The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.

Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.

The Attentional Boost Effect in Older Adults: Examining the Vulnerable Boost Hypothesis.

INTRODUCTION: The Attentional Boost Effect (ABE) occurs whenever participants recognize stimuli paired earlier with to-be-responded targets better than stimuli earlier paired with to-be-ignored distractors or presented on their own (baseline). Previous studies showed that the ABE does not occur in older adults when the encoding time is too short (500 ms/word) or when encoding is incidental, likely due to aging-related reductions in cognitive resources or limitations of processing speed. METHOD: In the present study, younger and older adults encoded words presented for 1000 ms under intentional instructions. In addition, to determine the potential impact of the retention interval, the recognition task was performed after a delay of 2 minutes (Experiment 1) or 20 minutes (Experiment 2). RESULTS: Under these conditions, older adults showed a significant ABE and the size of the effect was comparable to that achieved by younger adults. The magnitude of the ABE was vulnerable to the passage of time because the recognition advantage of target-paired words decreased sharply from 2 to 20 minutes. CONCLUSIONS: Taken together, our data demonstrate that younger and older adults may have comparable ABE effects under specific conditions and are similarly sensitive to interference.

Advocating for the inclusion of kidney health outcomes in neonatal research: best practice recommendations by the Neonatal Kidney Collaborative.

Acute kidney injury (AKI) occurs in nearly 30% of sick neonates. Chronic kidney disease (CKD) can be detected in certain populations of sick neonates as early as 2 years. AKI is often part of a multisystem syndrome that negatively impacts developing organs resulting in short- and long-term pulmonary, neurodevelopmental, and cardiovascular morbidities. It is critical to incorporate kidney-related data into neonatal clinical trials in a uniform manner to better understand how neonatal AKI or CKD could affect an outcome of interest. Here, we provide expert opinion recommendations and rationales to support the inclusion of short- and long-term neonatal kidney outcomes using a tiered approach based on study design: (1) observational studies (prospective or retrospective) limited to data available within a center's standard practice, (2) observational studies involving prospective data collection where prespecified kidney outcomes are included in the design, (3) interventional studies with non-nephrotoxic agents, and (4) interventional studies with known nephrotoxic agents. We also provide recommendations for biospecimen collection to facilitate ancillary kidney specific research initiatives. This approach balances the costs of AKI and CKD ascertainment with knowledge gained. We advocate that kidney outcomes be included routinely in neonatal clinical study design. Consistent incorporation of kidney outcomes across studies will increase our knowledge of neonatal morbidity.

Effector-specific improvements in action prediction in left-handed individuals after short-term physical practice.

Research has established the influence of short-term physical practice for enhancing action prediction in right-handed (RH) individuals. In addition to benefits of physical practice for these later assessed perceptual-cognitive skills, effector-specific interference has been shown through action-incongruent secondary tasks (motor interference tasks). Here we investigated this experience-driven facilitation of action predictions and effector-specific interference in left-handed (LH) novices, before and after practicing a dart throwing task. Participants watched either RH (n = 19) or LH (n = 24) videos of temporally occluded dart throws, across a control condition and three secondary-task conditions: tone-monitoring, RH or LH force monitoring. These conditions were completed before and after physical practice throwing with the LH. Significantly greater improvement in prediction accuracy was shown post-practice for the LH- versus RH-video group. Consistent with previous work, effector-specific interference was shown, exclusive to the LH-video group. Only when doing the LH force monitoring task did the LH-video group show secondary task interference in prediction accuracy. These data support the idea that short-term physical practice resulted in the development of an effector-specific motor representation. The results are also consistent with other work in RH individuals (showing RH motor interference) and hence rule out the interpretation that these effector specific effects are due to the disruption of more generalized motor processes, thought to be lateralized to the left-hemisphere of the brain.

The Year in Aortic Surgery: Selected Highlights From 2023.

