Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into Chlamydia pathogenesis: Role of leukemia inhibitory factor

Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted infections worldwide. Since the symptoms of Ct infection are often subtle or absent, most people are unaware of their infection until they are tested or develop severe complications such as infertility. It is believed that the primary culprit of Ct-associated tissue damage is unresolved chronic inflammation, resulting in aberrant production of cytokines, chemokines, and growth factors, as well as dysregulated tissue influx of innate and adaptive immune cells. A member of the IL-6 cytokine family, leukemia inhibitory factor (LIF), is one of the cytokines induced by Ct infection but its role in Ct pathogenesis is unclear. In this article, we review the biology of LIF and LIF receptor (LIFR)-mediated signaling pathways, summarize the physiological role of LIF in the reproductive system, and discuss the impact of LIF in chronic inflammatory conditions and its implication in Ct pathogenesis. Under normal circumstances, LIF is produced to maintain epithelial homeostasis and tissue repair, including the aftermath of Ct infection. However, LIF/LIFR-mediated signaling – particularly prolonged strong signaling – can gradually transform the microenvironment of the fallopian tube by altering the fate of epithelial cells and the cellular composition of epithelium. This harmful transformation of epithelium may be a key process that leads to an enhanced risk of infertility, ectopic pregnancy and cancer following Ct infection.
The emerging double-edged sword role of Sirtuins in the gastric inflammation-carcinoma sequence revealed by bulk and single-cell transcriptomes

Histone modification and the inflammation-carcinoma sequence (ICS) have been acknowledgedly implicated in gastric carcinogenesis. However, the extremum expression of some histone modification genes (HMGs) in intestinal metaplasia (IM) rather than GC obscures the roles of HMGs in ICS. In this study, we assumed an explanation that the roles of HMGs in ICS were stage specific. Bulk RNA-seq on endoscopy biopsy samples from a total of 50 patients was accompanied by reanalysis of a set of published single-cell transcriptomes, which cross-sectionally profiled the transcriptomic features of chronic superficial gastritis (SG), atrophy gastritis (AG), IM, and early gastric cancer (GC). Differential analysis observed significantly peaked expression of SIRT6 and SIRT7 at IM. Weighted correlation network analysis on bulk transcriptome recognized significant correlations between SIRT1/6 and IM. The single-cell atlas identified one subgroup of B cells expressing high level of TFF1 (TFF1 hi naive B cell) that theoretically played important roles in defending microbial infection, while SIRT6 displayed a positive correlation with TFF1 low naive B cells. Moreover, gene set enrichment analysis at different lesions (SG-AG, AG-IM, and IM-GC) highlighted that gene sets contributing to IM, e.g., Brush Border, were largely enriched from co-expressing genes of Sirtuins (SIRTs) in AG-IM. Surveys of the genes negatively correlated with SIRT6 in public databases considered SIRT6 as tumor suppressors, which was confirmed by the cell proliferation and migration assays after transient transfection of SIRT6 overexpression vector into AGS cells. All the above observations were then confirmed by serial section-based immunohistochemistry against Ki-67, MUC2, MUC5AC, p53, and SIRT6 on the endoscopic submucosal dissection tissue. By contrast, the expression of the other HMGs varied even opposite within same family. Taken together, this study preliminarily demonstrated the two-edged sword role of SIRTs in ICS and, by extension, showed that the roles of HMGs in ICS were probably stage specific. Our study may provide new insights into and attract attention on gastric prevention and therapy targeting HMGs.
Thermodynamics of Black Holes: Semi-Classical Approaches and Beyond

This thesis is focussed to study various aspects of black hole physics. Our approach is a semi-classical type, where the spacetime geometry of black holes is considered to be classical but the fields moving in the background are quantum in nature. Some notable facets of this thesis are the following. We start by looking into the issue of generalized Smarr mass formula for arbitrary dimensional black holes in Einstein-Maxwell gravity. We derive this formula for these black holes and also demonstrate that such a formula can be expressed in the form of a dimension independent identity $K_{\chi^{\mu}}=2ST$ (where the l.h.s is the Komar conserved charge corresponding to the null Killing vector $\chi^{\mu}$ and in the r.h.s $S, T$ are the semi-classical entropy and temperature of a black hole) defined at the black hole event horizon. We highlight the role of exact differentials in computations involving black hole thermodynamics. Some results like the first law of black hole thermodynamics and semi-classical entropy are obtained without using the laws of black hole mechanics as usually done. The blackbody (Hawking) radiation spectrum for higher dimensional black holes is computed by using a density matrix technique of tunneling mechanism by considering both event and cosmological horizons. We also provide the modifications to the semi-classical Hawking temperature and Bekenstein-Hawking entropy due to various effects. These modifications are mainly found due to higher order (in $\hbar$) effects to the WKB ansatz used for the quantum tunneling formalism and non-commutative gravity inspired effects. Finally, in we discuss phase transition phenomena in black holes. We formulate a new methodology based on Clausius-Clapeyron and Ehrenfest's equations to exhibit and classify phase transitions in black holes in analogy to what is done in standard thermodynamics.
The relationship between gender, marital status and depression among Chinese middle-aged and older people: Mediation by subjective well-being and moderation by degree of digitization

