Developmental and temporal characteristics of clonal sperm mosaicism.

Throughout development and aging, human cells accumulate mutations resulting in genomic mosaicism and genetic diversity at the cellular level. Mosaic mutations present in the gonads can affect both the individual and the offspring and subsequent generations. Here, we explore patterns and temporal stability of clonal mosaic mutations in male gonads by sequencing ejaculated sperm. Through 300× whole-genome sequencing of blood and sperm from healthy men, we find each ejaculate carries on average 33.3 ± 12.1 (mean ± SD) clonal mosaic variants, nearly all of which are detected in serial sampling, with the majority absent from sampled somal tissues. Their temporal stability and mutational signature suggest origins during embryonic development from a largely immutable stem cell niche. Clonal mosaicism likely contributes a transmissible, predicted pathogenic exonic variant for 1 in 15 men, representing a life-long threat of transmission for these individuals and a significant burden on human population health.

Landscape-scale benefits of protected areas for tropical biodiversity.

The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines1. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear2-5. Unregulated hunting can empty PAs of large animals6, illegal tree felling can degrade habitat quality7, and parks can simply displace disturbances such as logging and hunting to unprotected areas of the landscape8 (a phenomenon called leakage). Alternatively, well-functioning PAs could enhance animal diversity within reserves as well as in nearby unprotected sites9 (an effect called spillover). Here we test whether PAs across mega-diverse Southeast Asia contribute to vertebrate conservation inside and outside their boundaries. Reserves increased all facets of bird diversity. Large reserves were also associated with substantially enhanced mammal diversity in the adjacent unprotected landscape. Rather than PAs generating leakage that deteriorated ecological conditions elsewhere, our results are consistent with PAs inducing spillover that benefits biodiversity in surrounding areas. These findings support the United Nations goal of achieving 30% PA coverage by 2030 by demonstrating that PAs are associated with higher vertebrate diversity both inside their boundaries and in the broader landscape.

Somatic mosaicism reveals clonal distributions of neocortical development.

The structure of the human neocortex underlies species-specific traits and reflects intricate developmental programs. Here we sought to reconstruct processes that occur during early development by sampling adult human tissues. We analysed neocortical clones in a post-mortem human brain through a comprehensive assessment of brain somatic mosaicism, acting as neutral lineage recorders1,2. We combined the sampling of 25 distinct anatomic locations with deep whole-genome sequencing in a neurotypical deceased individual and confirmed results with 5 samples collected from each of three additional donors. We identified 259 bona fide mosaic variants from the index case, then deconvolved distinct geographical, cell-type and clade organizations across the brain and other organs. We found that clones derived after the accumulation of 90-200 progenitors in the cerebral cortex tended to respect the midline axis, well before the anterior-posterior or ventral-dorsal axes, representing a secondary hierarchy following the overall patterning of forebrain and hindbrain domains. Clones across neocortically derived cells were consistent with a dual origin from both dorsal and ventral cellular populations, similar to rodents, whereas the microglia lineage appeared distinct from other resident brain cells. Our data provide a comprehensive analysis of brain somatic mosaicism across the neocortex and demonstrate cellular origins and progenitor distribution patterns within the human brain.

FLAN: feature-wise latent additive neural models for biological applications.

MOTIVATION: Interpretability has become a necessary feature for machine learning models deployed in critical scenarios, e.g. legal system, healthcare. In these situations, algorithmic decisions may have (potentially negative) long-lasting effects on the end-user affected by the decision. While deep learning models achieve impressive results, they often function as a black-box. Inspired by linear models, we propose a novel class of structurally constrained deep neural networks, which we call FLAN (Feature-wise Latent Additive Networks). Crucially, FLANs process each input feature separately, computing for each of them a representation in a common latent space. These feature-wise latent representations are then simply summed, and the aggregated representation is used for the prediction. These feature-wise representations allow a user to estimate the effect of each individual feature independently from the others, similarly to the way linear models are interpreted. RESULTS: We demonstrate FLAN on a series of benchmark datasets in different biological domains. Our experiments show that FLAN achieves good performances even in complex datasets (e.g. TCR-epitope binding prediction), despite the structural constraint we imposed. On the other hand, this constraint enables us to interpret FLAN by deciphering its decision process, as well as obtaining biological insights (e.g. by identifying the marker genes of different cell populations). In supplementary experiments, we show similar performances also on non-biological datasets. CODE AND DATA AVAILABILITY: Code and example data are available at https://github.com/phineasng/flan_bio.

