Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae)

Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite or whorled leaves. C. bungei, C. fargesii f. duclouxii and C. fargesii are sources of traditional precious wood in China, known as the “kings of wood”. Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within Catalpa. Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus Catalpa and analyzed their basic structure and evolutionary relationships. The chloroplast genome of Catalpa shows a typical tetrad structure with a total length ranging from 157,765 bp (C. fargesii) to 158,355 bp (C. ovata). The length of the large single-copy (LSC) region ranges from 84,599 bp (C. fargesii) to 85,004 bp (C. ovata), that of the small single-copy (SSC) region ranges from 12,662 bp (C. fargesii) to 12,675 bp (C. ovata), and that of the inverted repeat (IR) regions ranges from 30,252 bp (C. fargesii) to 30,338 bp (C. ovata). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus Catalpa formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of Catalpa, which will facilitate future research efforts.
A PBPK Model of Ternary Cyclodextrin Complex of ST-246 Was Built to Achieve a Reasonable IV Infusion Regimen for the Treatment of Human Severe Smallpox

ST-246 is an oral drug against pathogenic orthopoxvirus infections. An intravenous formulation is required for some critical patients. A ternary complex of ST-246/meglumine/hydroxypropyl-β-cyclodextrin with well-improved solubility was successfully developed in our institute. The aim of this study was to achieve a reasonable intravenous infusion regimen of this novel formulation by a robust PBPK model based on preclinical pharmacokinetic studies. The pharmacokinetics of ST-246 after intravenous injection at different doses in rats, dogs, and monkeys were conducted to obtain clearances. The clearance of humans was generated by using the allometric scaling approach. Tissue distribution of ST-246 was conducted in rats to obtain tissue partition coefficients (K p ). The PBPK model of the rat was first built using in vivo clearance and K p combined with in vitro physicochemical properties, unbound fraction, and cyclodextrin effect parameters of ST-246. Then the PBPK model was transferred to a dog and monkey and validated simultaneously. Finally, pharmacokinetic profiles after IV infusion at different dosages utilizing the human PBPK model were compared to the observed oral PK profile of ST-246 at therapeutic dosage (600 mg). The mechanistic PBPK model described the animal PK behaviors of ST-246 via intravenous injection and infusion with fold errors within 1.2. It appeared that 6h-IV infusion at 5 mg/kg BID produced similar Cmax and AUC as oral administration at 600 mg. A PBPK model of ST-246 was built to achieve a reasonable regimen of IV infusion for the treatment of severe smallpox, which will facilitate the clinical translation of this novel formulation.
Comparative Cardiovascular Outcomes of SGLT2 Inhibitors in Type 2 Diabetes Mellitus: A Network Meta-Analysis of Randomized Controlled Trials

Background A network meta-analysis of randomized controlled trials (RCTs) was conducted to explore the cardiovascular outcomes of all the kind and dosages of sodium-glucose cotransport-2 (SGLT2) inhibitors in type 2 diabetes mellitus (T2DM) patients. Method and Result The Cochrane Library, PubMed, and Embase databases were systematically searched for studies to compare the therapeutic effects of different SGLT2 inhibitors in T2DM patients. The effect measurements estimate chosen were odds ratios (ORs) and their corresponding 95% confidence interval (CI). Forty-seven RCTs involving a total of 70574 participants were eligible for direct and indirect comparisons. In direct comparison, treatment with dapagliflozin 5mg showed significantly lower risk of all-cause mortality compared with treatment with dapagliflozin 2.5mg (OR 0.09, 95% CI 0.01-0.70). According to NMA, interestingly, empagliflozin 10mg/25mg, and canagliflozin 100mg was associated with significantly lower risks of all-cause mortality compared with placebo (OR of 0.70, 95% CI 0.58-0.85; 0.69, 95% CI 0.57-0.84; and 0.83, 95% CI 0.73-0.95, respectively). Compared with placebo, dapagliflozin 10mg, empagliflozin 10mg and 25mg displayed the lower risks for cardiovascular events (OR 0.78, 95% CI 0.44-1.00; OR 0.47, 95% CI 0.22-0.93; and 0.43, 95% CI 0.24-0.74, respectively) by direct comparison. Moreover, canagliflozin 100/300mg showed significantly higher risks of cardiovascular events compared with empagliflozin 10mg (OR of 4.83, 95% CI 1.14-20.46 and 5.31, 95% CI 1.26-22.34, respectively) and empagliflozin 25mg (4.23, 95% CI 1.13-15.83 and 4.65, 95% CI 1.25-17.27, respectively) according to NMA. There were non-significant differences among all interventions in volume depletion in traditional pairwise meta-analysis. While in NMA, canagliflozin 100/300mg were associated with significantly increased risks of volume depletion compared with placebo (OR of 1.47, 95% CI 1.08-1.99 and 2.19, 95% CI 1.66-2.90, respectively). Conclusion In the limitations of the NMA, this study showed that empagliflozin might be better than other SGLT2 inhibitors with low risks of all-cause mortality and cardiovascular events in patients with T2DM suggesting the need for ad hoc RCTs.
Characteristics and Clinical Significance of T-Cell Receptor Repertoire in Hepatocellular Carcinoma

