Miracle-dz/UniFAR-FTUs huggingface dataset:
Upgrading of the general AMBER force field 2 for fluorinated alcohol biosolvents: A validation for water solutions and melittin solvation

The standard GAFF2 force field parameterization has been refined for the fluorinated alcohols 2,2,2‐trifluoroethanol (TFE), 1,1,1,3,3,3‐hexafluoro‐2‐propanol (HFIP), and 1,1,1,3,3,3‐hexafluoropropan‐2‐one (HFA), which are commonly used to study proteins and peptides in biomimetic media. The structural and dynamic properties of both proteins and peptides are significantly influenced by the biomimetic environment created by the presence of these cosolvents in aqueous solutions. Quantum mechanical calculations on stable conformers were used to parameterize the atomic charges. Different systems, such as pure liquids, aqueous solutions, and systems formed by melittin protein and cosolvent/water solutions, have been used to validate the new models. The calculated macroscopic and structural properties are in agreement with experimental findings, supporting the validity of the newly proposed models.
Public Insurance and Single-Guardian Households Are Associated with Diagnostic Delay in Slipped Capital Femoral Epiphysis

Background: Extensive literature documents the adverse sequelae of delayed diagnosis of slipped capital femoral epiphysis (SCFE), including worsening deformity and surgical complications. Less is known about predictors of delayed diagnosis of SCFE, particularly the effects of social determinants of health. The purpose of this study was to evaluate the impact of insurance type, family structure, and neighborhood-level socioeconomic vulnerability on the delay of SCFE diagnosis. Methods: We reviewed medical records of patients who underwent surgical fixation for stable SCFE at a tertiary pediatric hospital from 2002 to 2021. We abstracted data on demographic characteristics, insurance status, family structure, home address, and symptom duration. We measured diagnostic delay in weeks from the date of symptom onset to diagnosis. We then geocoded patient addresses to determine their Census tract-level U.S. Centers for Disease Control and Prevention (CDC) and Agency for Toxic Substances and Disease Registry (ATSDR) Social Vulnerability Index (SVI), using U.S. Census and American Community Survey data. We performed 3 separate logistic regression models to examine the effects of (1) insurance status, (2) family structure, and (3) SVI on a delay of ≥12 weeks (reference, <12 weeks). We adjusted for age, sex, weight status, number of siblings, and calendar year. Results: We identified 351 patients with SCFE; 37% (129) had a diagnostic delay of ≥12 weeks. In multivariable logistic regression models, patients with public insurance were more likely to have a delay of ≥12 weeks than patients with private insurance (adjusted odds ratio [OR], 1.83 [95% confidence interval (CI), 1.12 to 2.97]; p = 0.015) and patients from single-guardian households were more likely to have a delay of ≥12 weeks than patients from multiguardian households (adjusted OR, 1.95 [95% CI, 1.11 to 3.45]; p = 0.021). We did not observe a significant increase in the odds of delay among patients in the highest quartile of overall SVI compared with patients from the lower 3 quartiles, in both the U.S. comparison (adjusted OR, 1.43 [95% CI, 0.79 to 2.58]; p = 0.24) and the Massachusetts comparison (adjusted OR, 1.45 [95% CI, 0.79 to 2.66]; p = 0.23). Conclusions: The delay in diagnosis of SCFE remains a concern, with 37% of patients with SCFE presenting with delay of ≥12 weeks. Public insurance and single-guardian households emerged as independent risk factors for diagnostic delay. Interventions to reduce delay may consider focusing on publicly insured patients and those from single-guardian households. Level of Evidence: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Non-vaccination Against COVID-19 Among Venezuelan Refugees and Migrants Adults in Peru: A Cross-sectional Study, 2022