Recombination resolves the cost of horizontal gene transfer in experimental populations of Helicobacter pylori.

Horizontal gene transfer (HGT) is important for microbial evolution, yet we know little about the fitness effects and dynamics of horizontally transferred genetic variants. In this study, we evolve laboratory populations of Helicobacter pylori, which take up DNA from their environment by natural transformation, and measure the fitness effects of thousands of transferred genetic variants. We find that natural transformation increases the rate of adaptation but comes at the cost of significant genetic load. We show that this cost is circumvented by recombination, which increases the efficiency of selection by decoupling deleterious and beneficial genetic variants. Our results show that adaptation with HGT, pervasive in natural microbial populations, is shaped by a combination of selection, recombination, and genetic drift not accounted for in existing models of evolution.

Peroxisomal ß-oxidation enzyme, DECR2, regulates lipid metabolism and promotes treatment resistance in advanced prostate cancer.

BACKGROUND: Peroxisomes are central metabolic organelles that have key roles in fatty acid homoeostasis. As prostate cancer (PCa) is particularly reliant on fatty acid metabolism, we explored the contribution of peroxisomal ß-oxidation (perFAO) to PCa viability and therapy response. METHODS: Bioinformatic analysis was performed on clinical transcriptomic datasets to identify the perFAO enzyme, 2,4-dienoyl CoA reductase 2 (DECR2) as a target gene of interest. Impact of DECR2 and perFAO inhibition via thioridazine was examined in vitro, in vivo, and in clinical prostate tumours cultured ex vivo. Transcriptomic and lipidomic profiling was used to determine the functional consequences of DECR2 inhibition in PCa. RESULTS: DECR2 is upregulated in clinical PCa, most notably in metastatic castrate-resistant PCa (CRPC). Depletion of DECR2 significantly suppressed proliferation, migration, and 3D growth of a range of CRPC and therapy-resistant PCa cell lines, and inhibited LNCaP tumour growth and proliferation in vivo. DECR2 influences cell cycle progression and lipid metabolism to support tumour cell proliferation. Further, co-targeting of perFAO and standard-of-care androgen receptor inhibition enhanced suppression of PCa cell proliferation. CONCLUSION: Our findings support a focus on perFAO, specifically DECR2, as a promising therapeutic target for CRPC and as a novel strategy to overcome lethal treatment resistance.

The interplay of perceptual processing demands and practice in modulating voluntary and involuntary motor responses.

Understanding how sensory processing demands affect the ability to ignore task-irrelevant, loud auditory stimuli (LAS) during a task is key to performance in dynamic environments. For example, tennis players must ignore crowd noise to perform optimally. We investigated how practice affects this ability by examining the effects of delivering LASs during preparatory phase of an anticipatory timing (AT) task on the voluntary and reflexive responses in two conditions: lower and higher visual processing loads. Twenty-four participants (mean age = 23.1, 11 females) completed the experiment. The AT task involved synchronizing a finger abduction response with the last visual stimulus item in a sequence of four Gabor grating patches briefly flashed on screen. The lower demand condition involved only this task, and the higher demand condition required processing the orientations of the patches to report changes in the final stimulus item. Our results showed that higher visual processing demands affected the release of voluntary actions, particularly in the first block of trials. When the perceptual load was lower, responses were released earlier by the LAS compared to the high-load condition. Practice reduced these effects largely, but high perceptual load still led to earlier action release in the second block. In contrast, practice led to more apparent facilitation of eyeblink latency in the second block. These findings indicate that a simple perceptual load manipulation can impact the execution of voluntary motor actions, particularly for inexperienced participants. They also suggest distinct movement preparation influences on voluntary and involuntary actions triggered by acoustic stimuli.

