bluuebunny/crossref_metadata_2025_split huggingface dataset:
The importance of early recognition of extraintestinal manifestations of digestive tract dysfunction following gastrointestinal surgery
Authors: Pang Michelle , Kuwada Scott 
Published: May 2024

Abstract
We report a case of a 47-year-old male who presented with altered mental status. A review of his records revealed a weight loss of 20 lbs over the past 6 years, a recent hospitalization for idiopathic polyneuropathy with failure to thrive, and prior surgeries for peptic ulcer disease and small bowel obstruction. He was alert but had retrograde amnesia and peripheral neuropathy. A diagnosis was made, and the patient improved with treatment but was unfortunately left with irreversible neurological deficits. We discuss the importance of recognizing the extraintestinal manifestations of gastrointestinal dysfunction following gastrointestinal surgery.
To Calm and to Commend: Veterans’ Musical Preferences Anticipating End of Life
Authors: Krauss Beatrice J 
Published: May 2024

ABSTRACT

Introduction
Since World War 1, physicians have noted the calming effects of music for military personnel experiencing “shell shock,” Post Traumatic Stress Disorder (PTSD), or stress. Researchers have documented that stress or PTSD-like symptoms re-emerge for veterans at the end of life, triggered by hospital-like settings, co-occurring conditions, and debilitation. Dying veterans also face integration of their service and combat experiences into summations of their lives. In response, there has been a national movement for bedside ceremonies, often with music, to honor veterans.

Materials and Methods
The project elicited veterans’ musical preferences for calming and for music for honor services, using non-hospitalized veterans as surrogates for veterans in hospice. Respondent-driven sampling protected confidentiality and likely resulted in participants being representative of US veterans in terms of ethnicity, gender, and military branch. Recruitment materials contained all elements of informed consent, with consent collected in the introduction to the online survey. The survey had embedded links to musical performances, as well as write-in musical choices, and allowed US veterans from the Army, Air Force, Marines, and Navy to note their preferences both for music that was calming and music to be used in honor ceremonies. Online queries also asked about stress during service, usual coping strategies for stress, and current or past symptoms of PTSD. Links to hot lines were provided. The study was approved by the University of Arizona Institutional Review Board.

Results
Listening to music was the most prevalent of the 20 coping mechanisms for stress in this sample of 30 veterans. Musical preferences were stable across age groups. For calming, music at resting heartbeat rhythms was chosen. Music from early adulthood or from the timelessness of the classics was selected most often. Modern music with lyrics has themes of duty, affirmation, gratitude, and relief. The nearly universal soothing effects of lullabies were recognized. For music for honor ceremonies, desires were often independent of the military branch. Patriotic songs, or songs recognizing multiple service branches, or with themes of peace and affirmation were more often chosen than music from a particular service branch.

Conclusion
Listening to music is a frequent coping strategy for veterans. While themes representing classical music choices are readily available in anthologies, other music chosen by this sample is not; the veterans’ preferred music is rarely found in compilations of popular, movie, and TV music. Hospice and hospital intakes that document and communicate veterans’ musical preferences to music therapists and therapeutic musicians may better support service men and women. Further research may examine veterans’ preference for live or recorded music at end of life given the importance of meaning-making and the presence of others documented in the literature.
Cluster cosmology redux: a compact representation for the halo mass function
Authors: Norton Cameron E , Adams Fred C , Evrard August E 
Published: May 2024

ABSTRACT
Groups and clusters of galaxies imprint coherent, arcminute-scale features across the spectrophotometric sky, especially optical-IR clusters of galaxies, spectral distortions in the cosmic microwave background, and extended sources of X-ray emission. The space–time density of the host dark matter halo population – the halo mass function (HMF) – is a common theoretical basis for modelling such observable features. We explore a compact representation – a dual-quadratic (DQ-HMF) form – that features readily interpretable parameters representing polynomial expansions of the space–time number density surface, first in terms of log-mass, then in redshift. The DQ-HMF form fits Mira-Titan N-body emulator expectations for halo masses $10^{13.7-14.5} \, h^{-1}\, {\rm M}_\odot$ over redshifts, 0.1 &lt; z &lt; 1.5 to within $\sim \! 5~{{\ \rm per\ cent}}$. We provide best-fitting parameters for a Planck 2018 cosmology and demonstrate model self-similarity in the Ωm−$\, \sigma _8$ plane. Convolving with a minimal mass–observable relation (MOR) yields closed-form expressions for counts, mean mass, and mass variance of cluster samples characterized by an observable property. Performing information-matrix forecasts of potential parameter constraints from existing and future surveys, we demonstrate the potential for percent-level constraints on model parameters by an LSST-like optical cluster survey of 300 000 clusters and a richness–mass variance of 0.32. Even better constraints could potentially be achieved by a survey with one-tenth the sample size but with a reduced selection property variance of 0.12. Potential benefits and extensions to the basic MOR parametrization are discussed.
Increasing AGN sample completeness using long-term near-infrared variability
Authors: Green K , Elmer E , Maltby D T , Almaini O , Merrifield M , Hartley W G 
Published: May 2024