Objectives The purpose of this study was to determine factors associated with non-vaccination against coronavirus disease 2019 (COVID-19) among the Venezuelan immigrant population residing in Peru. Methods A cross-sectional study was conducted using data obtained from the Second Survey of the Venezuelan Population Residing in Peru in 2022. The dependent variable was vaccination status against COVID-19. The independent variables included socio-demographic, economic, and migratory characteristics of the included population. Crude and adjusted generalized linear Poisson-family models were used to calculate prevalence ratios with 95% confidence intervals (CIs). Results A total of 7739 Venezuelan migrants aged 18 years or older were included. The proportion of non-vaccination against COVID-19 was 5.7%. Regarding associated factors, unemployment (adjusted prevalence ratio [aPR], 1.31; 95% CI, 1.04 to 1.65) was linked to an increased likelihood of not being vaccinated against COVID-19. In contrast, women (aPR, 0.76; 95% CI, 0.61 to 0.95), possessing a migration permit (aPR, 0.41; 95% CI, 0.31 to 0.54), and having health insurance (aPR, 0.47; 95% CI, 0.27 to 0.81) were associated with a decreased likelihood of being unvaccinated. Conclusions The primary governmental and non-governmental institutions responsible for supporting and protecting the Venezuelan migrant and refugee population should improve vaccination access by issuing migration permits and providing health insurance.
The influence of childhood emotional neglect experience on brain dynamic functional connectivity in young adults

ABSTRACT Background: Childhood emotional neglect (CEN) confers a great risk for developing multiple psychiatric disorders; however, the neural basis for this association remains unknown. Using a dynamic functional connectivity approach, this study aimed to examine the effects of CEN experience on functional brain networks in young adults. Method: In total, 21 healthy young adults with CEN experience and 26 without childhood trauma experience were recruited. The childhood trauma experience was assessed using the childhood trauma questionnaire (CTQ), and eligible participants underwent resting-state functional MRI. Sliding windows and k-means clustering were used to identify temporal features of large-scale functional connectivity states (frequency, mean dwell time, and transition numbers). Result: Dynamic analysis revealed two separate connection states: state 1 was more frequent and characterized by extensive weak connections between the brain regions. State 2 was relatively infrequent and characterized by extensive strong connections between the brain regions. Compared to the control group, the CEN group had a longer mean dwell time in state 1 and significantly decreased transition numbers between states 1 and 2. Conclusion: The CEN experience affects the temporal properties of young adults’ functional brain connectivity. Young adults with CEN experience tend to be stable in state 1 (extensive weak connections between the brain regions), reducing transitions between states, and reflecting impaired metastability or functional network flexibility. HIGHLIGHTS We focus solely on the childhood emotional neglect experience and its long-term effects on brain function. Eligible participants with and without childhood emotional neglect were identified through a large-scale screen among young adults. The results found childhood emotional neglect experiences have a long-term impact on brain flexibility.
Missed nursing care in relation to registered nurses' level of education and self-reported evidence-based practice.

BACKGROUND Patient safety is one of the cornerstones of high-quality healthcare systems. Evidence-based practice is one way to improve patient safety from the nursing perspective. Another aspect of care that directly influences patient safety is missed nursing care. However, research on possible associations between evidence-based practice and missed nursing care is lacking. AIM The aim of this study was to examine associations between registered nurses' educational level, the capability beliefs and use of evidence-based practice, and missed nursing care. METHODS This study had a cross-sectional design. A total of 228 registered nurses from adult inpatient wards at a university hospital participated. Data were collected with the MISSCARE Survey-Swedish version of Evidence-Based Practice Capabilities Beliefs Scale. RESULTS Most missed nursing care was reported within the subscales Basic Care and Planning. Nurses holding a higher educational level and being low evidence-based practice users reported significantly more missed nursing care. They also scored significantly higher on the Evidence-based Practice Capabilities Beliefs Scale. The analyses showed a limited explanation of the variance of missed nursing care and revealed that being a high user of evidence-based practice indicated less reported missed nursing care, while a higher educational level meant more reported missed nursing care. LINKING EVIDENCE TO ACTION Most missed nursing care was reported within the subscales Planning and Basic Care. Thus, nursing activities are deprioritized in comparison to medical activities. Nurses holding a higher education reported more missed nursing care, indicating that higher education entails deeper knowledge of the consequences when rationing nursing care. They also reported varied use of evidence-based practice, showing that higher education is not the only factor that matters. To decrease missed nursing care in clinical practice, and thereby increase the quality of care, educational level, use of evidence-based practice, and organizational factors must be considered.
Nervous system-related tropism of SARS-CoV-2 and autoimmunity in COVID-19 infection.

