Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth of HIV-1 Molecular Transmission Clusters in New York City

Background HIV-1 genetic sequences can be used to infer viral transmission history and dynamics. Throughout the United States, HIV-1 sequences from drug resistance testing are reported to local public health departments. Methods We investigated whether inferred HIV transmission network dynamics can identify individuals and clusters of individuals most likely to give rise to future HIV cases in a surveillance setting. We used HIV-TRACE, a genetic distance-based clustering tool, to infer molecular transmission clusters from HIV-1 pro/RT sequences from 65736 people in the New York City surveillance registry. Logistic and LASSO regression analyses were used to identify correlates of clustering and cluster growth, respectively. We performed retrospective transmission network analyses to evaluate individual- and cluster-level prioritization schemes for identifying parts of the network most likely to give rise to new cases in the subsequent year. Results Individual-level prioritization schemes predicted network growth better than random targeting. Across the 3600 inferred molecular transmission clusters, previous growth dynamics were superior predictors of future transmission cluster growth compared to individual-level prediction schemes. Cluster-level prioritization schemes considering previous cluster growth relative to cluster size further improved network growth predictions. Conclusions Prevention efforts based on HIV molecular epidemiology may improve public health outcomes in a US surveillance setting.
Attention-deficit hyperactivity disorder and addictions (substance and behavioral): Prevalence and characteristics in a multicenter study in France

Aim The aim of this study is to determine the possible links between attention-deficit hyperactivity disorder (ADHD) and the presence of concomitant addictions with or without substance use in a French student population. Measures A battery of questionnaire measuring socioeconomic characteristics, university curriculum, ADHD (Wender Utah Rating Scale and Adult ADHD Self-Report Scale), substance consumptions (alcohol, tobacco, and cannabis), and behavioral addictions [(eating disorders (SCOFF)], Internet addiction (Internet Addiction Test), food addiction (Yale Food Addiction Scale), compulsive buying (Echeburua’s), and problem gambling (The Canadian Problem Gambling Index)] and measures of physical activity (Godin’s Leisure Time Exercise Questionnaire) was filled up by university students in Rouen and Nanterre in France. Results A total of 1,517 students were included (472 from Paris Nanterre and 1,042 from Rouen). The mean age was 20.6 years (SD = 3.6) and the sex ratio male to female was 0.46. The prevalence of ADHD among the students (current ADHD with a history of ADHD in childhood) was 5.6%. A quarter (25.7%) of students had already repeated their university curriculum, compared to 42.2% among the students with ADHD. Students with possible ADHD had repeated classes more often and believed to have a lower academic level than the students without ADHD. Significant differences were found as students with ADHD were less likely to succeed in their studies (repeated classes more often) than non-ADHD students, and considered their academic level to be lower. They also had significantly higher scores on substance (alcohol, cannabis, and tobacco) as well as behavioral addictions (gambling, compulsive buying disorder, eating disorders, and Internet addiction). Conclusion It seems essential to determine students’ problems and propose interventions adapted to students’ needs, in order to reduce the negative impact on their future academic and global successes.
Value of bone marrow biopsy in Hodgkin lymphoma patients staged by FDG PET: results from the German Hodgkin Study Group trials HD16, HD17, and HD18