ABSTRACT
In this work, we use 8 years of deep near-infrared imaging to select and study a new set of 601 active galaxies identified through long-term near-infrared (NIR) variability in the UKIDSS Ultra Deep Survey (UDS). These objects are compared to 710 X-ray bright Active Galactic Nuclei (AGN) detected by the Chandra X-ray observatory. We show that infrared variability and X-ray emission select distinct sets of active galaxies, finding only a 37 per cent overlap of galaxies detected by both techniques and confirming NIR-variable AGN to be typically X-ray quiet. Examining the mass functions of the active galaxies shows that NIR variability detects AGN activity in galaxies over a significantly wider range of host stellar mass compared to X-ray detection. For example, at z ∼ 1, variable AGN are identified among approximately 1 per cent of galaxies in a roughly flat distribution above the stellar mass completeness limit ($\gt 10^{9}\rm \, {\rm M}_{\odot }$), while X-ray detection primarily identifies AGN in galaxies of higher mass ($\gt 10^{10}\rm \, {\rm M}_{\odot }$). We conclude that long-term near-infrared variability provides an important new tool for obtaining more complete samples of AGN in deep survey fields.
HYMALAIA: a hybrid lagrangian model for intrinsic alignments
Authors: Maion Francisco , Angulo Raul E , Bakx Thomas , Chisari Nora Elisa , Kurita Toshiki , Pellejero-Ibáñez Marcos 
Published: May 2024

ABSTRACT
The intrinsic alignment of galaxies is an important ingredient for modelling weak-lensing measurements, and a potentially valuable cosmological and astrophysical signal. In this paper, we present HYbrid Model Advected from LAgrangian space for IA (HYMALAIA): a new model to predict the intrinsic alignments of biased tracers. HYMALAIA is based on a perturbative expansion of the statistics of the Lagrangian shapes of objects, which is then advected to Eulerian space using the fully non-linear displacement field obtained from N-body simulations. We demonstrate that HYMALAIA is capable of consistently describing monopole and quadrupole of halo shape–shape and matter–shape correlators, and that, without increasing the number of free parameters, it does so more accurately than other perturbatively inspired models such as the non-linear alignment model and the tidal-alignment-tidal-torquing model.
Structure of an internal loop motif with three consecutive U•U mismatches from stem–loop 1 in the 3′-UTR of the SARS-CoV-2 genomic RNA
Authors: Vögele Jennifer , Duchardt-Ferner Elke , Bains Jasleen Kaur , Knezic Bozana , Wacker Anna , Sich Christian , Weigand Julia E , Šponer Jiří , Schwalbe Harald , Krepl Miroslav , Wöhnert Jens 
Published: May 2024

Abstract
The single-stranded RNA genome of SARS-CoV-2 is highly structured. Numerous helical stem–loop structures interrupted by mismatch motifs are present in the functionally important 5′- and 3′-UTRs. These mismatches modulate local helical geometries and feature unusual arrays of hydrogen bonding donor and acceptor groups. However, their conformational and dynamical properties cannot be directly inferred from chemical probing and are difficult to predict theoretically. A mismatch motif (SL1-motif) consisting of three consecutive U•U base pairs is located in stem–loop 1 of the 3′-UTR. We combined NMR-spectroscopy and MD-simulations to investigate its structure and dynamics. All three U•U base pairs feature two direct hydrogen bonds and are as stable as Watson–Crick A:U base pairs. Plasmodium falciparum 25S rRNA contains a triple U•U mismatch motif (Pf-motif) differing from SL1-motif only with respect to the orientation of the two closing base pairs. Interestingly, while the geometry of the outer two U•U mismatches was identical in both motifs the preferred orientation of the central U•U mismatch was different. MD simulations and potassium ion titrations revealed that the potassium ion-binding mode to the major groove is connected to the different preferred geometries of the central base pair in the two motifs.
Protein phosphatase PP1 regulation of RNA polymerase II transcription termination and allelic exclusion of VSG genes in trypanosomes
Authors: Kieft Rudo , Zhang Yang , Yan Haidong , Schmitz Robert J , Sabatini Robert 
Published: May 2024

