bluuebunny/crossref_metadata_2025_split huggingface dataset:
2024 Clinical Practice Guideline Update by the Infectious Diseases Society of America on Complicated Intra-abdominal Infections: Diagnostic Imaging of Suspected Acute Appendicitis in Adults, Children, and Pregnant People
Authors: Bonomo Robert A , Tamma Pranita D , Abrahamian Fredrick M , Bessesen Mary , Chow Anthony W , Dellinger E Patchen , Edwards Morven S , Goldstein Ellie , Hayden Mary K , Humphries Romney , Kaye Keith S , Potoski Brian A , Rodríguez-Baño Jesús , Sawyer Robert , Skalweit Marion , Snydman David R , Donnelly Katelyn , Loveless Jennifer 
Published: July 2024

Abstract
This paper is part of a clinical practice guideline update on the risk assessment, diagnostic imaging, and microbiological evaluation of complicated intra-abdominal infections in adults, children, and pregnant people, developed by the Infectious Diseases Society of America (IDSA). In this paper, the panel provides recommendations for diagnostic imaging of suspected acute appendicitis. The panel's recommendations are based on evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.
2024 Clinical Practice Guideline Update by the Infectious Diseases Society of America on Complicated Intra-abdominal Infections: Diagnostic Imaging of Suspected Acute Intra-abdominal Abscess in Adults, Children, and Pregnant People
Authors: Bonomo Robert A , Tamma Pranita D , Abrahamian Fredrick M , Bessesen Mary , Chow Anthony W , Dellinger E Patchen , Edwards Morven S , Goldstein Ellie , Hayden Mary K , Humphries Romney , Kaye Keith S , Potoski Brian A , Rodríguez-Baño Jesús , Sawyer Robert , Skalweit Marion , Snydman David R , Donnelly Katelyn , Loveless Jennifer 
Published: July 2024

Abstract
This article is part of a clinical practice guideline update on the risk assessment, diagnostic imaging, and microbiological evaluation of complicated intra-abdominal infections in adults, children, and pregnant people, developed by the Infectious Diseases Society of America. In this article, the panel provides recommendations for diagnostic imaging of suspected acute intra-abdominal abscess. The panel's recommendations are based on evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach.
2024 Clinical Practice Guideline Update by the Infectious Diseases Society of America on Complicated Intra-abdominal Infections: Utility of Intra-abdominal Fluid Cultures in Adults, Children, and Pregnant People
Authors: Bonomo Robert A , Humphries Romney , Abrahamian Fredrick M , Bessesen Mary , Chow Anthony W , Dellinger E Patchen , Edwards Morven S , Goldstein Ellie , Hayden Mary K , Kaye Keith S , Potoski Brian A , Rodríguez-Baño Jesús , Sawyer Robert , Skalweit Marion , Snydman David R , Tamma Pranita D , Donnelly Katelyn , Loveless Jennifer 
Published: July 2024

Abstract
This paper is part of a clinical practice guideline update on the risk assessment, diagnostic imaging, and microbiological evaluation of complicated intra-abdominal infections in adults, children, and pregnant people, developed by the Infectious Diseases Society of America. In this paper, the panel provides recommendations for obtaining cultures of intra-abdominal fluid in patients with known or suspected intra-abdominal infection. The panel's recommendations are based on evidence derived from systematic literature reviews and adhere to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach.
Secondary tricuspid regurgitation: incidence, types, and outcomes in atrial fibrillation vs. sinus rhythm
Authors: Naser Jwan A , Castrichini Matteo , Ibrahim Hossam H , Scott Christopher G , Lin Grace , Lee Eunjung , Mankad Rekha , Siontis Konstantinos C , Eleid Mackram F , Pellikka Patricia A , Michelena Hector I , Pislaru Sorin V , Nkomo Vuyisile T 
Published: July 2024

Abstract

Background and Aims
Incidence and types of secondary tricuspid regurgitation (TR) are not well defined in atrial fibrillation (AFib) and sinus rhythm (SR). Atrial secondary TR (A-STR) is associated with pre-existing AFib; however, close to 50% of patients with A-STR do not have AFib. The aim of this study was to assess incidence, types, and outcomes of ≥ moderate TR in AFib vs. SR.

Methods
Adults with and without new-onset AFib without structural heart disease or ≥ moderate TR at baseline were followed for the development of ≥ moderate TR. Tricuspid regurgitation types were pacemaker, left-sided valve disease, left ventricular (LV) dysfunction, pulmonary hypertension (PH), isolated ventricular, and A-STR.

Results
Among 1359 patients with AFib and 20 438 in SR, 109 and 378 patients developed ≥ moderate TR, respectively. The individual types of TR occurred more frequently in AFib related to the higher pacemaker implantation rates (1.12 vs. 0.19 per 100 person-years, P &lt; .001), larger right atrial size (median 78 vs. 53 mL, P &lt; .001), and higher pulmonary pressures (median 30 vs. 28 mmHg, P &lt; .001). The most common TR types irrespective of rhythm were LV dysfunction-TR and A-STR. Among patients in SR, those with A-STR were older, predominantly women with more diastolic abnormalities and higher pulmonary pressures. All types of secondary TR were associated with all-cause mortality, highest in PH-TR and LV dysfunction-TR.