Several studies have demonstrated that the T-cell receptor (TCR) repertoire is associated with prognosis and immune therapy response in several types of cancer. However, the comprehensive features of TCR repertoire in tumor-infiltrating and circulating T cells, as well as its clinical significance of diagnosis in hepatocellular carcinoma (HCC) patients, are still unknown. In this study, we perform paired tumor/peritumoral tissues and peripheral blood samples from 58 patients with HCC and sequenced them with high-throughput TCR to comprehensively analyze the characteristics of TCR and the clinical significance of peripheral TCR sequence. By exploring the abundance and diversity of TCR repertoires, we observe that there was a significantly higher TCR diversity in peripheral blood than in tumoral and peritumoral tissues, while tumoral and peritumoral tissues showed similar TCR diversity. A substantial difference in the usage frequencies of several Vβ, Jβ genes, and TCRβ VJ pairings was found among three types of tissues. Moreover, we reveal that HCC patients have a unique profile of TCR repertoire in peripheral blood in contrast to healthy individuals. We further establish an HCC diagnostic model based on TCRβ VJ pairing usage in peripheral blood, which yields a best-fit area under the curve (AUC) of 0.9746 ± 0.0481 (sensitivity = 0.9675 ± 0.0603, specificity = 0.9998 ± 0.0007, average of 100 repeats) in the test set. Our study describes the characteristics of tissue infiltration and circulating T-cell bank in patients with HCC and shows the potential of using circulating TCR sequence as a biomarker for the non-invasive diagnosis of patients with HCC.
V-QBA vs. QBA—How Do Video and Live Analysis Compare for Qualitative Behaviour Assessment?

Animal welfare is an inextricable part of livestock production and sustainability. Assessing welfare, beyond physical indicators of health, is challenging and often relies on qualitative techniques. Behaviour is a key component of welfare to consider and Qualitative Behaviour Assessment (QBA) aims to achieve this by systematically scoring behaviour across specific terms. In recent years, numerous studies have conducted QBA by using video footage, however, the method was not originally developed using video and video QBA (V-QBA) requires validation. Forty live QBAs were conducted, by two assessors, on housed beef cattle to help fill this validation gap. Video was recorded over the assessment period and a second video assessment was conducted. Live and video scores for each term were compared for both correlation and significant difference. Principle component analysis (PCA) was then conducted and correlations and differences between QBA and V-QBA for the first two components were calculated. Of the 20 terms, three were removed due to an overwhelming majority of scores of zero. Of the remaining 17 terms, 12 correlated significantly, and a significant pairwise difference was found for one (“Bored”). QBA and V-QBA results correlated across both PC1 (defined as “arousal”) and PC2 (defined as “mood”). Whilst there was no significant difference between the techniques for PC1, there was for PC2, with V-QBA generally yielding lower scores than QBA. Furthermore, based on PC1 and PC2, corresponding QBA and V-QBA scores were significantly closer than would be expected at random. Results found broad agreement between QBA and V-QBA at both univariate and multivariate levels. However, the lack of absolute agreement and muted V-QBA results for PC2 mean that caution should be taken when implementing V-QBA and that it should ideally be treated independently from live QBA until further evidence is published. Future research should focus on a greater variety of animals, environments, and assessors to address further validation of the method.
Procrastination Among University Students: Differentiating Severe Cases in Need of Support From Less Severe Cases

