Miracle-dz/UniFAR-FTUs huggingface dataset:
Sperm DNA fragmentation testing: Summary evidence and clinical practice recommendations

We herein summarise the evidence concerning the impact of sperm DNA fragmentation in various clinical infertility scenarios and the advances on sperm DNA fragmentation tests. The collected evidence was used to formulate 41 recommendations. Of these, 13 recommendations concern technical aspects of sperm DNA fragmentation testing, including pre‐analytical information, clinical thresholds and interpretation of results. The remaining 28 recommendations relate to indications for sperm DNA fragmentation testing and clinical management. Clinical scenarios like varicocele, unexplained infertility, idiopathic infertility, recurrent pregnancy loss, intrauterine insemination, in vitro fertilisation/intracytoplasmic sperm injection, fertility counselling for men with infertility risk factors and sperm cryopreservation have been contemplated. The bulk evidence supporting the recommendations has increased in recent years, but it is still of moderate to low quality. This guideline provides clinicians with advice on best practices in sperm DNA fragmentation testing. Also, recommendations are provided on possible management strategies to overcome infertility related to sperm DNA fragmentation, based on the best available evidence. Lastly, we identified gaps in knowledge and opportunities for research and elaborated a list of recommendations to stimulate further investigation.
Validation of insomnia questionnaires in the general population: The Nord‐Trøndelag Health Study (HUNT)

The primary aim was to validate questionnaire‐based insomnia diagnoses from a modified Karolinska Sleep Questionnaire (KSQ) and the Insomnia Severity Index (ISI), by age category (< or >65 years), against a semi‐structured face‐to‐face interview. Secondary aims were to split validity by diagnostic certainty of the interview and to compare prevalence estimates of questionnaire‐ and interview‐based diagnoses. A total of 232 out of 1,200 invited (19.3%) from the fourth Nord‐Trøndelag Health Study (HUNT4) completed questionnaires, including the KSQ and ISI, shortly before attending a face‐to‐face diagnostic interview for insomnia based on the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM‐5). Both a tentative (DSM‐5 criteria A–E) and a definite (criteria A–H) interview diagnosis was evaluated. Cohen’s kappa statistic quantified questionnaire validity. In all, 33% (95% confidence interval 27–39%) of participants had definite insomnia: 40% of women and 21% of men. The ISI (cut‐off 12) and several KSQ‐based diagnoses showed very good validity (κ ≤0.74) against the tentative, versus good validity (κ ≤0.61) against the definite interview diagnosis. Short questionnaires, requiring a daytime symptom at least three times a week, may underestimate insomnia prevalence. Validity was consistently higher for persons aged below versus above 65 years (definite insomnia: κ ≤0.64 vs. κ ≤0.56). Our results have implications for epidemiological population‐based studies utilising insomnia questionnaires.
VDRF: Sensing the defect information to risk level of vehicle recall based on bert communication model

The recall of defective automobile products is one of the important measures to promote the quality of product quality and protect consumers' pyhsical safety and property security. In order to assess the risk level of defect cases, automobile recall management experts need to analyze and discuss the defect information by personal. A risk level prediction method based on language pre-training Bert model is proposed in this paper, which can transform the defect information into rick level of the vehicle and then predict vehicle recall automatically, in which a seq2seq model is proposed to multi-label the vehicle complaint data. The outputs of the seq2seq model combined with other static and dynamic information are used as the input of the Bert communication model. Substantial comparative experiments of different feature combinations on different methods show that the proposed VDRF method achieves F1 value with 79% in vehicle recall risk prediction, which outperforms the traditional method.
Multi-source domain adaptation for decoder calibration of intracortical brain-machine interface

