bluuebunny/crossref_metadata_2025_split huggingface dataset:
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation
Authors: Blin Kai , Shaw Simon , Augustijn Hannah E , Reitz Zachary L , Biermann Friederike , Alanjary Mohammad , Fetter Artem , Terlouw Barbara R , Metcalf William W , Helfrich Eric J N , van Wezel Gilles P , Medema Marnix H , Weber Tilmann 
Published: May 2023

Abstract
Microorganisms produce small bioactive compounds as part of their secondary or specialised metabolism. Often, such metabolites have antimicrobial, anticancer, antifungal, antiviral or other bio-activities and thus play an important role for applications in medicine and agriculture. In the past decade, genome mining has become a widely-used method to explore, access, and analyse the available biodiversity of these compounds. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ (https://antismash.secondarymetabolites.org/) has supported researchers in their microbial genome mining tasks, both as a free to use web server and as a standalone tool under an OSI-approved open source licence. It is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in archaea, bacteria, and fungi. Here, we present the updated version 7 of antiSMASH. antiSMASH 7 increases the number of supported cluster types from 71 to 81, as well as containing improvements in the areas of chemical structure prediction, enzymatic assembly-line visualisation and gene cluster regulation.
TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning
Authors: Yin Rui , Ribeiro-Filho Helder V , Lin Valerie , Gowthaman Ragul , Cheung Melyssa , Pierce Brian G 
Published: May 2023

Abstract
The cellular immune system, which is a critical component of human immunity, uses T cell receptors (TCRs) to recognize antigenic proteins in the form of peptides presented by major histocompatibility complex (MHC) proteins. Accurate definition of the structural basis of TCRs and their engagement of peptide–MHCs can provide major insights into normal and aberrant immunity, and can help guide the design of vaccines and immunotherapeutics. Given the limited amount of experimentally determined TCR–peptide–MHC structures and the vast amount of TCRs within each individual as well as antigenic targets, accurate computational modeling approaches are needed. Here, we report a major update to our web server, TCRmodel, which was originally developed to model unbound TCRs from sequence, to now model TCR–peptide–MHC complexes from sequence, utilizing several adaptations of AlphaFold. This method, named TCRmodel2, allows users to submit sequences through an easy-to-use interface and shows similar or greater accuracy than AlphaFold and other methods to model TCR–peptide–MHC complexes based on benchmarking. It can generate models of complexes in 15 minutes, and output models are provided with confidence scores and an integrated molecular viewer. TCRmodel2 is available at https://tcrmodel.ibbr.umd.edu.
Solitude and Soul in Restoration Britain
Authors: Taylor Barbara 
Published: May 2023

Abstract
In 1672 John Evelyn, Restoration courtier, diarist and polymath, formed a platonic soul union with Margaret Blagge (later Godolphin), a young maid of honour in Queen Catherine’s household. Both were devout Anglicans whose religious practices were shaped by their love of ‘recesse’. For four years they enacted a spiritual solitude à deux in an emotionally charged relationship lived out through private prayer and epistolary devotional exchanges, until Margaret’s marriage and death in childbirth. Solitude was then, as it had long been, highly contentious. In the 1660s Evelyn had debated it with a Scottish lawyer named George Mackenzie. In a spirit of mock argument common at the time, Evelyn had taken the anti-solitude side. Yet despite the playfulness of the debate, it highlighted tensions in Evelyn’s love of solitude that played out across his life, reaching an emotional peak in his soul union with Margaret. For Margaret, too, life with Evelyn was fraught as she struggled with melancholic miseries long associated with solitude, compounded by a conflict between her reclusive devotional life with him and her engagement to the courtier Sidney Godolphin. Tracking the story of this complex spiritual partnership provides intimate insights into the psychological stakes of the solitude tradition and its varying implications for women and men in Restoration Britain.
L’utilisation du monoxyde d’azote inhalé chez les nouveau-nés
Authors: Mitra Souvik , Altit Gabriel 
Published: May 2023