The purposes of this study were to investigate the effects of gender and marital status on depression among middle-aged and older people in China, and to explore the mediating effect of subjective well-being and the moderating effect of degree of digitization in the relationship between subjective well-being and depression. A total of 15,586 Chinese middle-aged and older people (≥ 45 years old) were included in the study using data from the 2018 China Health and Retirement Longitudinal Survey (CHARLS). T-test, ANOVA, hierarchical regression and Bootstrap methods were adopted to test the mediating role of subjective well-being and the moderating role of degree of digitization. The results showed that middle-aged and older women were more likely to suffer from depression than men, and married middle-aged and older people were less likely to be depressed than those who were separated or divorced, widowed and never married. Subjective well-being partially mediated the relationship between gender and depression, and masked the relationship between marital status and depression, and all five dimensions it contains also played a mediating role. Degree of digitization moderated the effect of subjective well-being on depression. Simple slope tests indicated that the effect of subjective well-being on depression increased as degree of digitization increased. In conclusion, to address the mental health problems of middle-aged and older people brought about by the ageing and digital society, we should start by improving their subjective well-being and promoting their integration into the digital society.
Fusion primer driven racket PCR: A novel tool for genome walking

The limitations of the current genome-walking strategies include strong background and cumbersome experimental processes. Herein, we report a genome-walking method, fusion primer-driven racket PCR (FPR-PCR), for the reliable retrieval of unknown flanking DNA sequences. Four sequence-specific primers (SSP1, SSP2, SSP3, and SSP4) were sequentially selected from known DNA (5'→3′) to perform FPR-PCR. SSP3 is the fragment that mediates intra-strand annealing (FISA). The FISA fragment is attached to the 5′ end of SSP1, generating a fusion primer. FPR-PCR comprises two rounds of amplification reactions. The single-fusion primary FPR-PCR begins with the selective synthesis of the target first strand, then allows the primer to partially anneal to some place(s) on the unknown region of this strand, producing the target second strand. Afterward, a new first strand is synthesized using the second strand as the template. The 3′ end of this new first strand undergoes intra-strand annealing to the FISA site, followed by the formation of a racket-like DNA by a loop-back extension. This racket-like DNA is exponentially amplified in the secondary FPR-PCR performed using SSP2 and SSP4. We validated this FPR-PCR method by identifying the unknown flanks of Lactobacillus brevis CD0817 glutamic acid decarboxylase genes and the rice hygromycin gene.
Higher-achieving children are better at estimating the number of books at home: Evidence and implications

The number of books at home is commonly used as a proxy for socioeconomic status in educational studies. While both parents’ and students’ reports of the number of books at home are relatively strong predictors of student achievement, they often disagree with each other. When interpreting findings of analyses that measure socioeconomic status using books at home, it is important to understand how findings may be biased by the imperfect reliability of the data. For example, it was recently suggested that especially low-achieving students tend to underestimate the number of books at home, so that use of such data would lead researchers to overestimate the association between books at home and achievement. Here we take a closer look at how students’ and parents’ reports of the number of books at home relate to literacy among fourth grade students, by analyzing data from more than 250,000 students in 47 countries participating in 2011 PIRLS. Contrary to prior claims, we find more downward bias in estimates of books at home among high-achieving students than among low-achieving students, but unsystematic errors appear to be larger among low-achieving students. This holds within almost every country. It also holds between countries, that is, errors in estimates of books at home are larger in low-achieving countries. This has implications for studies of the association between books at home and achievement: the strength of the association will generally be underestimated, and this problem is exacerbated in low-achieving countries and among low-achieving students.
Internet-based cognitive behavioral therapy in children and adolescents with obsessive-compulsive disorder: A randomized controlled trial