Abstract
The genomes of Leishmania and trypanosomes are organized into polycistronic transcription units flanked by a modified DNA base J involved in promoting RNA polymerase II (Pol II) termination. We recently characterized a Leishmania complex containing a J-binding protein, PP1 protein phosphatase 1, and PP1 regulatory protein (PNUTS) that controls transcription termination potentially via dephosphorylation of Pol II by PP1. While T. brucei contains eight PP1 isoforms, none purified with the PNUTS complex, complicating the analysis of PP1 function in termination. We now demonstrate that the PP1-binding motif of TbPNUTS is required for function in termination in vivo and that TbPP1-1 modulates Pol II termination in T. brucei and dephosphorylation of the large subunit of Pol II. PP1-1 knock-down results in increased cellular levels of phosphorylated RPB1 accompanied by readthrough transcription and aberrant transcription of the chromosome by Pol II, including Pol I transcribed loci that are typically silent, such as telomeric VSG expression sites involved in antigenic variation. These results provide important insights into the mechanism underlying Pol II transcription termination in primitive eukaryotes that rely on polycistronic transcription and maintain allelic exclusion of VSG genes.
The p21CIP1-CDK4-DREAM axis is a master regulator of genotoxic stress-induced cellular senescence
Authors: Schmidt Ariane , Allmann Sebastian , Schwarzenbach Christian , Snyder Petra , Chen Jia-Xuan , Nagel Georg , Schöneis Anna , Rasenberger Birgit , Beli Petra , Loewer Alexander , Hofmann Thomas G , Tomicic Maja T , Christmann Markus 
Published: May 2024

Abstract
Cellular senescence, a major driver of aging, can be stimulated by DNA damage, and is counteracted by the DNA repair machinery. Here we show that in p16INK4a-deficient cells, senescence induction by the environmental genotoxin B[a]P or ionizing radiation (IR) completely depends on p21CIP1. Immunoprecipitation-based mass spectrometry interactomics data revealed that during senescence induction and maintenance, p21CIP1 specifically inhibits CDK4 and thereby activates the DREAM complex. Genome-wide transcriptomics revealed striking similarities in the response induced by B[a]P and IR. Among the top 100 repressed genes 78 were identical between B[a]P and IR and 76 were DREAM targets. The DREAM complex transcriptionally silences the main proliferation-associated transcription factors E2F1, FOXM1 and B-Myb as well as multiple DNA repair factors. Knockdown of p21CIP1, E2F4 or E2F5 diminished both, repression of these factors and senescence. The transcriptional profiles evoked by B[a]P and IR largely overlapped with the profile induced by pharmacological CDK4 inhibition, further illustrating the role of CDK4 inhibition in genotoxic stress-induced senescence. Moreover, data obtained by live-cell time-lapse microscopy suggest the inhibition of CDK4 by p21CIP1 is especially important for arresting cells which slip through mitosis. Overall, we identified the p21CIP1/CDK4/DREAM axis as a master regulator of genotoxic stress-induced senescence.
Trends and socioeconomic inequality of the burden of congenital abnormalities of the kidney and urinary tract among children and adolescents
Authors: He Guohua , Liu Yunfei , Bagga Arvind , Onubogu Chinyere Ukamaka , Schaefer Franz , Zou Zhiyong , Smoyer William E , Xiao Nianzhou , Lin Tianxin , Lanewala Ali Asghar , Kang Hee Gyung , Waheed Muhammad Zeeshan , Park Seungkyo , Jiang Xiaoyun , Song Yi , Ding Jie 
Published: May 2024

ABSTRACT

Background
Although congenital abnormalities of the kidney and urinary tract (CAKUT) is the leading cause of childhood-onset chronic kidney disease and kidney failure, comprehensive information on the disease burden among children and adolescents globally is lacking. We aim to report the trends and socioeconomic inequality of CAKUT burden for people aged 0–24 years from 1990 to 2019.

Methods
We reported the prevalence, mortality and disability-adjusted life-years (DALYs) for CAKUT based on the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, quantified the association of disease burden and socio-demographic index (SDI), and calculated the slope index of inequality, the relative index of inequality and concentration index.