Implementing living-donor pediatric liver transplantation in Southern Vietnam: 15-year results and perspectives.

BACKGROUND: ND2 in Ho Chi Minh City is currently the only public center that performs PLT in Southern Vietnam. In 2005, the first PLT was successfully performed, with support from Belgian experts. This study reviews the implementation of PLT at our center and evaluates the results and challenges. METHODS: Implementation of PLT at ND2 required medico-surgical team building and extensive improvement of hospital facilities. Records of 13 transplant recipients from 2005 to 2020 were studied retrospectively. Short- and long-term complications, as well as the survival rates, were reported. RESULTS: The mean follow-up time was 8.3 ± 5.7 years. Surgical complications included one case of hepatic artery thrombosis that was successfully repaired, one case of colon perforation resulting in death from sepsis, and two cases of bile leak that were drained surgically. PTLD was observed in five patients, of whom three died. There were no cases of retransplantation. The 1-year, 5-year, and 10-year patient survival rates were 84.6%, 69.2%, and 69.2%, respectively. There were no cases of complication or death among the donors. CONCLUSION: Living-donor PLT was developed at ND2 for providing a life-saving treatment to children with end-stage liver disease. Early surgical complication rate was low, and the patient survival rate was satisfactory at 1 year. Long-term survival decreased considerably due to PTLD. Future challenges include surgical autonomy and improvement of long-term medical follow-up with a particular emphasis on prevention and management of Epstein-Barr virus-related disease.

Clinical characteristics of COVID-19 patients treated in emergency COVID-19 hospitals in Vietnam: Experience from Phutho province, Vietnam.

Background: This study aimed to evaluate the clinical characteristics, patient's management approaches, and outcomes of the COVID-19 patients in Phu Tho Province, Vietnam. Methods: A retrospective, multicenter study of 2166 COVID-19 patients in 13 hospitals in Phutho Province, Vietnam. The subjects were divided into 3 groups based on vaccination status: unvaccinated group, 1st dose of vaccine group, 2nd dose of vaccine group. The clinical characteristics, management approaches, and outcomes were collected and compared between the 3 groups. Results: The hospitalization rate of the 3 groups decreased from the unvaccinated group, the 1st dose of vaccinated group, to the 2nd dose of vaccinated group, 42.61%; 30,24% and 27,15% respectively. The 19-40 years old group had the highest hospitalization rate (38,1%) together with the group that had not accepted the full COVID 19 vaccination dose (57,64%). The 2nd dose of vaccinated group had the lowest percentages of high temperature, cough, dyspnea, chest pain and sore throat. The unvaccinated group had the highest heart rate, respiratory rate and SpO2 compared to the two other groups. The percentage needing Immunomodulation and Anticoagulant Therapy was highest (6.8% and 1.4 % respectively) in the unvaccinated group. The percentage receiving Antiviral Therapy was highest (42,5%) in those who had received the 2nd dose of vaccine. Conclusions: COVID-19 vaccination improved the symptoms of the patients and should be accepted in all ages.

The impact of recreational cannabis legalization on ED visit rates for acute cannabis intoxication.