Objective. For nonstationarity of neural recordings, daily retraining is required in the decoder calibration of intracortical brain-machine interfaces (iBMIs). Domain adaptation (DA) has started to be applied in iBMIs to solve the problem of daily retraining by taking advantage of historical data. However, previous DA studies used only a single source domain, which might lead to performance instability. In this study, we proposed a multi-source DA algorithm, by fully utilizing the historical data, to achieve a better and more robust decoding performance while reducing the decoder calibration time. Approach. The neural signals were recorded from two rhesus macaques using intracortical electrodes to decode the reaching and grasping movements. A principal component analysis (PCA)-based multi-source domain adaptation (PMDA) algorithm was proposed to apply the feature transfer to diminish the disparities between the target domain and each source domain. Moreover, the multiple weighted sub-classifiers based on multi-source domain data and small current sample set were constructed to accomplish the decoding. Main results. Our algorithm was able to make use of the multi-source domain data and achieve better and more robust decoding performance compared with other methods. Only a small current sample set was needed by our algorithm in order for the decoder calibration time to be effectively reduced. Significance. (1) The idea of the multi-source DA was introduced into the iBMIs to solve the problem of time consumption in the daily decoder retraining. (2) Instead of using only single-source domain data in the previous study, our algorithm made use of multi-day historical data, resulting in better and more robust decoding performance. (3) Our algorithm could be accomplished with only a small current sample set, and it can effectively reduce the decoder calibration time, which is important for further clinical applications.
CircTET1 Inhibits Retinoblastoma Progression via Targeting miR-492 and miR-494-3p through Wnt/β-catenin Signaling Pathway

ABSTRACT Purpose: Retinoblastoma (RB) is a frequent intraocular malignancy in children. Circular RNA (circRNA) plays an essential role in regulating the occurrence and development of tumors. This study aimed at investigating the function and molecular basis of hsa_circ_0093996 (circTET1) in RB. Methods: The expression of circTET1, miR-492 and miR-494-3p was examined using quantitative real-time polymerase chain reaction. Cell proliferation, cycle arrest, apoptosis, migration and invasion of RB cells were detected using Cell Counting Kit-8 (CCK-8), colony formation assay, flow cytometry, scratch assay and transwell analysis, respectively. The levels of matrix metalloproteinase (MMP) 2, MMP9 and Wnt/β-catenin pathway-related proteins were measured via western blot assay. The association between circTET1 and miR-492/miR-494-3p was validated via dual-luciferase reporter assay and RNA pull-down assay. Xenograft assay was employed to analyze tumor growth in vivo. Results: CircTET1 level was reduced, while miR-492 and miR-494-3p levels were increased in RB tissues and cells. Overexpression of circTET1 inhibited proliferation, migration and invasion, and promoted apoptosis and cell cycle arrest in Y79 and WERI-Rb1 cells. Moreover, circTET1 impeded RB cell progression by sponging miR-492/miR-494-3p. Also, up-regulation of circTET1 restrained Wnt/β-catenin pathway via regulating miR-492 and miR-494-3p. Furthermore, circTET1 suppressed tumor growth in xenograft models. Conclusion: CircTET1 inhibited RB progression by sponging miR-492/miR-494-3p and inactivating the Wnt/β-catenin pathway, which provided new insights for RB treatment.
Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding

The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CAP, which entails repositioning of DNA recognition helices (F-helices) in the DBD to dock favorably to the target DNA. Despite considerable progress, much remains to be understood about the mechanistic details of DNA recognition by CAP and about the map of allosteric pathways involved in CAP-mediated gene transcription. The present study uses molecular dynamics and umbrella sampling simulations to investigate the mechanism of cAMP- and DNA-induced changes in the conformation and energetics of F-helices observed during the allosteric regulation of CAP by cAMP and the subsequent binding to the DNA promoter region. Using novel collective variables, the free energy profiles associated with the orientation and dynamics of F-helices in the unliganded, cAMP-bound, and cAMP-DNA-bound states of CAP are calculated and compared. The binding-induced alterations in the resultant free energy profiles reveal important flexibility constraints imposed on DBD upon cAMP and DNA binding. A comprehensive analysis of residue-wise interaction maps reveals potential allosteric pathways between CBD and DBD that facilitate the allosteric transduction of regulatory signals in CAP. The revelation that the predicted allosteric pathways crisscross the intersubunit interface offers important clues on the microscopic origin of the intersubunit cooperativity and dimer stability of CAP.
Stress and burnout in psychology doctoral students