The effects of SARS-CoV-2 in COVID-19 on the nervous system are incompletely understood. SARS-CoV-2 can infect endothelial cells, neurons, astrocytes, and oligodendrocytes with consequences for the host. There are indications that infection of these central nervous system-resident cells may result in long term effects, including emergence of neurodegenerative diseases. Indirect effects of infection with SARS-CoV-2 relate to the induction of autoimmune disease involving molecular mimicry or/and bystander activation of T- and B cells and emergence of autoantibodies against various self-antigens. Data obtained in preclinical models of coronavirus induced disease gives important clues for understanding of nervous system related assault of SARS-CoV-2. The pathophysiology of long-COVID syndrome and post-COVID syndrome in which autoimmunity and immune dysregulation might be the driving forces are still incompletely understood. Better understanding of nervous-system-related immunity in COVID-19 might support development of therapeutic approaches. In this review, the current understanding of SARS-CoV-2 tropism for the nervous system, the associated immune responses and diseases are summarized. The data indicates that there is viral tropism of SARS-CoV-2 for the nervous system resulting into various disease conditions. Prevention of SARS-CoV-2 infection by means of vaccination is currently the best strategy for prevention of subsequent tissue damage involving the nervous system. This article is protected by copyright. All rights reserved.
Management of early-stage hepatocellular carcinoma: challenges and strategies for optimal outcomes

Although hepatocellular carcinoma (HCC) is associated with a poor prognosis, management of early-stage HCC is often successful with highly efficacious treatment modalities such as liver transplantation, surgical resection, and radiofrequency ablation. However, unfavorable clinical outcomes have been observed under certain circumstances, even after efficient treatment. Factors that predict unsuitable results after treatment include tumor markers, inflammatory markers, imaging findings reflecting tumor biology, specific outcome indicators for each treatment modality, liver functional reserve, and the technical feasibility of the treatment modalities. Various strategies may overcome these challenges, including the application of reinforced treatment indication criteria with predictive markers reflecting tumor biology, compensation for technical issues with up-to-date technologies, modification of treatment modalities, downstaging with locoregional therapies (such as transarterial chemotherapy or radiotherapy), and recently introduced combination immunotherapies. In this review, we discuss the challenges to achieving optimal outcomes in the management of early-stage HCC and suggest strategies to overcome these obstacles.
SAVE Testis-sparing score: a multicenter retrospective study of a novel predictive tool for quantifying testicular tumors

Background: Testis-sparing surgery (TSS) is a safe treatment for patients with benign testicular tumors. Presently, assessments for evaluating the suitability of TSS are poorly standardized, partially because testicular anatomical elements cannot be quantitatively described. Materials and methods: The authors developed a scoring method known as the SAVE testis-sparing score based on four critical and accessible anatomical features of a testicular tumor. The SAVE score ranges from 0 to 8 and is divided into four risk classes (low, medium, high, and extremely high) to evaluate the feasibility of TSS, wherein low-risk indicates high feasibility and vice versa. This study included 444 testicular tumor patients from eight centers. Among them, 216 patients (model group: 151 patients, validation group: 65 patients) were included in the modeling analysis, and the other 228 patients from children’s centers were included in the proportion analysis. Using retrospective data, patient characteristics associated with surgical methods were identified. Furthermore, a multivariate logistic regression model was built quantify the associations between these characteristics and the surgery method. The receiver operator characteristic curve was used to evaluate the classification efficiency of SAVE. Results: The SAVE testis-sparing score includes size (tumor size as maximal diameter), available testicular tissue volume, volume ratio of the tumor to the testis, and the exophytic/endophytic properties of the tumor. The SAVE scoring system accurately classified the suitability of TSS based on the complexity of benign testicular tumors. Conclusion: The SAVE score is a reproducible and robust tool for quantitatively describing the anatomical characteristics of benign testicular tumors and guide the preoperative evaluation of TSS.
Chest MRI and CT Predictors of 10-Year All-Cause Mortality in COPD