BACKGROUND: In December 2018 the Michigan Regulation and Taxation of Marihuana Act legalized the recreational use of cannabis in Michigan. There are now high potency forms of cannabis readily available in the state, which could result in increased emergency department (ED) visit rates due to intoxication in adults and children. Although cannabis related visits account for a small percentage of all adult and pediatric ED visits, they impose a significant burden on the health care system's resources. This study aimed to assess the impact of the legalization of recreational marijuana on the rate of ED visits for acute cannabis intoxication. METHODS AND DESIGN: We utilized the legalization of marijuana in the state of Michigan to conduct a natural experiment utilizing a retrospective observational cohort design of ED visits for acute intoxication before and after legalization. The study was conducted at a health system composed of eight hospitals in southeast Michigan, including both academic and community hospitals serving a diverse patient population. We estimated monthly cannabis-related ED visits based on cannabis-related ICD-10 discharge codes and total ED visits using electronic health record data from 2016 to 2022. A negative-binomial (NB) regression model was used to estimate the immediate and cumulative changes in cannabis-related ED visit rate after legalization. RESULTS: There were a total of 2177 ED visits from 2066 patients for cannabis intoxication in our study cohort. Of the 2177 visits, 671 were before and 1506 were after legalization. In the univariate analysis, recreational cannabis legalization was associated with an increase in the average cannabis-related ED visit rate (Rate Ratio [RR]:1.70, 95% CI: (1.49, 1.94), p-value <0.001). In the multivariate analysis adjusting for age, results remain significant (RR 1.47, 95% CI (1.29, 1.70), p-value <0.001). The increased visit rate occurred in the first month after legalization; however, the slope of the increasing rate of ED visits were similar before and after cannabis legalization (RR, 1.28, 95% CI (1.07, 1.54), p-value <0.001). CONCLUSIONS: The legalization of recreational cannabis in Michigan was associated with an immediate increase in ED visit rates for acute cannabis intoxications across all ages, especially among middle-aged adults, in the context of an stably increasing ED visit rate.

Purchasing medicines and functional foods on the internet: a cross-sectional study investigating the knowledge, attitudes, and experience of Vietnamese people in 2023.

OBJECTIVE: To investigate Vietnamese people's knowledge, attitudes, and experience in purchasing medicines and functional foods online. METHODS: Via an online survey, the data of 1,070 participants were collected, including their general characteristics, Internet use, previous experience, knowledge, and attitudes towards purchasing medicines/functional foods online. Factors associated with their knowledge and attitudes were identified via multivariate linear regression models. RESULTS: During 2022-2023, about 97.2% of participants used the Internet to seek health information (self-diagnosis: 65.0%, self-medication: 72.6%). Roughly 52.8% bought medicines and/or functional foods online. Among 565 buyers, 41.8% felt satisfied. Only 19.9% understood that selling medicines online was illegal in Vietnam. The main benefits of purchasing medicines/functional foods online that many people agreed on included convenience (87.1%), freedom from location (84.8%), and being able to order/buy products after opening hours (84.7%). Many people felt worried about the ability to buy counterfeit or substandard products (87.7%), inaccurate product information (85.0%), the lack of supervision of the authorities (83.7%), and increasing risks of drug abuse, self-medication, and treatment non-adherence (82.5%). Roughly 84.3% found distinguishing between legal and illegal online pharmacies difficult. Participants' average knowledge and attitude scores were 6.514 ± 2.461 (range: 0-16) and 89.330 ± 13.720 (range: 23-115), respectively. The main factors associated with people's knowledge and attitudes towards purchasing these products online included their frequency of Internet use, seeking health information online for self-medication, feeling satisfied with previous experience, and having at least one chronic disease. CONCLUSIONS: Many Vietnamese people's knowledge about purchasing medicines/functional foods online was limited. With the increasing need for online shopping, enhancing their knowledge is paramount. In the forthcoming years, when the Ministry of Health and relevant authorities publish legal documents and enact laws involving online pharmacies and trading medicines on the Internet, ways to recognize licensed online pharmacies must be widely propagated and disseminated in the community.

Rad21l1 cohesin subunit is dispensable for spermatogenesis but not oogenesis in zebrafish.