Background Bone marrow (BM) involvement defines advanced-stage Hodgkin lymphoma and thus has impact on the assignment to treatment. Our aim was to evaluate whether the established BM biopsy may be omitted in patients if 18F-fluorodeoxyglucose positron emission tomography (PET) scanning is carried out during staging. Patients and methods Our analysis set consisted of 832 Hodgkin lymphoma patients from the German Hodgkin Study Group trials HD16, HD17, and HD18 who underwent both PET scanning and BM biopsy before treatment. All PET studies were centrally reviewed and BM was categorized as showing focal involvement or not. Results Taking BM biopsy as reference standard, baseline PET showed a negative predictive value of 99.9% [95% confidence interval (CI) 99.2% to 100%] with true-negative results in 702 of 703 cases. The sensitivity of PET for detecting BM involvement was 95.0% (95% CI 75.1% to 99.9%) as it could identify 19 out of 20 patients with positive BM biopsy. Moreover, PET found 110 additional subjects with focal BM lesions who would have been considered negative by biopsy. Conclusions When compared with BM biopsy, PET was able to detect focal BM lesions in a large number of additional patients. This indicates that conventional BM biopsy may substantially underestimate the actual incidence of BM involvement. Given the high negative predictive value, baseline PET scanning can safely be used to exclude BM involvement in Hodgkin lymphoma. BM biopsy should be considered only in such patients in whom PET-detected lesions lead to a change of treatment protocol. Registered trials The trials included in this analysis were registered at ClinicalTrials.gov: HD16-NCT00736320, HD17-NCT01356680, and HD18-NCT00515554.
Aqueous Synthesis of Ultrathin Platinum/Non-Noble Metal Alloy Nanowires for Enhanced Hydrogen Evolution Activity.

Although aqueous synthesis of nanocrystals is advantageous in terms of the cost, convenience, environmental friendliness, and surface cleanness of the product, nanocrystals of Pt and non-noble metal alloys are difficult to obtain with controlled morphology and composition from this synthesis owing to a huge gap between the reduction potentials of respective metal salts. This huge gap could now be remedied by introducing a sulfite into the aqueous synthesis, which is believed to resemble an electroless plating mechanism, giving rise to a colloid of Pt-M (M=Ni, Co, Fe) alloy nanowires with an ultrasmall thickness (ca. 2.6 nm) in a high yield. The sulfite also leads to the formation of surface M-S bonds and thus atomic-level Pt/M-S(OH) interfaces for greatly boosted hydrogen evolution kinetics under alkaline conditions. An activity of 75.3 mA cm-2 has been achieved with 3 μg of Pt in 1 m KOH at an overpotential of 70 mV, which is superior to previously reported catalysts.
Cooperating yet distinct brain networks engaged during naturalistic paradigms: A meta-analysis of functional MRI results

Cognitive processes do not occur by pure insertion and instead depend on the full complement of co-occurring mental processes, including perceptual and motor functions. As such, there is limited ecological validity to human neuroimaging experiments that use highly controlled tasks to isolate mental processes of interest. However, a growing literature shows how dynamic, interactive tasks have allowed researchers to study cognition as it more naturally occurs. Collective analysis across such neuroimaging experiments may answer broader questions regarding how naturalistic cognition is biologically distributed throughout the brain. We applied an unbiased, data-driven, meta-analytic approach that uses k-means clustering to identify core brain networks engaged across the naturalistic functional neuroimaging literature. Functional decoding allowed us to, then, delineate how information is distributed between these networks throughout the execution of dynamical cognition in realistic settings. This analysis revealed seven recurrent patterns of brain activation, representing sensory, domain-specific, and attentional neural networks that support the cognitive demands of naturalistic paradigms. Though gaps in the literature remain, these results suggest that naturalistic fMRI paradigms recruit a common set of networks that that allow both separate processing of different streams of information and integration of relevant information to enable flexible cognition and complex behavior.
Dual effects of baicalin on osteoclast differentiation and bone resorption

Osteoclasts (OC) are critical cells responsible for many bone diseases such as osteoporosis. It is of great interest to identify agents that can regulate the activity of OC to treat osteolytic bone diseases. In this study, we found that baicalin exerted a two‐way regulatory effect on OC in a concentration‐dependent manner in vitro and in vivo. In detail, baicalin at a low concentration (below 1 μmol/L) enhanced OC differentiation and bone resorption, but baicalin at a high concentration (above 2 μmol/L) exhibited inhibitory effects on OC. We demonstrated that baicalin at low concentrations enhanced the mitogen‐activated protein kinase (MAPK) (ERK) signalling pathway and activated c‐Fos and NFATc1 expression, and thus enhanced gene expression, OC differentiation and bone resorption. However, baicalin at higher levels not only suppressed ERK phosphorylation and c‐fos and NFATc1 expression, but also altered the expression of apoptosis‐related proteins, and therefore inhibiting OC function. This dual effect was further verified in an LPS‐induced mouse calvarial osteolysis model, evidenced by enhanced osteolysis at a lower concentration but reduced bone loss at a higher concentration. Overall, our findings indicate that baicalin exerts dose‐dependent effects on OC formation and function. Therefore, caution should be applied when using baicalin to treating OC‐related bone diseases.
Accumulation of Multiple Mutations In Vivo Confers Cross-Resistance to New and Existing Integrase Inhibitors