Abstract Pulmonary imaging measurements using magnetic resonance imaging (MRI) and computed tomography (CT) have the potential to deepen our understanding of chronic obstructive pulmonary disease (COPD) by measuring airway and parenchymal pathologic information that cannot be provided by spirometry. Currently, MRI and CT measurements are not included in mortality risk predictions, diagnosis, or COPD staging. We evaluated baseline pulmonary function, MRI and CT measurements alongside imaging texture-features to predict 10-year all-cause mortality in ex-smokers with (n = 93; 31 females; 70 ± 9years) and without (n = 69; 29 females, 69 ± 9years) COPD. CT airway and vessel measurements, helium-3 (3He) MRI ventilation defect percent (VDP) and apparent diffusion coefficients (ADC) were quantified. MRI and CT texture-features were extracted using PyRadiomics (version2.2.0). Associations between 10-year all-cause mortality and all clinical and imaging measurements were evaluated using multivariable regression model odds-ratios. Machine-learning predictive models for 10-year all-cause mortality were evaluated using area-under-receiver-operator-characteristic-curve (AUC), sensitivity and specificity analyses. DLCO (%pred) (HR = 0.955, 95%CI: 0.934-0.976, p < 0.001), MRI ADC (HR = 1.843, 95%CI: 1.260-2.871, p < 0.001), and CT informational-measure-of-correlation (HR = 3.546, 95% CI: 1.660-7.573, p = 0.001) were the strongest predictors of 10-year mortality. A machine-learning model trained on clinical, imaging, and imaging textures was the best predictive model (AUC = 0.82, sensitivity = 83%, specificity = 84%) and outperformed the solely clinical model (AUC = 0.76, sensitivity = 77%, specificity = 79%). In ex-smokers, regardless of COPD status, addition of CT and MR imaging texture measurements to clinical models provided unique prognostic information of mortality risk that can allow for better clinical management.Clinical Trial Registration: www.clinicaltrials. gov NCT02279329
Ventilatory efficiency in post‐COVID‐19 athletes

Limitation in exercise capacity has not been described in athletes affected by SARS‐CoV‐2 infection. However, patients who have recovered from COVID‐19 without cardiopulmonary impairment show exaggerated ventilatory response during exercise. Therefore, we aimed to evaluate the ventilatory efficiency (VEf) in competitive athletes recovered from COVID‐19 and to characterize the ventilation versus carbon dioxide relationship (VE/VCO2) slope in this population. Thirty‐seven competitive athletes with COVID‐19 were recruited for this study. All participants underwent spirometry, echocardiography, and cardiopulmonary exercise testing (CPET). z‐FVC values and end‐title pressure of CO2 (PETCO2) were lower in the third tertile compared with the first tertile: −0.753 ± 0.473 vs. 0.037 ± 0.911, p = 0.05; 42.2 ± 2.7 vs. 37.1 ± 2.5 mmHg, p < 0.01. VE/VCO2 slope was significantly correlated to maximal VCO2/VE and maximal VO2/VE: coefficient = −0.5 R2 = 0.58, p < 0.0001 and coefficient = −0.3 R2 = 0.16, p = 0.008. Competitive athletes affected by SARS‐CoV‐2 infection, without cardio‐respiratory disease sequel, may present ventilatory inefficiency (ViE), without exercise capacity limitation. FVC is higher in athletes with better ventilatory performance during exercise, and increased VE/VCO2 slope is inversely correlated to max VCO2/VE and max VO2/VE.
‘We are suffering. Nothing is changing.’ Black mother's experiences, communication, and support in the neonatal intensive care unit in the United States: A Qualitative Study