This article reviews the recent and relevant literature to the field of aortic surgery. Specific areas highlighted include outcomes of Stanford type A dissection, management of acute aortic syndromes, management of aortic aneurysms, and traumatic aortic injury. Although the focus was on articles from 2023, literature from prior years also was included, given that this article is the first of a series. Notably, the pertinent sections from the 2022 American College of Cardiology/American Heart Association Guidelines for the Diagnosis and Management Aortic Disease are discussed.

Mavacamten in Right Ventricular Outflow Tract Obstruction.

Right ventricular outflow tract (RVOT) obstruction is a rare complication of ventricular hypertrophy in patients with hypertrophic cardiomyopathy (HCM). This study presents an unusual case of a patient with HCM with severe RVOT obstruction that was relieved successfully through the use of mavacamten.

Clinical manifestations and treatment outcomes for patients with Pseudomonas endocarditis.

OBJECTIVES: To investigate clinical outcomes of patients with Pseudomonas endocarditis and identify factors associated with treatment failure. METHODS: Adult patients meeting definitive Duke's criteria for Pseudomonas endocarditis at 11 hospitals were identified between May 2000 and February 2024. Failure was defined as death or microbiological failure by day 42. First-line therapy consisted of cefepime, piperacillin/tazobactam, ceftazidime or ceftolozane/tazobactam alone or in combination. RESULTS: Forty-eight patients met inclusion criteria; 29% were persons who inject drugs and 13% were organ transplant recipients. Pseudomonas aeruginosa was the causative species in 98% of cases. Patients who experienced 42 day cure were more likely to be initially managed with first-line ß-lactam agents compared with those who experienced clinical failure (97% versus 62%, P = 0.004). Treatment with first-line ß-lactams was associated with shorter time to treatment initiation and a lower likelihood of infection due to MDR Pseudomonas spp. In the univariate model, patients who experienced 90 day mortality were more likely to have prosthetic valve endocarditis (57% versus 24%, P = 0.02), an intracardiac complication (36% versus 9%, P = 0.04) and a higher median (IQR) Pitt bacteraemia score [2.5 (2-3.8) versus 1 (0-2), P = 0.048]. Combination therapy did not improve clinical outcomes but did increase the rate of adverse effects resulting in drug discontinuation compared with monotherapy, (21% versus 0%, P = 0.08). CONCLUSIONS: This is the largest study of Pseudomonas endocarditis to date. We identified improved clinical outcomes when cefepime, piperacillin/tazobactam, ceftazidime or ceftolozane/tazobactam were used for initial treatment. We did not identify a clinical benefit for combination treatment.

Pairwise Comparison of Heavy Dynamic Strength and Fast Dynamic Strength Interventions on Sprint Performance: A Systematic Review and Meta-Analysis.

ABSTRACT: Pairwise comparison of heavy dynamic strength and fast dynamic strength interventions on sprint performance: a systematic review and meta-analysis. J Strength Cond Res 38(8): 1509-1520, 2024-Previous studies have shown that both heavy dynamic strength (HDS) and fast dynamic strength (FDS) training can be used to improve sprint performance; however, a review and meta-analysis investigating pairwise studies that compare these two training interventions have not been performed. The aims of the study were to systematically review and analyze HDS and FDS training methodologies and evaluate their effect size difference, in pairwise comparison studies to determine and compare their effects on sprint performance. Databases were systematically searched using Boolean phrasing to identify eligible articles, and meta-analyses were performed on the extracted data. Seven studies met the inclusion criteria, which resulted in data from 138 subjects across 24 separate sprint assessments. Overall, there was a small effect in favor of FDS (standardized mean difference = 0.27, 95% confidence intervals [-0.07; 0.60], 95% prediction intervals [-1.01; 1.55]), but this was deemed not significant because of the wide-ranging prediction intervals. There is no distinguishable difference between HDS and FDS training on sprint performance. The wide-ranging prediction intervals suggest the variability is too great to determine whether one training type is more effective than the other. Practitioners should consider the individual needs of their athletes when deciding which training type to use for long-term sprint development.