Bictegravir (BIC) and cabotegravir (CAB) are the latest available HIV integrase inhibitors in clinical trials. The combination of major integrase inhibitor substitutions G140S/Q148H has been shown to confer high-level resistance to the approved integrase inhibitors raltegravir (RAL) and elvitegravir (EVG) but not necessarily dolutegravir (DTG). We assayed recombinant viruses made from patient-derived RNA extracts for resistance phenotype for a panel of viruses containing G140S/Q148H with additional accessory substitutions. The accumulation of multiple integrase substitutions confers high-level resistance to all 5 integrase inhibitors. There is extensive cross-resistance between DTG, BIC, and CAB (r = 0.96-0.97).
Hadamard Coding for Supervised Discrete Hashing

In this paper, we propose a learning-based supervised discrete hashing (SDH) method. Binary hashing is widely used for large-scale image retrieval as well as video and document searches, because the compact binary code representation is essential for data storage and reasonable for query searches using bit operations. The recently proposed SDH method efficiently solves mixed-integer programming problems by alternating optimization and the discrete cyclic coordinate descent (DCC) method. Based on some preliminary experiments, we show that the SDH method can be simplified without performance degradation. We analyze the simplified model and provide a mathematically exact solution thereof; we reveal that the exact binary code is provided by a “Hadamard matrix. ” Therefore, we named our method Hadamard coded-SDH (HC-SDH). In contrast to the SDH, our model does not require an alternating optimization algorithm and does not depend on initial values. The HC-SDH is also easier to implement than the iterative quantization. Experimental results involving a large-scale database show that the Hadamard coding outperforms the conventional SDH in terms of precision, recall, and computational time. On the large data sets SUN-397 and ImageNet, the HC-SDH provides a superior mean average of precision (mAP) and top-accuracy compared with the conventional SDH methods with the same code length and FastHash. The training time of the HC-SDH is 170 times faster than the conventional SDH and the testing time including the encoding time is seven times faster than the FastHash which encodes using a binary-tree.
Effects of anesthesia on cerebral blood flow, metabolism, and neuroprotection

Administration of anesthetic agents fundamentally shifts the responsibility for maintenance of homeostasis from the patient and their intrinsic physiological regulatory mechanisms to the anesthesiologist. Continuous delivery of oxygen and nutrients to the brain is necessary to prevent irreversible injury and arises from a complex series of regulatory mechanisms that ensure uninterrupted cerebral blood flow. Our understanding of these regulatory mechanisms and the effects of anesthetics on them has been driven by the tireless work of pioneers in the field. It is of paramount importance that the anesthesiologist shares this understanding. Herein, we will review the physiological determinants of cerebral blood flow and how delivery of anesthesia impacts these processes.
Targeting glypican‐4 overcomes 5‐FU resistance and attenuates stem cell–like properties via suppression of Wnt/β‐catenin pathway in pancreatic cancer cells

The existences of cancer stem cells in patients with pancreatic cancer are considered as pivotal factors contributing to chemoresistance and disease relapse. Glypican‐4 (GPC4) is one of the members of the glypicans family, which underlies human congenital malformations and multiple diseases. However, its potential biological function in pancreatic cancer still remains elusive. In this study, we are the first to demonstrate that GPC4 was involved in 5‐fluorouracil (5‐FU) resistance and pancreatic cancer stemness through comprehensive bioinformatical analysis. Functional experiments showed that knockdown of GPC4 sensitized pancreatic cancer cells to 5‐FU and attenuated stem cell–like properties. In terms of mechanism research, knockdown of GPC4 suppressed the activation of Wnt/β‐catenin pathway and its downstream targets. Furthermore, the expression of GPC4 was significantly upregulated in pancreatic cancer tissues compared with normal tissues and remarkably correlated with patients’ overall survival according to the data derived from the Cancer Genome Atlas database. Taken together, our results suggest that GPC4 is a key regulator in chemoresistance and pancreatic cancer stemness. Thus, targeting GPC4 may serve as a promising strategy for pancreatic cancer therapy.
Attentive Linear Transformation for Image Captioning