Résumé
Le monoxyde d’azote inhalé (NOi), un vasodilatateur pulmonaire sélectif, est utilisé pour le traitement des nouveau-nés en insuffisance respiratoire hypoxémique (IRH) associée à une hypertension pulmonaire persistante du nouveau-né. Idéalement, il doit commencer à être administré après la confirmation échocardiographique de ce type d’hypertension. L’utilisation de NOi est recommandée chez les nouveau-nés peu prématurés ou à terme chez qui survient une IRH malgré des stratégies d’oxygénation ou de ventilation optimales. Cependant, il n’est pas recommandé d’y recourir systématiquement chez les nouveau-nés prématurés sous assistance respiratoire. On peut l’envisager comme traitement de secours chez les nouveau-nés prématurés en IRH précoce associée à une rupture prolongée des membranes ou à un oligoamnios, ou en IRH tardive en cas d’hypertension pulmonaire liée à une dysplasie bronchopulmonaire et accompagnée d’une insuffisance ventriculaire droite marquée. On peut aussi l’envisager chez les nouveau-nés atteints d’une hernie diaphragmatique congénitale qui présentent une IRH persistante, malgré un recrutement pulmonaire optimal, des signes échocardiographiques d’hypertension pulmonaire suprasystémique et un fonctionnement ventriculaire gauche approprié.
Highly differentiated genomic properties underpin the different cell walls of Poaceae and eudicots
Authors: Pancaldi Francesco , Schranz Michael Eric , van Loo Eibertus N , Trindade Luisa M 
Published: May 2023

Abstract
Plant cell walls of Poaceae and eudicots differ substantially, both in the content and composition of their components. However, the genomic and genetic basis underlying these differences is not fully resolved. In this research, we analyzed multiple genomic properties of 150 cell wall gene families across 169 angiosperm genomes. The properties analyzed include gene presence/absence, copy number, synteny, occurrence of tandem gene clusters, and phylogenetic gene diversity. Results revealed a profound genomic differentiation of cell wall genes between Poaceae and eudicots, often associated with the cell wall diversity between these plant groups. For example, overall patterns of gene copy number variation and synteny were clearly divergent between Poaceae and eudicot species. Moreover, differential Poaceae–eudicot copy number and genomic contexts were observed for all the genes within the BEL1-like HOMEODOMAIN 6 regulatory pathway, which respectively induces and represses secondary cell wall synthesis in Poaceae and eudicots. Similarly, divergent synteny, copy number, and phylogenetic gene diversification were observed for the major biosynthetic genes of xyloglucans, mannans, and xylans, potentially contributing to the differences in content and types of hemicellulosic polysaccharides differences in Poaceae and eudicot cell walls. Additionally, the Poaceae-specific tandem clusters and/or higher copy number of PHENYLALANINE AMMONIA-LYASE, CAFFEIC ACID O-METHYLTRANSFERASE, or PEROXIDASE genes may underly the higher content and larger variety of phenylpropanoid compounds observed in Poaceae cell walls. All these patterns are discussed in detail in this study, along with their evolutionary and biological relevance for cell wall (genomic) diversification between Poaceae and eudicots.
Quantifying the rebound of influenza epidemics after the adjustment of zero-COVID policy in China
Authors: Lei Hao , Yang Lei , Yang Mengya , Tang Jing , Yang Jiaying , Tan Minju , Yang Shigui , Wang Dayan , Shu Yuelong 
Published: May 2023

Abstract
The coexistence of coronavirus disease 2019 (COVID-19) and seasonal influenza epidemics has become a potential threat to human health, particularly in China in the oncoming season. However, with the relaxation of nonpharmaceutical interventions (NPIs) during the COVID-19 pandemic, the rebound extent of the influenza activities is still poorly understood. In this study, we constructed a susceptible–vaccinated–infectious–recovered–susceptible (SVIRS) model to simulate influenza transmission and calibrated it using influenza surveillance data from 2018 to 2022. We projected the influenza transmission over the next 3 years using the SVIRS model. We observed that, in epidemiological year 2021–2022, the reproduction numbers of influenza in southern and northern China were reduced by 64.0 and 34.5%, respectively, compared with those before the pandemic. The percentage of people susceptible to influenza virus increased by 138.6 and 57.3% in southern and northern China by October 1, 2022, respectively. After relaxing NPIs, the potential accumulation of susceptibility to influenza infection may lead to a large-scale influenza outbreak in the year 2022–2023, the scale of which may be affected by the intensity of the NPIs. And later relaxation of NPIs in the year 2023 would not lead to much larger rebound of influenza activities in the year 2023–2024. To control the influenza epidemic to the prepandemic level after relaxing NPIs, the influenza vaccination rates in southern and northern China should increase to 53.8 and 33.8%, respectively. Vaccination for influenza should be advocated to reduce the potential reemergence of the influenza epidemic in the next few years.
Federalism and State Restructuring in Africa: A Comparative Analysis of Origins, Rationales, and Challenges
Authors: Yimenu Bizuneh 
Published: May 2023