During meiosis I, ring-shaped cohesin complexes play important roles in aiding the proper segregation of homologous chromosomes. RAD21L is a meiosis-specific vertebrate cohesin that is required for spermatogenesis in mice but is dispensable for oogenesis in young animals. The role of this cohesin in other vertebrate models has not been explored. Here, we tested if the zebrafish homolog Rad21l1 is required for meiotic chromosome dynamics during spermatogenesis and oogenesis. We found that Rad21l1 localizes to unsynapsed chromosome axes. It is also found between the axes of the mature tripartite synaptonemal complex (SC) in both sexes. We knocked out rad21l1 and found that nearly all rad21l1-/- mutants develop as fertile males, suggesting that the mutation causes a defect in juvenile oogenesis, since insufficient oocyte production triggers female to male sex reversal in zebrafish. Sex reversal was partially suppressed by mutation of the checkpoint gene tp53, suggesting that the rad21l1 mutation activates Tp53-mediated apoptosis or arrest in females. This response, however, is not linked to a defect in repairing Spo11-induced double-strand breaks since deletion of spo11 does not suppress the sex reversal phenotype. Compared to tp53 single mutant controls, rad21l1-/- tp53-/- double mutant females produce poor quality eggs that often die or develop into malformed embryos. Overall, these results indicate that the absence of rad21l1-/- females is due to a checkpoint-mediated response and highlight a role for a meiotic-specific cohesin subunit in oogenesis but not spermatogenesis.

Laparoscopic and thoracoscopic whole-stomach esophagectomy with preoperative pyloric balloon dilatation for esophageal cancer: a prospective multicenter case-series outcome.

INTRODUCTION: To mitigate gastroparesis as well as other post-operative complications, we undertook a prospective multicenter study to assess the feasibility, safety, and efficacy in the short-term outcomes of laparoscopic and thoracoscopic whole stomach esophagectomy with preoperative pyloric balloon dilatation. METHODS: A prospective descriptive study on 37 patients with laparoscopic and thoracoscopic whole stomach esophagectomy with preoperative pyloric balloon dilatation from January 2019 to March 2023. The perioperative indications, clinical data, intra-operative index, pathological postoperative specimens, postoperative complications, and follow-up results were retrospectively evaluated. RESULTS: In our study, all patients were male, with dysphagia as the predominant symptom (45.9%). Esophageal cancer incidence was similar between middle and lower thirds. Nodules were the primary finding on esophagoscopy (48.6%). Preoperative pyloric dilation averaged 31.2 min without complications. Surgical duration ranged from 225 to 400 min (mean 305). Gastric tube fluid volume averaged 148.9 ± 110.66 ml per day. Among 34 post-operative cases underwent gastric transit scans, most had non-dilated stomachs with efficient pyloric drug circulation. Three cases required prolonged ventilation, precluding pyloric circulation scans. Four patients developed chylous fistula, one requiring chest tube embolization. Recurrent laryngeal nerve damage occurred in 10.8% of cases. CONCLUSION: After evaluating esophageal cancer patients undergoing laparoscopic whole-stomach esophagectomy with preoperative pyloric balloon dilatation, it was found that this procedure is safe, effective, and significantly reduces postoperative gastroparesis and related complications.

The mediation model of social status on the link between parental attachment, aggressive behavior, and psychological well-being: Evidence from two studies in Vietnamese adolescents and young adults.

Little is known about how insecure attachment affects aggressive behavior and well-being among Vietnamese youth. Using structural equation modeling, we investigate the mediating role of subjective social status (SSS) on the paths from insecure attachment to overt aggressive behavior (OAB) and psychological well-being (PW) in a sample of 1753 Vietnamese adolescents (Mage = 16.136, SD = 0.784) and test whether the results will be replicated in another sample of 601 Vietnamese young adults (Mage = 19.93, SD = 1.35). Participants complete a survey comprising demographic information, attachment styles, SSS, OAB, and PW questionnaires. Our main findings include: (a) anxious attachment positively related to OAB in both samples, (b) anxious attachment was only negatively associated with adolescents' PW, (c) avoidant attachment was positively correlated to OAB in adolescents but negatively correlated in young adults, and (d) avoidant attachment was negatively related to PW in both samples. In addition, (e) in adolescents, the mediation role of SSS was significant in all paths, but (f) SSS only mediated the link from avoidant attachment to PW of young adults. The present study suggests that aggressive behavior might not be associated with social status or attachment in the same way in adolescents compared to young adult Vietnamese samples.