We propose a novel attention framework called attentive linear transformation (ALT) for automatic generation of image captions. Instead of learning the spatial or channel-wise attention in existing models, ALT learns to attend to the high-dimensional transformation matrix from the image feature space to the context vector space. Thus ALT can learn various relevant feature abstractions, including spatial attention, channel-wise attention, and visual dependence. Besides, we propose a soft threshold regression to predict the spatial attention probabilities. It preserves more relevant local regions than popular softmax regression. Extensive experiments on the MS COCO and the Flickr30k data sets all demonstrate the superiority of our model compared with other state-of-the-art models.
Women's self-perceptions in the aftermath of trauma: The role of trauma-centrality and trauma-type.

OBJECTIVE Traumatic events tend to play a major role in the way we perceive ourselves. Whereas the links between posttraumatic stress disorder (PTSD) and self-perceptions are well examined, less is known regarding other factors that may be involved in the erosion of self-perceptions. We sought to examine the contribution of trauma-centrality and trauma-type to the erosion of self-perceptions following trauma. Our hypotheses were (a) trauma-centrality is significantly related to impairments in self-perceptions, (b) sexual assault (SA) is related to greater erosion in self-perceptions compared with motor vehicle accident (MVA) and to unexpected death (bereavement), and (c) the effects of trauma-centrality and trauma-type on self-perceptions remain significant when statistically controlling for levels of PTSD symptoms. METHOD Adult American women (N = 108: SA = 48, MVA = 38, bereavement = 22) were recruited via online labor market and completed self-report measures of trauma history, PTSD symptoms, trauma-centrality, and several aspects of self-perceptions. RESULTS PTSD symptoms, trauma-centrality, and trauma-type were each found to contribute to the prediction of certain aspects of self-perceptions. Specifically, trauma-centrality was related to negative posttraumatic cognitions above and beyond the effects of PTSD symptoms. In addition, SA was related to greater impairments in global and domain-specific self-perceptions compared with MVA and bereavement. CONCLUSION Our findings highlight the roles of trauma-centrality and trauma-type in the erosion of self-perceptions following trauma. Our data emphasize the importance of considering the multiple factors influencing self-perceptions and of adopting a multifaceted conceptualization of the self in trauma-related research and clinical practice. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Oral and maxillofacial trauma in motorcyclists in an Iranian subpopulation

BACKGROUND/AIMS Road traffic accidents are considered a major cause of oral and maxillofacial trauma. Given that many traumatic injuries and deaths involve motorcyclists, the aim of this study was to investigate this vulnerable group in terms of oral and maxillofacial injuries following accidents. MATERIALS AND METHODS This cross-sectional study was conducted on 330 patients with oral and maxillofacial injuries at Shahid Rajaee Hospital in Shiraz, Iran, from April to September 2017. A questionnaire with questions regarding age, gender, helmet use, and driver's license was completed for all the patients and their injury type (including dental injuries). Data were analyzed using descriptive statistics and the chi-squared test with a significance level of 95%. RESULTS Of the 330 patients, 291 (88.2%) were male and 39 (11.8%) were female. There were 283 (85.75%) patients aged 21-30 years, and their mean age was 27.2 ± 6.5. Most of them (287, 87%) had not been wearing helmets at the time of the accident. Dental injuries were observed in 168 (50.9%) of the patients. Uncomplicated crown fractures were diagnosed in 25.4% of the patients, luxation injuries in 23.2%, and avulsion in 18.9%. Only 19.9% of the patients under the age of 25 had suffered facial injuries. CONCLUSION Most injuries in motorcycle accidents were dental trauma in men due to not wearing a helmet. Dental injuries had the highest frequency of damage.
The role of meta-analyses and umbrella reviews in assessing the harms of psychotropic medications: beyond qualitative synthesis