ABSTRACT Objectives Black mothers experience markedly disproportionate maternal morbidity and mortality in the United States, with racism often cited as the root cause manifesting through several pathways. The study examined Black mothers’ perceived provider communication, support needs, and overall experiences in the neonatal intensive care unit (NICU). Design This study used grounded theory embedded in the Black feminist theoretical (BFT) framework to generate new ideas grounded in the data. Data was collected through semi-structured interviews using videoconferencing, with questions related to the mother's overall NICU experiences, communication within the NICU, and perceived support needs. Data were analyzed using thematic analysis. Results Twelve mothers participated in the study; most were married (n = 10), had a cesarean birth, had a previous pregnancy complication (e.g., diabetes, hypertension), had attained a graduate degree or more (n = 9), earned an annual household income of $75,000 or more, and were between 35–44 years of age (n = 7). Three broad domains with several accompanying themes and sub-themes were identified, explicating the mother's experiences in the NICU. Specifically, factors influencing NICU hospitalization for mothers included maternal care/nursing experiences, interactions in the NICU, and the perceived support need that might attenuate negative care and birthing experiences. Conclusion The study adds to the growing literature championing Black maternal health equity and multilevel quality improvement strategies to foster equitable maternal health. Our study reinforces the need for racially congruent interventions and policy reformations to protect Black birthing people regardless of socioeconomic factors and social class using life course, holistic approaches, and intersectionality mindset. Importantly, using the BFT, this study calls for culturally sensitive research to capture the nuances associated with the multiplicity of experiences of Black people.
Current and novel percutaneous epicardial access techniques for electrophysiological interventions: A comparison of procedural success and safety

Accessing the pericardial space safely and efficiently is an important skill for interventional cardiac electrophysiologist. With the increased recognition of the complexity of the 3‐dimensional arrhythmogenic substrate due to advances in imaging and mapping technologies there has been an expansion of epicardial procedures in recent years. Equally, minimally invasive implantation of epicardial pacing, cardiac resynchronization, or defibrillation leads is expanding in specific patients where transvenous systems are contraindicated or their long term sequelae should be ideally avoided. Selective delivery of intrapericardial pharmacological antiarrhythmic therapy is yet another potential indication, albeit still investigational. The expanding indications for percutaneous epicardial procedures is contrasted by the still substantial risk and challenges associated with accessing the pericardial space. Myocardial perforation, coronary artery laceration, and damage to the surrounding organs are all recognized and feared complications. A number of innovative epicardial access techniques have been proposed to overcome the difficulties and risks of traditional dry subxiphoid punctures and may allow for more widespread use of epicardial access in the future. We review 10 different established and novel subxiphoidal epicardial access techniques describing procedural success rates, safety profile and overall experience. The technical aspects as well as access times and costs for extra equipment will be reviewed. Finally, an outlook of reported preclinical techniques awaiting in‐human feasibility studies is provided.
Mathematical models assessing the importance of disease on ecological invasions

A general understanding of the role that both shared disease and competition may play in ecological invasions is lacking. We develop a theoretical framework to determine the role of disease, in addition to competition, in invasions. We first investigate the effect of disease characteristics on the replacement time of a native species by an invader. The outcome is critically dependent on the relative effects that the disease has on the two species and less dependent on the basic epidemiological characteristics of the interaction. This framework is extended to investigate the effect of disease on the spatial spread of an invader and indicates that a wave of disease spreads through a native population in advance of the replacement. A probabilistic simulation model is developed to examine the particular example of the replacement of red squirrels by grey squirrels in the United Kingdom. This model is used to examine conservation strategies employed within red squirrel refuges and compared to observations from Sefton Coast Red Squirrel Refuge. Our findings indicate that culling greys may be effective at protecting red populations from replacement, but none of the conservation strategies currently employed can prevent periodic outbreaks of infection within red squirrel refuges.