Abstract
This article assesses federalism in the five African federations: Ethiopia, Nigeria, Somalia, South Africa, and South Sudan. By using Varieties of Democracy (V-Dem) and Afrobarometer data, it systematically investigates in what respect federalism succeeded and failed and whether the success rate varies across the states. It shows that federalism is successful in maintaining the states’ territorial integrity, but its success in conflict reduction is limited. Federalism helped reduce conflict in South Africa but not Nigeria and Ethiopia due to a lack of essential ingredients enabling federalism to flourish in multinational states. Federalism enabled South Africa and Nigeria to accommodate diversity by reducing identity-based exclusion and improving diverse groups’ access to power. In Ethiopia, it facilitated cultural and linguistic plurality but was unsuccessful in reducing exclusion and improving groups’ equal access to power. Africa illustrates that federalism fails to manage conflict unless incumbents embrace democracy, curtail centralism, and are loyal to federalism.
A Case for Social Workers as Investigators in Public Defender Offices
Authors: Hurd Amy L 
Published: May 2023

Abstract
Social workers play a critical role in modern public defender offices, whether performing mitigation work for pretrial negotiations and sentencing hearings or helping clients to secure access to basic human needs. Although social workers have held in-house positions in public defender offices since at least the 1970s, their service is largely limited to mitigation practice and traditional social work. This article raises an opportunity for social workers to broaden their capacity within public defense by pursuing investigator positions. A case is made for interested social workers to draw upon their education, training, and experience to showcase the alignment between their talents and the requisite skills and performance required of investigative work. Evidence is offered to support the notion that social workers bring skills and a social justice orientation to investigative work that can provide for fresh insight and innovation in investigation and defense strategy. The value brought to investigation by social workers throughout a legal defense is specified, as are considerations for applying and interviewing for investigator positions as social workers.
Rhabdomyolysis After Intravenous Iron Sucrose Infusion During Pregnancy
Authors: Ge Christina , Reyes Jessica , Queenan Ruth Anne , Gherman Robert B. 
Published: May 2023

BACKGROUND:
Iron infusions have become increasingly common in the treatment of iron-deficiency anemia during pregnancy. Although iron infusions are generally well tolerated, adverse reactions have been reported.

CASE:
A pregnant patient was diagnosed with rhabdomyolysis after receiving a second dose of intravenous (IV) iron sucrose at 32 6/7 weeks of gestation. On admission to the hospital, creatine kinase was 2,437 units/L, sodium was 132 mEq/L, and potassium was 2.1 mEq/L. Intravenous fluids and electrolyte repletion were administered, with improvement of symptoms within 48 hours. Creatinine kinase normalized 1 week after hospital discharge.

CONCLUSION:
Rhabdomyolysis can be associated with IV iron infusion during pregnancy.
Confirmation of Heart Malformations in Fetuses in the First Trimester Using Three-Dimensional Histologic Autopsy
Authors: Ruican Dan , Petrescu Ana-Maria , Istrate-Ofiţeru Anca-Maria , Roșu Gabriela Camelia , Zorilă George-Lucian , Dîră Laurenţiu Mihai , Nagy Rodica Daniela , Mogoantă Laurenţiu , Pirici Daniel , Iliescu Dominic Gabriel 
Published: May 2023

BACKGROUND:
We aimed to evaluate the usefulness of three-dimensional (3D) reconstruction of histology slides to confirm congenital heart disease (CHD) detected by first-trimester fetal cardiac ultrasonography. Conventional autopsy is hindered by the small size of the first-trimester fetal heart, and current CHD confirmation studies employ the use of highly specialized and expensive methods.

TECHNIQUE:
An extended first-trimester ultrasound examination protocol was used to diagnose fetal heart anomalies. Medical termination of pregnancies was followed by fetal heart extraction. The specimens were sliced, and the histology slides were stained and scanned. The resulting images were processed, and volume rendering was performed using 3D reconstruction software. The volumes were analyzed by a multidisciplinary team of maternal–fetal medicine subspecialists and pathologists and compared with ultrasound examination findings.