Objectives Obsessive-compulsive disorder (OCD) in childhood and adolescence often leads to significant impairment in various areas of life and has a high risk of becoming chronic. Cognitive behavioral therapy (CBT) is the recommended first-line treatment, but it is too rarely implemented in accordance with guidelines and is often not available close to the patient’s home. Importantly, internet-based CBT could help to reduce this gap in care. Having previously successfully demonstrated the feasibility of an internet-based CBT approach, we aimed to assess its effectiveness in a waiting list controlled randomized trial. Methods Children and adolescents aged 6–18 years with a principal diagnosis of OCD received 14 sessions of therapist-delivered CBT via videoconference distributed over 16 weeks. After inclusion, participants were randomly assigned to either the treatment or waiting list group. Participants in the treatment group began treatment immediately after baseline diagnostics, and participants in the waiting list group began treatment after a 16-week waiting period. The primary outcome was a pre-post comparison of OCD symptoms as measured with the Children’s Yale-Brown Obsessive Compulsive Scale (CY-BOCS). Additionally, remission was an important outcome measure. Follow-up assessments were conducted for all measures 16 and 32 weeks after completion of treatment. Results A total of 60 children and adolescents were included into the analyses. Over the course of the treatment, OCD symptoms according to the CY-BOCS significantly decreased in the treatment group compared to the waiting-list control group. Cohen’s d between groups was 1.63. After the patients in the waiting list group also received the treatment, the OCD symptoms decreased significantly in this group as well. This improvement of symptoms increased over the course of the follow-up assessments. Remission rate peaked at the 32-week follow-up, with 68% in the treatment group and 79% in the waiting list group. Importantly, patient satisfaction with treatment was high to very high. Conclusion In our study, OCD symptoms decreased significantly and remission rate was high after internet-based CBT. Those effects were comparable to those found in studies of face-to-face treatment. Although further evidence is needed, these are early indications that our approach may be a viable way to provide access to adequate treatment for children and adolescents affected by OCD. Clinical trial registration [www.ClinicalTrials. gov], identifier [NCT05037344].
Fire blight resistance, irrigation and conducive wet weather improve Erwinia amylovora winter survival in cankers

Erwinia amylovora causes fire blight, a disease responsible for enormous economic losses in the pome fruit-producing areas where it is present. Despite the abundant research on fire blight, information about E. amylovora population dynamics and survival in fire blight cankers and the plant defense responses to this pathogen in the infected bark are limited. In our study, we obtained fire blight cankers in apple, pear, and Asian pear cultivars showing differing resistance to the disease by shoot inoculation with E. amylovora. We collected cankers from irrigated and non-irrigated trees every 3 months in two independent field experiments and analyzed samples by viability digital PCR. We also assessed the expression of pathogenicity-related (PR) genes in the bark of selected apple and Asian pear cultivars. A logistic regression analysis revealed the impact of environmental and host factors on E. amylovora detection rates in cankers. The chances of detecting live E. amylovora cells in cankers increased significantly in those collected from irrigated trees, in July, and/or during an experiment performed in a year with an expected average rainfall when compared to samples from non-irrigated trees, collected in January, and/or during an experiment performed under environmental conditions dominated by drought. We found a positive correlation between the pathogen detection rates in cankers and the host resistance to fire blight that might be explained by lower E. amylovora survival rates in more damaged tissues of susceptible hosts. The genes PR-1, PR-2, PR-5, and PR-8 were induced in the bark surrounding apple and Asian pear fire blight cankers. Our study, involving the analysis of more than 800 canker samples, provides new knowledge about the fire blight disease cycle and lays the foundation for improved fire blight management and eradication strategies in pome fruit orchards.
Combinatorial classes on the moduli space of curves are tautological

The combinatorial description via ribbon graphs of the moduli space of Riemann surfaces makes it possible to define combinatorial cycles in a natural way. Witten and Kontsevich first conjectured that these classes are polynomials in the tautological classes. We answer affirmatively to this conjecture and find recursively all the polynomials.
The learning curve for robot-assisted radical cystectomy with total intracorporeal urinary diversion based on radical cystectomy pentafecta

Objective To analyze the learning curve for robot- assisted radical cystectomy (RARC) with total intracorporeal urinary diversion (ICUD) in terms of both time efficiency and quality of surgery based on radical cystectomy (RC)-pentafecta. Patients and methods We identified 203 consecutive patients who underwent RARC with ICUD of the ileal conduit (IC, 85) and orthotopic neobladder (ONB, 118) performed by a single surgeon between 2011 and 2021. We grouped ten consecutive patients into time-associated blocks according to the operation order. Process efficiency and operation quality were measured based on the surgeon’s console time and attainment/score sum of RC-pentafecta. The overcoming point of the learning curve was defined graphically and statistically. Results The mean follow-up period was 44.5 ± 30.7 months. Of the 203 patients, 109 (53.7%) attained the five criteria of RC-pentafecta (ONB vs IC, 50.6% vs. 55.9%, p = 0.35). The attainment rate and sum of the RC-pentafecta score of the third group were not significantly different from those of all patients (40.0% vs. 53.7%, p = 0.369, 4.00 ± 1.05 vs. 4.41 ± 0.75, p = 0.137, respectively), and the proficiency in operation quality was satisfactory in the third group. The console times continually improved and stabilized after the 140th case (IC, 60; ONB, 80), and the attainment rate and sum of the RC-pentafecta were significantly different between before and after the 140th case (p<0.001). Conclusion A single surgeon’s learning curve for RARC with ICUD and pelvic lymph node dissection (PLND) showed an acceptable level of proficiency after 30 consecutive cases in terms of the operation quality. However, for an expert surgeon, 140 cases were required to reach a plateau in time efficiency and second leap with the RC-pentafecta. RARC with ICUD and PLND can be performed safely without compromising functional outcomes and complications through sharing and transmission of standardized techniques.
Sub-surface plasma flows and the flare productivity of solar active regions