Procrastination refers to voluntarily postponing an intended course of action despite expecting to be worse off for this delay, and students are considered to be especially negatively affected. According to estimates in the literature, at least half of the students believe procrastination impacts their academic achievements and well-being. As of yet, evidence-based ideas on how to differentiate severe from less severe cases of procrastination in this population do not exist, but are important in order to identify those students in need of support. The current study recruited participants from different universities in Sweden to participate in an anonymous online survey investigating self-rated levels of procrastination, impulsivity, perfectionism, anxiety, depression, stress, and quality of life. Furthermore, diagnostic criteria for pathological delay (PDC) as well as self-report items and open-ended questions were used to determine the severity of their procrastination and its associated physical and psychological issues. In total, 732 participants completed the survey. A median-split on the Pure Procrastination Scale (PPS) and the responses to the PDC were used to differentiate two groups; “less severe procrastination” (PPS ≤ 2.99; n = 344; 67.7% female; M age = 30.03; SD age = 9.35), and “severe procrastination” (PPS ≥ 3.00; n = 388; 66.2% female; M age = 27.76; SD age = 7.08). For participants in the severe group, 96–97% considered procrastination to a problem, compared to 42–48% in the less severe group. The two groups also differed with regard to considering seeking help for procrastination, 35–38% compared to 5–7%. Participants in the severe group also reported more problems of procrastination in different life domains, greater symptoms of psychological issues, and lower quality of life. A thematic analysis of the responses on what physical issues were related to procrastination revealed that these were characterized by stress and anxiety, e.g., tension, pain, and sleep and rest, while the psychological issues were related to stress and anxiety, but also depression, e.g., self-criticism, remorse, and self-esteem. The current study recommends the PPS to be used as an initial screening tool, while the PDC can more accurately determine the severity level of procrastination for a specific individual.
Whole Genome Profiling of Lung Microbiome in Solid Organ Transplant Recipients Reveals Virus Involved Microecology May Worsen Prognosis

Solid organ transplantation (SOT) is the final therapeutic option for recipients with end-stage organ failure, and its long-term success is limited by infections and chronic allograft dysfunction. Viral infection in SOT recipients is considered an important factor affecting prognosis. In this study, we retrospectively analyzed 43 cases of respiratory infections in SOT recipients using metagenomic next-generation sequencing (mNGS) for bronchoalveolar lavage fluid (BALF). At least one virus was detected in 26 (60.5%) recipients, while 17 (39.5%) were virus-negative. Among virus-positive recipients, cytomegalovirus (CMV) was detected in 14 (32.6%), Torque teno virus (TTV) was detected in 9 (20.9%), and other viruses were detected in 6 (14.0%). Prognostic analysis showed that the mortality of the virus-positive group was higher than that of the virus-negative group regardless whether it is the main cause of infection. Analysis of different types of viruses showed that the mortality of the CMV-positive group was significantly higher than that of the CMV-negative group, but no significant difference was observed in other type of virus groups. The diversity analysis of the lung microbiome showed that there was a significant difference between the virus-positive group and the negative group, in particular, the significant differences in microorganisms such as Pneumocystis jirovecii (PJP) and Moraxella osloensiswere detected. Moreover, in the presence of CMV, Pneumocystis jirovecii, Veillonella parvula, and other species showed dramatic changes in the lung of SOT patients, implying that high degree of co-infection between CMV and Pneumocystis jirovecii may occur. Taken together, our study shows that the presence of virus is associated with worse prognosis and dramatically altered lung microbiota in SOT recipients.
Types of Eating Disorder Prodrome in Adolescence: The Role of Decision Making in Childhood

Psychiatric disorders like eating disorders (EDs) might be underpinned by differences in decision making. However, little previous research has investigated this potential relationship using longitudinal data. This study aimed to understand how components of decision making (delay aversion, risk adjustment, risk taking, quality of decision making and deliberation time) measured by the Cambridge Gambling Task in the United Kingdom’s Millennium Cohort Study (MCS; n = 11,303; female = 50.17%) at age 11 might explain clusters/types of ED prodrome involving body dissatisfaction, intention to lose weight, dietary restraint, excessive exercise and significant under/overweight measured in the MCS at age 14. Latent class analysis revealed two groups within the cohort: a non-prodromal eating pathology group, who were more likely to be of “average” weight, according to the UK90, with minimal disordered attitudes and behaviors in relation to eating and weight; and a second group with prodromal eating pathology, who had more body dissatisfaction, a desire to lose weight, were using dietary restriction and exercise to influence weight and were more likely to be “overweight” according to the UK90. Logistic regression showed that, after adjustment for confounding, higher risk-taking scores were associated with a 60% greater probability of being in the prodromal eating pathology group (b = 0.47, OR = 1.60, p < 0.01), and higher scores on quality of decision making were associated with a 30% lower probability of being in the prodromal eating pathology group (b = −0.34, OR = 0.70, p < 0.05). Helping young people to engage in moderate risk taking and improving decision making might reduce the later presence of ED prodromes.
Preoperative Electrophysiology in Patients With Ulnar Nerve Entrapment at the Elbow-Prediction of Surgical Outcome and Influence of Age, Sex and Diabetes