EXPERIENCE:
Six fetuses with heart malformations were evaluated using histologic 3D imaging: two with hypoplastic left heart syndrome, two with atrioventricular septal defects, one with an isolated ventricular septal defect, and one with transposition of the great arteries. The technique allowed us to confirm ultrasound-detected anomalies and also identified additional malformations.

CONCLUSION:
After pregnancy termination or loss, histologic 3D imaging can be used to confirm the presence of fetal cardiac malformations detected during first-trimester ultrasound examination. Additionally, this technique has the potential to refine the diagnosis for counseling regarding recurrence risk and retains the advantages of standard histology.
Wellness Opportunities for Migrant Beginnings, Kansas City, Missouri
Authors: Sekhon Subhjit , Smith Lucy , Morales Pedro 
Published: May 2023

OBJECTIVE:
To create a collaboration among health care professionals and community organizers to advance health equity and increase access to high-quality perinatal health care for Afghan refugees.

PROJECT SUMMARY:
This project was developed to create relationships among the health care industry, community partners, and nonprofit organizations to improve the perinatal health status of the refugee population of Kansas City, Missouri. Meetings were held among leaders of three medical systems (Samuel U. Rodgers Clinic, Swope Health, and University Health) and the two major resettlement agencies (Della Lamb and Jewish Vocational Services) to discuss barriers to care. These included communication, coordination of care, time limitations, and misunderstandings of the system. The following focus areas were identified, and interventions then were implemented:
1. Education
a. Seminars for health care professionals regarding specific perinatal health care needs
b. Tours and classes for refugees during which they were introduced to the facility, including labor and delivery, and prenatal, antenatal, and postpartum care
2. Communication
a. Medical passports for patients to better facilitate perinatal care among organizations, because all facilities provide care but deliveries occur only at University Health
3. Research
a. Performing surveillance activities and disseminating findings to aid other communities
The project is now expanding to include all refugee populations in the Kansas City area. Regular meetings are held quarterly with community leaders for continued quality improvement.

OUTCOME:
Primary outcomes focus on our refugee patients: increased patient autonomy, adherence to prenatal and postpartum visits, and developing trust in the system. Secondary outcomes include improved communication between clinics and resettlement agencies and improved cultural awareness among obstetric care professionals.

RELEVANCE TO WOMEN'S HEALTH:
Equity in perinatal care requires individualized services when serving a diverse population. Refugees in particular have a unique perspective and unique needs. Through collaboration, we were able to improve the health status of the most vulnerable members of our community.
Efficacy of the combination of tadalafil and tamsulosin versus tadalafil alone as a medical expulsive therapy for stone L1/3 ureter 10 mm or less: A prospective comparative placebo-controlled study
Authors: Reda Ahmed , Kamel Mostafa , Loay Mohamed , Abdelsalam Yaser M. , Zarzour Mohamed A. 
Published: May 2023

Abstract

Background
The lifetime occurrence of urinary stones is approximately 1%–15%, and the peak age of occurrence is 30 years. Approximately one fifths of urinary tract stones are found in the ureter, of which two thirds are in the distal ureter. Many drugs, including phosphodiesterase-5 inhibitors (PDE5Is) and α-blockers, are used to relax the smooth muscles in medical expulsive therapy (MET). We aimed to compare the combination of tadalafil and tamsulosin versus tadalafil alone as MET for stones in the L1/3 ureter of 10 mm or less.

Materials and methods
A total of 150 patients with L1/3 ureteric stones measuring 10 mm or less were enrolled in the study and randomly assigned to one of 3 equal groups using a computer-generated random number. Patients in group A prescribed tadalafil 10 mg/d. However, those in group B were prescribed tamsulosin 0.4 mg and tadalafil 10 mg/d, whereas those in group C received a placebo once daily. Stone expulsion rate and pain recurrence were evaluated after 14 days.

Results
The stone expulsion rate was significantly higher in the tadalafil and tamsulosin groups and the tamsulosin group than in the placebo group in the current study by 68% in the combination group, 64% in the tadalafil alone group, and 42% in the placebo group (p = 0.019). In the current study, a combination was associated with lower pain recurrence than tadalafil alone or placebo, with means of 1.06, 1.9, 2.98 (with a p value of 0.001). Stone size was not effective in any group.