ABSTRACT Psychology Doctoral Students (PDS) have to deal with highly emotional situations with their clients and academic demands that can cause stress. However, there is limited research examining stress and burnout in PDS. This study aimed to examine levels of stress in PDS students compared to the general population and to analyze levels of stress and burnout per year in the program. An online survey was distributed among both PDS currently enrolled in APA-accredited clinical and counseling psychology doctoral programs and individuals in the general population. A total of 204 (67.3%) participants were PDS and 99 (32.7%) were from the general population. There were no significant differences in levels of stress between the PDS and participants from the general population. Third- and fourth-year students (grouped together) reported a significantly higher level of stress than PDS in other years (p=.00). Similarly, third- and fourth-year students (grouped together) reported significantly higher scores in the burnout emotional exhaustion subscale, than the rest of the students (p=.04). Stress levels in PDS were similar to those in the general population. Within PDS those in their third and fourth year of their programs presented higher levels of stress and more emotional exhaustion. Implications will be discussed.
Hospitalised COVID-19 patients of the Mount Sinai Health System: a retrospective observational study using the electronic medical records

Objective To assess association of clinical features on COVID-19 patient outcomes. Design Retrospective observational study using electronic medical record data. Setting Five member hospitals from the Mount Sinai Health System in New York City (NYC). Participants 28 336 patients tested for SARS-CoV-2 from 24 February 2020 to 15 April 2020, including 6158 laboratory-confirmed COVID-19 cases. Main outcomes and measures Positive test rates and in-hospital mortality were assessed for different racial groups. Among positive cases admitted to the hospital (N=3273), we estimated HR for both discharge and death across various explanatory variables, including patient demographics, hospital site and unit, smoking status, vital signs, lab results and comorbidities. Results Hispanics (29%) and African Americans (25%) had disproportionately high positive case rates relative to their representation in the overall NYC population (p<0.05); however, no differences in mortality rates were observed in hospitalised patients based on race. Outcomes differed significantly between hospitals (Gray’s T=248.9; p<0.05), reflecting differences in average baseline age and underlying comorbidities. Significant risk factors for mortality included age (HR 1.05, 95% CI 1.04 to 1.06; p=1.15e-32), oxygen saturation (HR 0.985, 95% CI 0.982 to 0.988; p=1.57e-17), care in intensive care unit areas (HR 1.58, 95% CI 1.29 to 1.92; p=7.81e-6) and elevated creatinine (HR 1.75, 95% CI 1.47 to 2.10; p=7.48e-10), white cell count (HR 1.02, 95% CI 1.01 to 1.04; p=8.4e-3) and body mass index (BMI) (HR 1.02, 95% CI 1.00 to 1.03; p=1.09e-2). Deceased patients were more likely to have elevated markers of inflammation. Conclusions While race was associated with higher risk of infection, we did not find racial disparities in inpatient mortality suggesting that outcomes in a single tertiary care health system are comparable across races. In addition, we identified key clinical features associated with reduced mortality and discharge. These findings could help to identify which COVID-19 patients are at greatest risk of a severe infection response and predict survival.
Genetic analysis of an improved tilapia line selected for high growth in saline water

To date, commercial strains of Nile tilapia (Oreochromis niloticus, L.) are not available for aquaculture in saline water environments. The overarching objective of my PhD thesis was to develop a genetically improved strain of Nile tilapia not only having fast growth but also with good adaptation to a range of production systems. Specific aims of this study/thesis were: i) To assess genetic progress achieved from a selection program for high growth in moderately saline water (15 – 20 ppt); ii) Examine whether selection in a challenging environment produces Nile tilapia genotypes that can thrive in a range of production systems; iii) Estimate genetic variation for novel traits such as early survival of Nile tilapia fry during the early phase of rearing in brackish water environment (5 – 10 ppt); iv) Evaluate growth, physiological parameters, flesh and eating qualities of three genetically improved tilapia strains reared in fresh and saline waters; and v) Identify genes and gene expression associated with growth and salinity tolerance in the selected line cultured in both moderate saline- and fresh-water. Genetic evaluation of the selection program involved 36,145 animals with individual body traits records collected over seven generations from 2007 to 2014. They were offspring of 564 sires and 754 dams. Restricted Maximum Likelihood (REML) method applied to a multi-trait mixed model analysis showed a significant improvement in growth performance with an average genetic gain of 7 – 8% per generation (one generation was completed per year). The selection program for high growth, however, did not have detrimental effects on survival rate during grow-out. The estimate of heritability for the selection criterion (i.e. body weight) was moderate, suggesting that the population will continue showing response to future selection. ; Submitted in the fulfilment of the requirements of the degree of Doctor of Philosophy, University of the Sunshine Coast, 2017.
Post-antibiotic Effects and Post-sub-minimal Inhibitory Concentration Effects of Cetylpyridinium Chloride on Streptococcus gordonii and Streptococcus mutans