The impact of preoperative electrophysiology on outcome of surgical treatment in ulnar nerve entrapment at the elbow (UNE) is not clarified. Our aim was to evaluate influence of preoperative electrophysiologic grading on outcome and analyse how age, sex, and in particular diabetes affect such grading. Electrophysiologic protocols for 406 UNE cases, surgically treated at two hand surgery units reporting to the Swedish National Quality Register for Hand Surgery (HAKIR; 2010-2016), were retrospectively assessed, and graded as normal, reduced conduction velocity, conduction block or axonal degeneration. Outcome of surgery after primary and revision surgery was evaluated using QuickDASH and a doctor reported outcome measure (DROM) grading. No differences in QuickDASH or DROM were found between the four groups with different electrophysiologic grading preoperatively, or at three and 12 months or at follow up, respectively. When dichotomizing the electrophysiologic grading into normal and pathologic electrophysiology, cases with normal electrophysiology had worse QuickDASH than cases with pathologic electrophysiology preoperatively (p=0.046). Presence of a conduction block or axonal degeneration indicated a worse outcome by DROM grading (p=0.011). Primary surgeries had electrophysiologic more pronounced nerve pathology compared to revision surgeries (p=0.017). Cases of older age, men, and those with diabetes had more severe electrophysiologic nerve affection (p<0.0001). In the linear regression analysis, increasing age (unstandardized B=0.03, 95% CI 0.02-0.04; p<0.0001) and presence of diabetes (unstandardized B=0.60, 95% CI 0.25-0.95; p=0.001) were associated with a higher risk of a worse electrophysiologic classification. Female sex was associated with a better electrophysiologic grading (unstandardized B=-0.51, 95% CI -0.75- -0.27; p<0.0001). We conclude that older age, male sex, and concomitant diabetes are associated with more severe preoperative electrophysiologic nerve affection. Preoperative electrophysiologic grade of ulnar nerve affection may influence surgical outcome.
Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins

Inteins catalyze their removal from a host protein through protein splicing. Inteins that contain an additional site-specific endonuclease domain display genetic mobility via a process termed “homing” and thereby act as selfish DNA elements. We elucidated the crystal structures of two archaeal inteins associated with an active or inactive homing endonuclease domain. This analysis illustrated structural diversity in the accessory domains (ACDs) associated with the homing endonuclease domain. To augment homing endonucleases with highly specific DNA cleaving activity using the intein scaffold, we engineered the ACDs and characterized their homing site recognition. Protein engineering of the ACDs in the inteins illuminated a possible strategy for how inteins could avoid their extinction but spread via the acquisition of a diverse accessory domain.
The use of a neural network to minimize the risks of positive assessment of academically dishonest students

The issue of neural network learning and research in this area are important criteria for measuring the technical level of research institutions, educational establishments, or enterprises. The possibilities of using neural networks have not been exhaustively studied so far. For many years to come, they will be a means for information technology development and will require highly qualified IT specialists. In Ukraine, a whole set of methods for assessing academic achievements, both in full-time and part-time studies, is being actively introduced into the educational process. Quality management is a key element of any modern educational system which requires effective means for objective control of students’ achievements and the elimination of academic dishonesty. The paper reviews and summarizes publications on neural network learning. It is proposed to use neural networks to identify dishonesty cases in examinations and tests and minimize the risks of incorrect determination of the attainment level of students.
De-problematizing masculinity among heterosexual African, Caribbean, and Black male youth and men

The dominant discourse in literature often constructs heterosexual African, Caribbean, and Black (ACB) masculinity as inherently problematic and in need of “correction, repair, or rescue. ” This discourse privileges hegemonic male standards and conceals the power relations that shape racialized masculinities. Our study of self-identified heterosexual ACB men and male youth examines how performative and perceptual attenuations of hegemonic masculinity can moderate social and behavioural vulnerabilities in the context of HIV prevention, transmission, and survival. We used descriptive qualitative methods informed by community-based participatory research. Individual in-depth interviews and focus group discussions were conducted with 63 ACB men and male youth (aged 16 and above) residing in Ottawa, Canada, including community leaders, HIV service providers, and decision makers. The interviews were transcribed verbatim, and thematically analyzed with NVivo software. Member-checking, peer debriefing, and external audit ensured trustworthiness of data. ACB men and male youth define masculinity by their ability to provide for, protect, love, and lead their families. Within ACB cultures, men demonstrate their masculinity through their traditional role as family breadwinners, and are expected to be strong, bold, and responsible. This positive view of masculinity is potentially beneficial to the well-being of ACB men and male youth, and challenges mainstream notions of Black masculinity as uncontrolled, risky, toxic, or even predatory. A positive view of masculinity among ACB heterosexual men and youth could support future practice and policy interventions aimed at strengthening community responses to HIV and health.