Results
In 2019, the global prevalence, mortality and DALYs of CAKUT among individuals aged 0–24 years were 167.11 (95% confidence interval 166.97, 167.25), 0.30 (0.29, 0.30) and 32.22 (32.16, 32.29), respectively, per 100 000 population. The greatest prevalence, mortality and DALYs were recorded in the 0–4 years age group. The greatest mortality and DALYs were recorded in low SDI countries and territories. During 1990 to 2019, the prevalence, mortality and DALYs decreased globally, while in low and low-middle countries and territories the reduction was much less slower. India, Nigeria and Pakistan had the highest DALYs. Saudi Arabia and China exhibited a markedly decrease of CAKUT burden. Globally for every 0.1 increase in SDI, there was a 20.53% reduction in mortality and a 16.31% decrease in DALYs, but a 0.38% rise in prevalence.

Conclusions
Inequality for disease burden of varying SDI was increasing globally. Thus, specific preventive and health service measures are needed to reduce the global burden from CAKUT.
Genomic ascertainment of primary central nervous system cancers in adolescents and young adults
Authors: Stewart Douglas R 
Published: May 2024

Abstract
Genomic ascertainment is the inversion of the traditional phenotype-first approach; with a “genome-first” approach, a cohort linked to electronic health records (EHR) undergoes germline sequencing (array, panel, exome, and genome) and deleterious variation of interest in a gene (or set of genes) are identified. Phenotype is then queried from the linked EHR and from call-back investigation and estimates of variant prevalence, disease penetrance, and phenotype can be determined. This should permit a better estimate of the full phenotypic spectrum, severity, and penetrance linked to a deleterious variant. For now, given the modest size, limited EHR, and age of participants in sequenced cohorts, genomic ascertainment approaches to investigate cancer in children and young adults will likely be restricted to descriptive studies and complement traditional phenotype-first work. Another issue is the ascertainment of the cohort itself: Participants need to survive long enough to enroll. Not accounting for this may lead to bias and incorrect estimates of variant prevalence. Adult-focused cohorts with EHR extending back into childhood, linked to cancer registries, and/or studies that permit recontact with participants may facilitate genomic ascertainment in pediatric cancer research. In summary, genomic ascertainment in pediatric primary brain cancer research remains largely untapped and merits further investigation.
No drug holidays in BRAFV600E glioma patients: An argument for dose reduction of targeted therapies
Authors: Bazer Danielle A , Kolchinski Anna , Bush Nancy A O , Clarke Jennifer L , Bagley Stephen J , Schreck Karisa C 
Published: May 2024

Abstract

Background
Combined BRAF and MEK inhibition is effective for some BRAFV600E-altered gliomas, a cancer for which there are few effective therapies. While recent clinical trials demonstrate objective response rates of 30%–40%, tolerable adverse event rates are 70%–90%, and 12%–15% of patients stop therapy for toxicity. There are no clear guidelines regarding the timing and reinitiation of BRAF-targeted therapies following drug holidays. Here, we describe 4 patients with rapid disease progression during periods of treatment interruption. All patients experienced a response upon resumption of targeted therapy.

Methods
This is a multi-institutional, retrospective review of 4 patients.

Results
Three patients were diagnosed with BRAFV600E mutated anaplastic pleomorphic xanthoastrocytoma (aPXA) and 1 with epithelioid glioblastoma. The age range was 32 to 46; 3 patients were female and one patient was male. All patients were initially treated with radiation and were subsequently treated with BRAF/MEK inhibitors after disease progression. All patients with aPXA required the targeted therapy to be held due to toxicity and 1 patient held the therapy prior to transitioning to a novel BRAF-targeted agent. All patients were restarted on BRAF/MEK inhibitors after a drug holiday. Three patients required a dose reduction and all improved clinically following reinitiation.

Conclusions
Clinical and radiographic progression may occur rapidly upon holding BRAF-targeted therapy, warranting judicious dose reductions and minimization of drug holidays.
Xuemei Chen: Original innovation often derives from free exploration
Authors: Gu Chao 
Published: May 2024

ABSTRACT
Xuemei Chen is a distinguished biologist. She was elected a member of the US National Academy of Sciences in 2013, and is now the Dean of the School of Life Sciences at Peking University. Her main research areas are flower development, plant microRNAs, and RNA modifications. In this interview, Xuemei Chen discussed the prospects of plant research, and emphasized the significance of free exploration to achieve the ground-breaking ‘0 to 1’ innovation—until free exploration leads to the discovery of the ‘1’, one may not know what the ‘0’ is and may not be able to intentionally seek it. She also introduced the upcoming Beijing Advanced Center of RNA Biology (BEACON), and expressed her views on organized scientific research.
Cabotegravir + Rilpivirine Long-Acting: Overview of Injection Guidance, Injection Site Reactions, and Best Practices for Intramuscular Injection Administration
Authors: Teichner Paula , Chamay Nadine , Elliot Emilie , Pascual-Bernáldez Miguel , Merrill Deanna , Garris Cindy , D’Amico Ronald , Felizarta Cecy , Torres Emma , Van Solingen-Ristea Rodica , Baugh Bryan , Patel Parul , Vannappagari Vani , Dakhia Samia , Polli Joseph W , Garside Louise , Grove Richard , Thiagarajah Shanker , Birmingham Eileen , van Wyk Jean 
Published: May 2024