Background and Objectives: When an antimicrobial agent is removed after the treatment of bacteria for a short period, it takes a long time for the bacteria to return to normal growth, despite the reduction in the antimicrobial agent concentration. This phenomenon is referred to the postantibiotic effect (PAE). The PAE of cetylpyridinium chloride, which is a common ingredient in oral mouthwash solutions, has not yet been elucidated. We evaluated the post-antibiotic effect (PAE), post-antibiotic sub-MIC effect (PA SME), and sub-MIC effect (SME) for cetylpyridinium chloride in Streptococcus gordonii, which is known to be an early colonizer of the tooth surface, and Streptococcus mutans, a causative agent of dental caries. Materials and Methods: After cetylpyridinium chloride was applied to bacteria, PAE, PASME and SME were measured to investigate the time to recovery of bacterial growth. Results: The mean PAE times for S. gordonii and S. mutans were 1 h and 1.07 h, respectively. Original Research Article Lee and Lee; JAMB, 9(2): 1-5, 2018; Article no.JAMB. 39739 2 When the PA SME was compared with the PAE, the PA SME was longer than the PAE in both S. gordonii and S. mutans. Conclusion: In this study, it was shown that cetylpyridinium chloride can cause a PAE, PA SME and SME; therefore, this pharmacodynamic effect should be expected in the clinical application of cetylpyridinium chloride.
The Monocyte/High Density Lipoprotein Cholesterol Ratio (MHR) as an Indicator of the Need for Amputation in Patients With Peripheral Artery Disease Developing Critical Limb Ischemia

The monocyte/high density lipoprotein cholesterol ratio (MHR) reflects the proatherogenic and antiatherogenic balance, and a high ratio is associated with the severity of atherosclerosis. We measured the MHR of patients with critical limb ischemia (CLI) due to peripheral artery disease (PAD) requiring amputation. Patients diagnosed with PAD were divided into 2 groups; those who underwent an amputation due to CLI without any sign of infection and those treated with surgical or percutaneous revascularization or followed up medically. A healthy control group was also included. In patients diagnosed with PAD (n = 563), the MHR value was higher for the control group (n = 200), (12.4 ± 0.42 vs 11.5 ± 0.28, P < .001). In the amputation group, the MHR was significantly higher for the group treated by other methods (15.7 ± 1.52 vs 12.8 ± 1.45, P < .001). Possible confounding factors affecting the MHR value were determined by the univariate regression analysis, and the multiple regression analysis revealed that MHR was an independent predictor of amputation in patients with PAD (P < .001). This study suggests that the MHR may be the predictor of amputation risk in patients with PAD and CLI.
Use of mannan oligosaccharide in broiler diets: an overview of underlying mechanisms

Antibiotic resistance has led poultry nutritionists to find alternatives for antibacterial growth promoters in broilers. Among these substitutes, one is mannan oligosaccharides (MOS), a yeast cell wall derived prebiotic. MOS decreases the load of pathogenic bacteria through 1) binding bacterial type-1 fimbriae 2) increasing goblet cells which produce bactericidal mucin and 3) providing favourable environment for the growth of beneficial bacteria leading to competitive exclusion. Balance between pathogenic and beneficial bacteria causes increase in villus length and decrease in crypt depth which are biomarkers for gut morphological improvement. As structure is equal to function, improvement in intestinal morphology increases activity of digestive enzymes and ultimately improves digestion. Besides these, immunomodulatory effect of MOS activates macrophages of gut associated lymphoid tissues resulting in improvement in cellular, humoral and cutaneous immunity. MOS also increases production of butyric acid and decrease pH of intestine in broilers. Though these combined mechanisms, MOS improves growth rate and performance of broilers.
Partially replacing sorghum silage with cactus (Opuntia stricta) cladodes in a soybean oil-supplemented diet markedly increases trans-11 18:1, cis-9, trans-11 CLA and 18:2 n-6 contents in cow milk.