Abstract ὠφελέειν, ἢ μὴ βλάπτειν (Primum non nocere) – Hιppocrates’ principle should still guide daily medical prescribing. Therefore, assessing evidence of psychopharmacologic agents’ safety and harms is essential. Randomised controlled trials (RCTs) and observational studies may provide complementary information about harms of psychopharmacologic medications from both experimental and real-world settings. It is considered that RCTs provide a better control of confounding variables, while observational studies provide evidence from larger samples, longer follow-ups, in more representative samples, which may be more reflective of real-life clinical scenarios. However, this may not always hold true. Moreover, in observational studies, safety data are poorly or inconsistently reported, precluding reliable quantitative synthesis in meta-analyses. Beyond individual studies, meta-analyses, which represent the highest level of ‘evidence’, can be misleading, redundant and of low methodological quality. Overlapping meta-analyses sometimes even reach different conclusions on the same topic. Meta-analyses should be assessed systematically. Descriptive reviews of reviews can be poorly informative. Conversely, ‘umbrella reviews’ can use a quantitative approach to grade evidence. In this editorial, we present the main factors involved in the assessment of psychopharmacologic agents’ harms from individual studies, meta-analyses and umbrella reviews. Study design features, sample size, number of the events of interest, summary effect sizes, p-values, heterogeneity, 95% prediction intervals, confounding factor adjustment and tests of bias (e.g., small-study effects and excess significance) can be combined with other assessment tools, such as AMSTAR and GRADE to create a framework for assessing the credibility of evidence.
No Evidence of "healthy neuroticism" in the Hawaii Personality and Health Cohort.

BACKGROUND Heterogeneity in the effects of trait neuroticism on mortality has inspired recent theories of "healthy neuroticism," or the possibility that neuroticism can lead people down either healthy or unhealthy behavioral pathways. The logical extension of this theory is that some construct-perhaps another trait, financial resource, or health-relevant situation-changes the relationship between neuroticism and health. The other possibility is that different components of neuroticism lead to different health behaviors and therefore different outcomes. PURPOSE The current study systematically examines the relationship between child and adult neuroticism and various health indicators including perceptions of health, behaviors, health outcomes, and biomarkers of health. Finally, we examine both potential moderators of the associations with neuroticism and examine its facet structure. METHODS The current study utilizes data from the Hawaii Longitudinal Study of Personality and Health, which includes both adult (IPIP-NEO) and childhood (teacher-reported) measures of personality and socioeconomic status, as well as a variety of health outcomes, from self-reported health and health behavior to biological markers, such as cholesterol and blood glucose levels. Sample sizes range from 299 to 518. RESULTS The relationship between neuroticism and health was not consistently moderated by any other variable, nor were facets of neuroticism differentially related to health. CONCLUSIONS Despite a systematic investigation of the potential "paths" which may differentiate the relationship of neuroticism to health, no evidence of healthy neuroticism was found.
Creating supportive school cultures for beginning teachers: Mitigating the cultural contextual factors

Our internationally focused, systematic review of research literature explored a variety of contextual factors that affect experiences of beginning teachers and how these factors are addressed in the programs of support for new and beginning teachers. The transition and socialization processes that accompany early-career teachers, as well as efforts focused on acculturation to school contexts and the profession, are commonly noted in the literature and provide insights for those who support novice teachers. In this article, we report our findings that focus specifically on the cultural contextual factors. We view the cultural context as the eclectic environment wherein these early-career teachers learn to organize their thoughts, emotions, and behaviours, based on shared norms, beliefs, values, customs, and traditions that are common to a group of people. Upon the initial review of the literature on teacher attrition, retention, induction, and mentorship, we discuss the overarching themes that we found from our exploration of the cultural factors affecting beginning teachers, the aspects of induction and mentoring programs that were designed to address these factors, and we offer conclusions and research implications.