Localized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress.

Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative stress, controlling protein fate and supporting stress defenses at several subcellular compartments. However, the rules driving subcellular ubiquitin localization to promote these concerted response mechanisms remain understudied. Here, we show that K63-linked ubiquitin chains, known to promote proteasome-independent pathways, accumulate primarily in non-cytosolic compartments during oxidative stress induced by sodium arsenite in mammalian cells. Our subcellular ubiquitin proteomic analyses of non-cytosolic compartments expanded 10-fold the pool of proteins known to be ubiquitinated during arsenite stress (2,046) and revealed their involvement in pathways related to immune signaling and translation control. Moreover, subcellular proteome analyses revealed proteins that are recruited to non-cytosolic compartments under stress, including a significant enrichment of helper ubiquitin-binding adaptors of the ATPase VCP that processes ubiquitinated substrates for downstream signaling. We further show that VCP recruitment to non-cytosolic compartments under arsenite stress occurs in a ubiquitin-dependent manner mediated by its adaptor NPLOC4. Additionally, we show that VCP and NPLOC4 activities are critical to sustain low levels of non-cytosolic K63-linked ubiquitin chains, supporting a cyclical model of ubiquitin conjugation and removal that is disrupted by cellular exposure to reactive oxygen species. This work deepens our understanding of the role of localized ubiquitin and VCP signaling in the basic mechanisms of stress response and highlights new pathways and molecular players that are essential to reshape the composition and function of the human subcellular proteome under dynamic environments.

RNA-binding protein PCBP2 regulates pancreatic ß cell function and adaptation to glucose.

Glucose plays a key role in shaping pancreatic ß cell function. Thus, deciphering the mechanisms by which this nutrient stimulates ß cells holds therapeutic promise for combating ß cell failure in type 2 diabetes (T2D). ß Cells respond to hyperglycemia in part by rewiring their mRNA metabolism, yet the mechanisms governing these changes remain poorly understood. Here, we identify a requirement for the RNA-binding protein PCBP2 in maintaining ß cell function basally and during sustained hyperglycemic challenge. PCBP2 was induced in primary mouse islets incubated with elevated glucose and was required to adapt insulin secretion. Transcriptomic analysis of primary Pcbp2-deficient ß cells revealed impacts on basal and glucose-regulated mRNAs encoding core components of the insulin secretory pathway. Accordingly, Pcbp2-deficient ß cells exhibited defects in calcium flux, insulin granule ultrastructure and exocytosis, and the amplification pathway of insulin secretion. Further, PCBP2 was induced by glucose in primary human islets, was downregulated in islets from T2D donors, and impacted genes commonly altered in islets from donors with T2D and linked to single-nucleotide polymorphisms associated with T2D. Thus, these findings establish a paradigm for PCBP2 in governing basal and glucose-adaptive gene programs critical for shaping the functional state of ß cells.

Detection of active SARS-CoV-2 in cough aerosols from COVID-19 patients.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an airborne pathogen, but detection of infectious SARS-CoV-2 in air and in particular the introduction of the virus into the environment by different human expiratory manoeuvres is not well studied. OBJECTIVES: The aim of this study was to investigate the presence of SARS-CoV-2 in cough from coronavirus disease of 2019 (COVID-19) in-patients and to study contamination of the virus in the patient's environment. METHODS: Detection of SARS-CoV-2 in cough was analyzed by PCR, culture and imaging. Detection in cough was compared to presence of the virus in air and on surfaces from patient rooms. RESULTS: Twenty-five patients in 21 rooms were included in the study. SARS-CoV-2 RNA was found in cough aerosols from 16 out of 22 patients that produced voluntary cough. As demonstrated by plaque-forming unit assays, active virus was isolated from 11 of these 16 patients. Using mainly molecular detection, the virus was also found in air, on high-contact surfaces, and no-touch surfaces from the room of the COVID-19 patients. CONCLUSIONS: These results show that infectious SARS-CoV-2 circulating in air can originate from patient cough and should be considered against the risk of acquiring COVID-19 through inhalation.

