared to previously reported literature. Randomized prospective trials are needed to better define the utility of various interventions.
End-of-life treatment preferences and advanced care planning among older adults

Abstract End-of-life treatment preferences (EOLTPs) refer to the amount of medical intervention an individual would wish to receive in a life-threatening scenario. This study aimed to investigate relationships between older adults’ EOLTPs and advance care planning (ACP). Using archival data from two interview surveys of community-dwelling older adults (study 1 n = 331, study 2 n = 338; age 60–102), results found that a desire for less end-of-life medical intervention was associated with greater EOL discussion with physicians. This relationship was explained by greater death preparation and younger age. Older adults may use ACP to limit unwanted medical interventions.
Non-opioid antinociceptive drugs : risk of respiratory depression and death related to concomitant use of gabapentinoids in addition to opioids

ABSTRACT Introduction Respiratory depression and opioid-related death are reported when opioids are associated with gabapentinoids. Meta-analyses of randomized clinical trials investigating efficacy and safety of such association failed to assess these risks because of the lack of data. The aim of this systematic review was to investigate the risk of respiratory depression or death during this combination in the scientific literature, including case reports or series, observational studies, and clinical trials. Areas covered PubMed®, Web of Science®, Embase®, and Google Scholar® were searched from their inception to December 2021, for original articles in English, French, and German. Data synthesis was done on a narrative approach by type of articles. Expert opinion The review included 25 articles (4 case reports, 2 cross-sectional, 3 case–control, 14 cohort studies, and 2 clinical trials). Respiratory depression or opioid-related death and co-exposure to gabapentinoids were associated in perioperative setting/chronic pain (odds ratios around 1.3) and in opioid maintenance treatment (hazard ratio 3.4). These findings are in agreement with experimental studies showing that a single dose of gabapentinoid may reverse opioid respiratory tolerance. Because the combination gabapentinoids–opioids is highly prevalent in all clinical context, all health care professionals and patients must be aware of this risk.
Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences

Abstract Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing—to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid—while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods—usually an expensive, complex, and/or time-consuming endeavor—phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid’s ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution. ]
Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil.

One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information is need to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root- system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH·) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a "cry for help" case wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.
Pathways to post-traumatic growth in Korean female cancer patients: the mediation effects of coping strategies and resilience

ABSTRACT Background: Cancer is a life-threatening disease in Korean women. Female cancer patients in Korea have reported poor physical functioning and psychological distress after diagnosis. However, some patients experience post-traumatic growth (PTG), which includes positive feelings and changes. Objective: The main purpose of this study was to examine the relationships between PTG and its associated factors in Korean female cancer patients to understand how female cancer patients achieve PTG while experiencing cancer diagnosis and treatment. This study aimed to improve the quality of life of many Korean female patients with cancer. Methods: This study investigated the structural model of the paths from the disruption of core beliefs (CBD), coping strategies, and resilience to PTG in a sample of female cancer patients. In total, 164 middle-aged women diagnosed with cancer were included in the final sample. Results: First, it was determined that the proposed structural model was substantial and had high fit indices. Second, problem-solving was positively associated by the CBD routes. Third, it was also favorably expected that problem-solving would lead to resilience and resilience would lead to PTG. These findings are important for developing future interventions for Korean female cancer patients and can be considered as an important variable to improve their PTG. HIGHLIGHTS The proposed structural model observed paths of how female cancer patients achieve post-traumatic growth while experiencing cancer diagnosis and treatment. Disruption of core beliefs as a factor positively associates problem-solving in Korean female cancer patients. Problem-solving and resilience as factors positively associate post-traumatic growth in Korean female cancer patients.
Serum and plasma protein biomarkers associated with frailty in patients with cirrhosis

Frailty, a clinical phenotype of decreased physiological reserve, is a strong determinant of adverse health outcomes in patients with cirrhosis. The only cirrhosis-specific frailty metric is the Liver Frailty Index (LFI), which must be administered in person and may not be feasible for every clinical scenario. We sought to discover candidate serum/plasma protein biomarkers that could differentiate frail from robust patients with cirrhosis. A total of 140 adults with cirrhosis awaiting liver transplantation in the ambulatory setting with LFI assessments and available serum/plasma samples were included. We selected 70 pairs of patients on opposite ends of the frailty spectrum (LFI>4.4 for frail and LFI<3.2 for robust) who were matched by age, sex, etiology, HCC, and Model for End-Stage Liver Disease-Sodium. Twenty-five biomarkers with biologically plausible associations with frailty were analyzed using ELISA by a single laboratory. Conditional logistic regression was used to examine their association with frailty. Of the 25 biomarkers analyzed, we identified 7 proteins that were differentially expressed between frail and robust patients. We observed differences in 6 of the 7 proteins in the expected direction: (a) higher median values in frail versus robust with growth differentiation factor-15 (3682 vs. 2249 pg/mL), IL-6 (17.4 vs. 6.4 pg/mL), TNF-alpha receptor 1 (2062 vs. 1627 pg/mL), leucine-rich alpha-2 glycoprotein (44.0 vs. 38.6 μg/mL), and myostatin (4066 vs. 6006 ng/mL) and (b) lower median values in frail versus robust with alpha-2-Heremans-Schmid glycoprotein (0.11 vs. 0.13 mg/mL) and free total testosterone (1.2 vs. 2.4 ng/mL). These biomarkers represent inflammatory, musculoskeletal, and endocrine/metabolic systems, reflecting the multiple physiological derangements observed in frailty. These data lay the foundation for confirmatory work and development of a laboratory frailty index for patients with cirrhosis to improve diagnosis and prognostication.
Remarkable Changes in the Near-Infrared Spectrum of the Nova-like Variable V4332 Sagittarii