Based on low 18:0 contents observed in milk fat of cows fed cactus cladodes (CC), we hypothesized that including Opuntia stricta cladodes in a soybean oil (SO)-supplemented diet would promote incomplete rumen biohydrogenation of supplemental PUFA, leading to increased trans-11 18:1 and cis-9, trans-11 CLA contents in milk. Twelve Holstein cows were used in a two-period study: (a) Baseline: all cows received a total mixed ration (TMR) composed of sorghum silage (SS) and a concentrate containing no SO for 14 days; (b) Treatment: cows received one of the following SO-supplemented diets for 21 days: (1) SS-TMR: a TMR composed of SS and a SO-enriched concentrate, (2) CC-TMR: a TMR containing CC as a partial substitute for SS plus the SO-enriched concentrate, and (3) CC-PMR: same diet as in treatment 2, but CC were mixed with the SO-enriched concentrate and fed as a partial mixed ration (PMR). Both CC diets increased relative abundances of trans-11 18:1, cis-9, trans-11 CLA, and 18:2 n-6 in milk fat, whereas opposite effects were observed on 18:0 and cis-9 18:1. Proportion of 18:2 n-6 increased, and cis-9, trans-11 CLA tended to increase with CC-PMR as compared to CC-TMR, whereas 18:3 n-3 was higher with CC-PMR than with SS-TMR. Proportions of several odd- and branched-chain fatty acids, certain 18:1 isomers, and trans-9, cis-11 CLA changed with CC diets, notably with CC-PMR. Milk yield and intake of most nutrients (except fibre) increased or tended to increase with the CC diets, whereas gross milk composition was unaltered. Stearoyl-CoA desaturase-1 index for C18 (SCD18 ) was higher with CC-PMR than with SS-TMR, and milk n-6:n-3 FA ratio and apparent transfer of 18:2 n-6 to milk increased with CC diets. These results indicate that Opuntia stricta cladodes can be a valuable feed ingredient for improving the nutraceutical value of milk fat.
Design Comorbidity Portfolios to Improve Treatment Cost Prediction of Asthma Using Machine Learning

Comorbidity is an important factor to consider when trying to predict the cost of treating asthma patients. When an asthmatic patient suffered from comorbidity, the cost of treating such a patient becomes dependent on the nature of the comorbidity. Therefore, lack of recognition of comorbidity on asthmatic patient poses a challenge in predicting the cost of treatment. In this study, we proposed a comorbidity portfolio design that improves the prediction cost of treating asthmatic patients by regrouping frequently occurred comorbidities in different cost groups. In the experiment, predictive models, including logistic regression, random forest, support vector machine, classification regression tree, and backpropagation neural network were trained with real-world data of asthmatic patients from 2012 to 2014 in a large city of China. The 10-fold cross validation and random search algorithm were employed to optimize the hyper-parameters. We recorded significant improvements using our model, which are attributed to comorbidity portfolios in area under curve (AUC) and sensitivity increase of 46.89% (standard deviation: 4.45%) and 101.07% (standard deviation: 44.94%), respectively. In risk analysis of comorbidity on cost, respiratory diseases with a cumulative proportion in the adjusted odds ratio of 36.38% (95%CI: 27.61%, 47.86%) and circulatory diseases with a cumulative proportion in the adjusted odds ratio of 23.83% (95%CI: 15.95%, 35.22%) are the dominant risks of asthmatic patients that affects the treatment cost. It is found that the comorbidity portfolio is robust, and provides a better prediction of the high-cost of treating asthmatic patients. The preliminary characterization of the joint risk of multiple comorbidities posed on cost are also reported. This study will be of great help in improving cost prediction and comorbidity management.