The extreme space weather conditions resulting from high energetic events likes solar flares and Coronal Mass Ejections demand for reliable space weather forecasting. The magnetic flux tubes while rising through the convection zone gets twisted by the turbulent plasma flows, energizing the system and resulting in flares. We investigate the relationship between the subsurface plasma flows associated with flaring active regions and their surface magnetic flux and current helicity. The near-surface horizontal velocities derived from the ring-diagram analysis of active region patches using Global Oscillation Network Group Doppler velocity measurements are used to compute the fluid dynamics descriptors like vertical divergence, vorticity and kinetic helicity used in this work. The flaring active regions are observed to have large value of vertical vorticity and kinetic helicity. Also, the horizontal flow divergence, vorticity, flux, kinetic and current helicities are observed to be significantly correlated and evolve in phase with each other. We observe that the integrated values of the above flow and magnetic parameters observed 1 day prior to the flare are significantly correlated with the integrated flare intensity of the active region. Hence, we show that strong vorticity/kinetic helicities lead to larger active region twisting, presumably generating high-intensity flares.
Commentary: Editorial—Whole-body electromyostimulation: A training technology to improve health and performance in humans? volume II

We read with interest the recent study by Kemmler et al., 2022 reporting the feasibility and ef ﬁ ciency of whole-body electromyostimulation (WB-EMS) training for addressing important health-related outcomes in different populations such as healthy adults, people with low back pain, people with knee osteoarthritis, frail older people, and critically ill patients. We commend the authors for addressing this valuable training method that should be further studied due to its increasing popularity, time ef ﬁ ciency, joint-friendliness, and individualized application, which has increasingly been the subject of scienti ﬁ c research. Therefore, we intend to contribute to discussing the bene ﬁ ts of WB-EMS training speci ﬁ cally for older people. Our recent systematic review (de Oliveira compiled data on 283 older people aged 69 and 83 with metabolic syndrome, sarcopenic obesity, and sedentary lifestyles. Based on a subgroup analysis of our meta-analysis, it was possible to observe some differences in health-related outcomes between training with WB-EMS performed at different time points with or without the addition of protein supplementation,
A web-based novel prediction model for predicting depression in elderly patients with coronary heart disease: A multicenter retrospective, propensity-score matched study

Background Depression is associated with an increased risk of death in patients with coronary heart disease (CHD). This study aimed to explore the factors influencing depression in elderly patients with CHD and to construct a prediction model for early identification of depression in this patient population. Materials and methods We used propensity-score matching to identify 1,065 CHD patients aged ≥65 years from four hospitals in Chongqing between January 2015 and December 2021. The patients were divided into a training set (n = 880) and an external validation set (n = 185). Univariate logistic regression, multivariate logistic regression, and least absolute shrinkage and selection operator regression were used to determine the factors influencing depression. A nomogram based on the multivariate logistic regression model was constructed using the selected influencing factors. The discrimination, calibration, and clinical utility of the nomogram were assessed by the area under the curve (AUC) of the receiver operating characteristic curve, calibration curve, and decision curve analysis (DCA) and clinical impact curve (CIC), respectively. Results The predictive factors in the multivariate model included the lymphocyte percentage and the blood urea nitrogen and low-density lipoprotein cholesterol levels. The AUC values of the nomogram in the training and external validation sets were 0.762 (95% CI = 0.722–0.803) and 0.679 (95% CI = 0.572–0.786), respectively. The calibration curves indicated that the nomogram had strong calibration. DCA and CIC indicated that the nomogram can be used as an effective tool in clinical practice. For the convenience of clinicians, we used the nomogram to develop a web-based calculator tool (https://cytjt007.shinyapps.io/dynnomapp_depression/). Conclusion Reductions in the lymphocyte percentage and blood urea nitrogen and low-density lipoprotein cholesterol levels were reliable predictors of depression in elderly patients with CHD. The nomogram that we developed can help clinicians assess the risk of depression in elderly patients with CHD.