We report on recent near-IR observations of V4332 Sgr—the nova-like variable that erupted in 1994. Its rapid, post-outburst evolution to a cool M-type giant/supergiant, soon after its outburst, showed that it was an unusual object differing from other eruptive variables, such as classical/symbiotic novae or born-again asymptotic giant branch stars. The present study of V4332 Sgr was motivated by the keen interest in the recent eruption of V838 Mon—an object with a spectacular light echo that, along with V4332 Sgr, is believed to belong to a new class of objects (we propose that they be called "quasi novae"). Our observations show new developments in the evolution of V4332 Sgr. The most striking feature is the detection of several molecular bands of AlO—a rarely seen molecule in astronomical spectra—in the JHK spectra. Many of these bands are being detected for the first time. The only other detection of some of these AlO bands is in V838 Mon, thereby showing further spectral similarities between the two objects. JHK photometry shows the development of a new dust shell around V4332 Sgr with a temperature of ~900 K and a lower limit on the derived mass of Mdust = 3.7 × 10-12 M☉. This dust shell does not appear to be associated with ejecta of the 1994 outburst but is due to a second mass-loss episode, which is not expected in a classical nova outburst. The cold molecular environment, suggested by the AlO emission, is also not expected in novae ejecta. We model the AlO bands and also discuss the possible formation mechanism of the AlO. These results show the need to monitor V4332 Sgr regularly for unexpected developments. The results can also be significant in predicting possible changes in the future evolution of V838 Mon.
The application of integral equation methods to the numerical solution of some exterior boundary-value problems

The application of integral equation methods to exterior boundary-value problems for Laplace’s equation and for the Helmholtz (or reduced wave) equation is discussed. In the latter case the straightforward formulation in terms of a single integral equation may give rise to difficulties of non-uniqueness; it is shown that uniqueness can be restored by deriving a second integral equation and suitably combining it with the first. Finally, an outline is given of methods for transforming the integral operators with strongly singular kernels which occur in the second equation.
α-Gd 2 S 3 -type structure in In 2 O 3 : Experiments and theoretical confirmation of a high-pressure polymorph in sesquioxide

A high-pressure phase, orthorhombic $\ensuremath{\alpha}{\text{-Gd}}_{2}{\text{S}}_{3}$ type, was found in ${\text{In}}_{2}{\text{O}}_{3}$ as a post-${\text{Rh}}_{2}{\text{O}}_{3}(\text{II})$ phase at pressures over 40 GPa by using an in situ x-ray diffraction method. This structure is composed of unusual sevenfold and eightfold coordinated cations, which has not been predicted for any sesquioxides to date. Compared with the known post-${\text{Rh}}_{2}{\text{O}}_{3}(\text{II})$ transition to the ${\text{CaIrO}}_{3}$ structure, this transition to $\ensuremath{\alpha}{\text{-Gd}}_{2}{\text{S}}_{3}$ yields a considerable volume change. Density functional lattice energy calculations also show that the transition to $\ensuremath{\alpha}{\text{-Gd}}_{2}{\text{S}}_{3}$ is more favorable than the transition to ${\text{CaIrO}}_{3}$ in ${\text{In}}_{2}{\text{O}}_{3}$.
DNA sensing in the pathological process of ischemic stroke

The innate immune response plays an important role in the pathological process of ischemic stroke. Increasing evidence suggests that the inflammatory response triggered by the innate immune system hinders neurological and behavioural recovery after stroke. The perception of abnormal DNA and its downstream effects are an essential part of the innate immune system. The abnormal DNA is the major inducing factor for innate immune response and is sensed by a series of DNA sensors. In this review, we discussed the multiple roles of DNA sensing in the pathological process of ischemic stroke, with a special focus on DNA sensors Toll‐like receptor 9 (TLR9), absent in melanoma 2 (AIM2) and cyclic GMP‐AMP synthase (cGAS).