Abstract

Background
Cabotegravir (CAB) + rilpivirine (RPV) dosed monthly or every 2 months is a complete long-acting (LA) regimen for the maintenance of human immunodeficiency virus type 1 virologic suppression. Across the phase 3/3b trials, the most frequently reported adverse events were injection site reactions (ISRs).

Methods
We present pooled ISR characteristics and outcomes for participants receiving CAB + RPV LA through week 96 of the FLAIR and ATLAS-2M studies, and survey results from healthcare providers (HCPs) giving injections (eg, injectors) in the ATLAS, FLAIR, and ATLAS-2M studies to determine optimal injection techniques. Surveys were anonymous, self-administered online questionnaires that queried provider demographics, injection experience, and techniques to minimize pre-/postinjection discomfort. Data were summarized using descriptive statistics.

Results
Overall, 8453 ISRs were reported by 801 participants receiving ≥1 injection of CAB LA/RPV LA. Most ISRs were mild to moderate in severity (grade 1–2, 99%), with a median duration of 3 days (interquartile range, 2–4 days), and rarely led to withdrawal (2%). Surveys were completed by 181 HCPs across 113 sites. Pushing the intramuscular injection at slow speed (66%), bringing the medication to room temperature (58%), and relaxing the gluteus muscle before injecting (53%) were ranked as effective preinjection/injection procedure practices for minimizing pain. Most injectors (60%) indicated that a prone position provided optimal patient comfort, and 41% had no preference on injection medication order.

Conclusions
Taken together, the data demonstrate favorable tolerability with CAB + RPV LA injections over the long term and simple techniques routinely used by injectors to help optimize the administration of CAB + RPV LA injections.
Varicella-Zoster Virus–Induced Neurologic Disease After COVID-19 Vaccination: A Multicenter Observational Cohort Study
Authors: Elbaz Meital , Hoffman Tomer , Yahav Dafna , Dovrat Sarah , Ghanem-Zoubi Nesrin , Atamna Alaa , Grupel Daniel , Reisfeld Sharon , Hershman-Sarafov Mirit , Ciobotaro Pnina , Najjar-Debbiny Ronza , Brosh-Nissimov Tal , Chazan Bibiana , Yossepowitch Orit , Wiener-Well Yonit , Halutz Ora , Reich Shelley , Ben-Ami Ronen , Paran Yael 
Published: May 2024

Abstract

Background
Early reports described an increased risk of herpes zoster following receipt of mRNA-based COVID-19 vaccines. The objective was to assess whether COVID-19 vaccine is associated with varicella-zoster virus–induced neurologic disease (VZV-ND).

Methods
This multicenter retrospective case-control study with a test-negative design was conducted at 12 hospitals in Israel. We included all patients admitted with VZV-ND between January 2020 and December 2021 and matched controls with a negative polymerase chain reaction result for VZV in cerebrospinal fluid.

Results
We identified 188 patients meeting the case definition of VZV-ND who were admitted during the study period. Cases were matched with 376 controls. There was no significant variation in the incidence of VZV-ND between 1 year preceding and 1 year following the deployment of BNT162b2 in Israel. Analysis of persons who had received at least 1 dose of COVID-19 vaccine (n = 259) showed similar proportions of VZV-ND and non–VZV-ND in 4 intervals (30, 42, 50, 60 days) following the last vaccine dose. The median time from the last vaccine dose to hospitalization with a neurologic syndrome was 53 days (IQR, 25–128) and 82 days (IQR, 36–132) for VZV-ND and non–VZV-ND, respectively, not reaching statistical significance (P = .056). The rate of VZV-ND in vaccinated patients was no different from the rate in the unvaccinated group (30.9% vs 35.4%, P = .2).

Conclusions
We did not find an association between COVID-19 vaccine and VZV-ND. Since COVID-19 vaccine is now recommended yearly, every fall and winter, establishing the safety of the vaccine is of great importance.