Formation of templated inclusions in a forebrain α-synuclein mouse model is independent of LRRK2.

Leucine-rich repeat kinase 2 (LRRK2) and α-synuclein share enigmatic roles in the pathobiology of Parkinson's disease (PD). LRRK2 mutations are a common genetic cause of PD which, in addition to neurodegeneration, often present with abnormal deposits of α-synuclein in the form of Lewy-related pathology. As Lewy-related pathology is a prominent neuropathologic finding in sporadic PD, the relationship between LRRK2 and α-synuclein has garnered considerable interest. However, whether and how LRRK2 might influence the accumulation of Lewy-related pathology remains poorly understood. Through stereotactic injection of mouse α-synuclein pre-formed fibrils (PFF), we modeled the spread of Lewy-related pathology within forebrain regions where LRRK2 is most highly expressed. The impact of LRRK2 genotype on the formation of α-synuclein inclusions was evaluated at 1-month post-injection. Neither deletion of LRRK2 nor G2019S LRRK2 knockin appreciably altered the burden of α-synuclein pathology at this early timepoint. These observations fail to provide support for a robust pathophysiologic interaction between LRRK2 and α-synuclein in the forebrain in vivo. There was, however, a modest reduction in microglial activation induced by PFF delivery in the hippocampus of LRRK2 knockout mice, suggesting that LRRK2 may contribute to α-synuclein-induced neuroinflammation. Collectively, our data indicate that the pathological accumulation of α-synuclein in the mouse forebrain is largely independent of LRRK2.

Cost of Acute and Sequelae Care for Japanese Encephalitis Patients, Bangladesh, 2011-2021.

Japanese encephalitis (JE) is associated with an immense social and economic burden. Published cost-of-illness data come primarily from decades-old studies. To determine the cost of care for patients with acute JE and initial and long-term sequelae from the societal perspective, we recruited patients with laboratory-confirmed JE from the past 10 years of JE surveillance in Bangladesh and categorized them as acute care, initial sequalae, and long-term sequelae patients. Among 157 patients, we categorized 55 as acute, 65 as initial sequelae (53 as both categories), and 90 as long-term sequelae. The average (median) societal cost of an acute JE episode was US $929 ($909), of initial sequelae US $75 ($33), and of long-term sequelae US $47 ($14). Most families perceived the effect of JE on their well-being to be extreme and had sustained debt for JE expenses. Our data about the high cost of JE can be used by decision makers in Bangladesh.

DECODE: a computational pipeline to discover T cell receptor binding rules.

MOTIVATION: Understanding the mechanisms underlying T cell receptor (TCR) binding is of fundamental importance to understanding adaptive immune responses. A better understanding of the biochemical rules governing TCR binding can be used, e.g. to guide the design of more powerful and safer T cell-based therapies. Advances in repertoire sequencing technologies have made available millions of TCR sequences. Data abundance has, in turn, fueled the development of many computational models to predict the binding properties of TCRs from their sequences. Unfortunately, while many of these works have made great strides toward predicting TCR specificity using machine learning, the black-box nature of these models has resulted in a limited understanding of the rules that govern the binding of a TCR and an epitope. RESULTS: We present an easy-to-use and customizable computational pipeline, DECODE, to extract the binding rules from any black-box model designed to predict the TCR-epitope binding. DECODE offers a range of analytical and visualization tools to guide the user in the extraction of such rules. We demonstrate our pipeline on a recently published TCR-binding prediction model, TITAN, and show how to use the provided metrics to assess the quality of the computed rules. In conclusion, DECODE can lead to a better understanding of the sequence motifs that underlie TCR binding. Our pipeline can facilitate the investigation of current immunotherapeutic challenges, such as cross-reactive events due to off-target TCR binding. AVAILABILITY AND IMPLEMENTATION: Code is available publicly at https://github.com/phineasng/DECODE. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Protein Phosphatase 2A Activation Via ApoER2 in Trophoblasts Drives Preeclampsia in a Mouse Model of the Antiphospholipid Syndrome.

[Figure: see text].