Contextual Triggers and Tic Severity Across Life Periods: A Retrospective Analysis in Adults with Tic Disorders.

In tic disorders (TD), tic expression varies across the lifespan and as a function of contextual factors. This study explored connections between tic expression and contextual triggers across life periods in 74 adults (Mage = 23.2) with TDs. The Tic History and Coping Strategies form assessed retrospective self-reports of contextual antecedents, consequences, and tic severity during four life periods (middle school; 9th/10th grade; 11th/12th grade; college/work) and past month. Tics reportedly worsened during and after school in school-aged years and worsened in the evening during college/work years. Stress and anxiety were reported to consistently trigger tics across time. The impact of activities, places, and emotions did not differ across life periods. Attention-based consequences, most prevalent during middle school, were more common than escape- or avoidance-related consequences across all periods. Findings illuminate how contextual factors may influence tics across life periods and underscore the consistent impact of tic-triggering emotions and attention-related consequences.

Neutral markers reveal complex population structure across the range of a widespread songbird.

Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.

Sex differences in cardiac transcriptomic response to neonatal sleep apnea.

Pediatric obstructive sleep apnea poses a significant health risk, with potential long-term consequences on cardiovascular health. This study explores the dichotomous nature of neonatal cardiac response to chronic intermittent hypoxia (CIH) between males and females, aiming to fill a critical knowledge gap in the understanding of sex-specific cardiovascular consequences of sleep apnea in early life. Neonates were exposed to CIH until p28 and underwent comprehensive in vivo physiological assessments, including whole-body plethysmography, treadmill stress-tests, and echocardiography. Results indicated that male CIH rats weighed 13.7% less than age-matched control males (p = 0.0365), while females exhibited a mild yet significant increased respiratory drive during sleep (93.94 ± 0.84 vs. 95.31 ± 0.81;p = 0.02). Transcriptomic analysis of left ventricular tissue revealed a substantial sex-based difference in the cardiac response to CIH, with males demonstrating a more pronounced alteration in gene expression compared to females (5986 vs. 3174 genes). The dysregulated miRNAs in males target metabolic genes, potentially predisposing the heart to altered metabolism and substrate utilization. Furthermore, CIH in males was associated with thinner left ventricular walls and dysregulation of genes involved in the cardiac action potential, possibly predisposing males to CIH-related arrhythmia. These findings emphasize the importance of considering sex-specific responses in understanding the cardiovascular implications of pediatric sleep apnea.

Let's talk about flux: the rising potential of autophagy rate measurements in disease.

Macroautophagy/autophagy is increasingly implicated in a variety of diseases, making it an attractive therapeutic target. However, many aspects of autophagy are not fully understood and its impact on many diseases remains debatable and context-specific. The lack of systematic and dynamic measurements in these cases is a key reason for this ambiguity. In recent years, Loos et al. 2014 and Beesabathuni et al. 2022 developed methods to quantitatively measure autophagy holistically. In this commentary, we pose some of the unresolved biological questions regarding autophagy and consider how quantitative measurements may address them. While the applications are ever-expanding, we provide specific use cases in cancer, virus infection, and mechanistic screening. We address how the rate measurements themselves are central to developing cancer therapies and present ways in which these tools can be leveraged to dissect the complexities of virus-autophagy interactions. Screening methods can be combined with rate measurements to mechanistically decipher the labyrinth of autophagy regulation in cancer and virus infection. Taken together, these approaches have the potential to illuminate the underlying mechanisms of various diseases.Abbreviation MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; R1: rate of autophagosome formation; R2: rate of autophagosome-lysosome fusion; R3: rate of autolysosome turnover.