Conclusions
The combination of PDE5Is and α-blockers effectively increases the expulsion of lower ureteric stones (5–10 mm), but with the same effect as PDE5Is alone, with the advantage of decreasing pain recurrence. Stone size did not affect the expulsion rate in patients who received MET for stones less than 1 cm in size.
The Role of Interleukin 6 in Substance Use Disorder Treatment Failure
Authors: Techau Aimee 
Published: May 2023

Abstract
Substance use disorders (SUDs) are often misunderstood as a reflection of an individual's lack of motivation or willpower or as a moral failing. SUDs are complex and require a biopsychosocial lens to understand the phenomenon, particularly treatment failure, which is described as a deficit in patients' willpower/self-regulation or dedication to managing their condition.
Recent evidence has implicated inflammatory cytokines such as interleukin 6 (IL-6) in the action of substance use by impairing executive functioning, which is an essential aspect of self-regulatory control. Emerging research indicates that inflammation may also shape social behavior, including social withdrawal and approach, thus having potential implications on health-seeking and health-sustaining behaviors often interpreted as a dedication to managing health conditions.
The aim of this two-part biobehavioral synthesis is to (a) examine the scientific evidence of the role of IL-6 in self-regulatory failure, (b) explore IL-6 as a common inflammatory mechanism across SUDs, and (c) investigate the role of IL-6 in social withdrawal and approach to gain an understanding of how this determinant may impact treatment failure.
Overall, the evidence supports a new paradigm of treatment failure that stresses the influence of IL-6 on self-regulatory failure by way of dual cognitive processing and the role of IL-6 in shaping social behavior central to health-seeking and health-sustaining behaviors. This discovery will help to minimize stigma and blame. Understanding the role of IL-6 in treatment failure may elucidate novel targets for intervention, improve treatment outcomes, and break the social disconnection cycle often seen in SUDs.
The Combined Effect of Delirium and Falls on Length of Stay and Discharge
Authors: Kalivas Benjamin , Zhang Jingwen , Harper Kristine , Dulin Jennifer , Heincelman Marc , Marsden Justin , Hunt Kelly J. , Mauldin Patrick D. , Moran William P. , Thomas Meghan K. 
Published: May 2023

ABSTRACT

Introduction:
Delirium or a fall are associated with many negative outcomes including increased length of stay (LOS) and discharge to a facility; however, this relationship is incompletely understood.

Methods:
A cross-sectional study of all hospitalizations in a large, tertiary care hospital evaluated the effect of delirium and a fall on the outcomes of LOS and risk of being discharged to a facility.

Results:
The study included 29,655 hospital admissions. A total of 3,707 (12.5%) patients screened positive for delirium and 286 (0.96%) had a reported fall. After adjustment for covariates, relative to patients without delirium or a fall, patients with delirium only had a 1.64-fold longer LOS; patients with fall only had a 1.96-fold longer LOS; and patients who had delirium and fall had a 2.84-fold longer LOS. The adjusted odds of discharge to a facility, relative to those without delirium or a fall, was 8.98 times higher in those with delirium and a fall.

Conclusions:
Delirium and falls influence LOS and likelihood of being discharged to a facility. The joint impact of falls and delirium on LOS and facility discharge was more than additive. Hospitals should consider the integrated management of delirium and falls.
Apathy Among Persons Living With HIV Is Associated With Lower Self-efficacy for Health Care Provider Interactions
Authors: Babicz Michelle A. , Matchanova Anastasia , Woods Steven Paul 
Published: May 2023

Abstract
Apathy is common in persons with HIV (PWH) and has been associated with a variety of health outcomes. We examined the association between apathy and self-efficacy for health care provider interactions in 142 PWH. A composite score comprised of the apathy subscale of the Frontal Systems Behavioral Scale and the vigor-activation scale of the Profile of Mood States was used to measure apathy. Self-efficacy for health care provider interactions was measured using the Beliefs Related to Medication Adherence – Dealing with Health Professional subscale. Higher levels of apathy were associated with lower self-efficacy for health care provider interactions at a medium effect size, independent of mood disorders, health literacy, and neurocognition. Findings suggest that apathy plays a unique role in self-efficacy for health care provider interactions and support the importance of assessment and management of apathy to maximize health outcomes among PWH.