Assessing athletes beyond routine screening: Incorporating essential factors to optimize cardiovascular health and performance.

The American Heart Association (AHA) has devised Life's Essential 8, a set of eight evidence-based health behaviors that play a crucial role in optimizing cardiovascular health and overall well-being. In addition to Life's Essential 8, enhanced screening for Cardiovascular-Kidney-Metabolic (CKM) Syndrome risk factors into routine athlete screening also provides a more comprehensive approach for ensuring athlete safety and long-term health. Incorporating Life's Essential 8 and CKM Syndrome metrics into athlete health evaluations will improve the sports performance of athletes and help optimize their long-term health.

A study comparing the cost-effectiveness of conventional and drug-eluting transarterial chemoembolisation (cTACE and DEB-TACE) for the treatment of hepatocellular carcinoma in an Australian public hospital.

INTRODUCTION: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality and transarterial chemoembolisation (TACE) is an established technique to treat patients with intermediate-stage HCC. The aim of this study was to generate accurate costing data on cTACE and DEB-TACE in an Australian setting and assess whether one of the procedures offers favourable cost-effectiveness. METHODS: Costing study using data from all TACE procedures performed at a single centre between January 2018 and December 2022. Data were included from all direct and indirect costs including operative costs, wages, overheads, ward costs, transfusion, pathology, pharmacy and ward support. Cost-effectiveness was assessed by dividing local costs by existing high-quality data on quality-adjusted life years (QALYs). RESULTS: 64 TACE treatments were performed on 44 patients. Mean age was 66.5 years and 91% were male. Overall median total cost per patient for the entire TACE treatment regime was AUD$7380 (range AUD$3719-$20,258). However, 39% of patients received more than one treatment, and the median cost per individual treatment was AUD$5270 (range AUD$3533-$15,818). The difference in median cost between cTACE (AUD$4978) and DEB-TACE (AUD$9202) was significant, P < 0.001. In calculating cost-effectiveness, each cTACE treatment cost AUD$2489 per QALY gained, while each DEB-TACE cost AUD$3834 per QALY gained. The incremental cost-effectiveness ratio (ICER) for DEB-TACE over cTACE was AUD$10,560 per QALY gained. CONCLUSION: Both cTACE and DEB-TACE are low-cost treatments in Australia. However, DEB-TACE offers a solution with an ICER of AUD$10,560 per QALY gained which is below the Australian government willingness to pay threshold and thus is a more cost-effective treatment.

Disruption of Plasmodium falciparum kinetochore proteins destabilises the nexus between the centrosome equivalent and the mitotic apparatus.

Plasmodium falciparum is the causative agent of malaria and remains a pathogen of global importance. Asexual blood stage replication, via a process called schizogony, is an important target for the development of new antimalarials. Here we use ultrastructure-expansion microscopy to probe the organisation of the chromosome-capturing kinetochores in relation to the mitotic spindle, the centriolar plaque, the centromeres and the apical organelles during schizont development. Conditional disruption of the kinetochore components, PfNDC80 and PfNuf2, is associated with aberrant mitotic spindle organisation, disruption of the centromere marker, CENH3 and impaired karyokinesis. Surprisingly, kinetochore disruption also leads to disengagement of the centrosome equivalent from the nuclear envelope. Severing the connection between the nucleus and the apical complex leads to the formation of merozoites lacking nuclei. Here, we show that correct assembly of the kinetochore/spindle complex plays a previously unrecognised role in positioning the nascent apical complex in developing P. falciparum merozoites.

AAP Recommended Cardiac Screening Questions in Preparticipation Physical Evaluation Forms.

To evaluate the utilization of the American Academy of Pediatrics' (AP) cardiovascular screening questions within preparticipation physical evaluation forms from the 50 state high school athletic associations. We found that fewer than half of state forms incorporated all 10 AAP questions; moreover, a subset failed to adhere to criteria recommended by either the AAP or American Heart Association.