Conclusions
New-onset AFib vs. SR conferred a higher risk of the individual TR types related to sequelae of AFib and higher pacemaker implantation rates, although the distribution of TR types was similar. Secondary TR was universally associated with increased mortality.
The relationship between psychological burden and providing assistance with taking medication among caregivers of patients with dementia: a cross-sectional study
Authors: Fuga Habuchi , Yamaoka Erika , Ishida Natsuko , Shitanda Koji , Hashimoto Masako , Matushita Ryo 
Published: July 2024

Abstract

Objectives
Previous studies have examined the psychological burden of caregivers of patients with dementia. However, although many caregivers struggle to assist patients with dementia with medication management, the relationship between assisting such patients with taking their medicines and the caregiver psychological burden is understudied. Therefore, this study identified the association between caregivers’ psychological burden and assisting patients with dementia with taking medication.

Methods
A cross-sectional survey was conducted among caregivers of patients with dementia in Japan. The survey questionnaire included questions that assessed the symptoms of patients with dementia, their status of taking medication through medication assistance from caregivers, and caregivers’ psychological burden using the Kessler Psychological Distress Scale and the Japanese version of the Perceived Stress Scale.

Key findings
A total of 57 caregivers participated in the study. Higher Kessler Psychological Distress Scale scores were significantly associated with unsuccessful assistance with taking regular medication (β = 0.35, 95% confidence interval [CI]: 2.23–12.0, P &lt; .05), depressive symptoms (β = 0.26, 95% CI: 0.10–8.53, P &lt; .05), and irritability (β = 0.38, 95% CI: 2.71–11.5, P &lt; .05). Likewise, higher scores on the Japanese version of the Perceived Stress Scale were significantly associated with irritability (β = 0.37, 95% CI: 1.87–12.5, P &lt; .05) among patients with dementia.

Conclusion
The findings suggest that caregiver psychological burden is associated with unsuccessful assistance with taking regular medication for patients with dementia.
Do Pregnant Persons Want Influenza Vaccines? Knowledge, Attitudes, Perceptions, and Practices Toward Influenza Vaccines in 8 Low- and Middle-Income Countries
Authors: McCarron Margaret , Yau Tat S , Griffin Chelsey , Marcenac Perrine , Ebama Malembe S , Lafond Kathryn E , Igboh Ledor S , Duca Lindsey M , Bino Silvia , Bettaieb Jihene , Dhaouadi Sonia , Sahakyan Gayane , Cherkaoui Imad , Alj Loubna , Coulibaly Daouda , Lutwama Julius J , Douba Alfred , N’Gattia Anderson , Khanthamaly Viengphone , Tengbriacheu Chankham , Patthammavong Chansay , Lambach Philipp , Otorbaeva Dinagul , Azziz-Baumgartner Eduardo , Bresee Joseph S 
Published: July 2024

Abstract

Background
Vaccination is the most effective way to prevent influenza infection and adverse outcomes; despite global recommendations to vaccinate pregnant persons, access to influenza vaccines remains low. We explored knowledge, attitudes, and practices of pregnant persons to inform actions to improve vaccine uptake.

Methods
We pooled data from cross-sectional surveys assessing pregnant persons’ attitudes toward influenza vaccines in 8 low- and middle-income countries. Countries used standard methods to measure attitudes and intents toward influenza vaccination. We stratified by presence/absence of a national influenza vaccination program, income group, geographic region, and individual-level factors.

Results
Our analysis included 8556 pregnant persons from 8 countries. Most pregnant persons (6323, 74%) were willing to receive influenza vaccine if it was offered for free. Willingness differed by presence of an existing influenza vaccination program; acceptance was higher in countries without programs (2383, 89%) than in those with programs (3940, 67%, P &lt; .001).

Conclusions
Most pregnant persons in middle-income countries, regardless of influenza vaccination program status, were willing to be vaccinated against influenza if the vaccine was provided free of charge. National investments in influenza vaccination programs present an opportunity to avert illness both in pregnant persons themselves and in their newborn babies.
Diverse roles of dendritic cell and regulatory T cell crosstalk in controlling health and disease
Authors: Yamazaki Sayuri 
Published: July 2024

Abstract
Dendritic cells (DCs) are specialized antigen-presenting cells for lymphocytes, including regulatory T (Treg) cells, a subset of CD4+ T cells expressing CD25 and Foxp3, a transcription factor. Treg cells maintain immunological self-tolerance in mice and humans, and suppress autoimmunity and other various immune responses such as tumor immunity, transplant rejection, allergy, responses to microbes, and inflammation. Treg-cell proliferation is controlled by antigen-presenting DCs. On the other hand, Treg cells suppress the function of DCs by restraining DC maturation. Therefore, the interaction between DCs and Treg cells, DC–Treg crosstalk, could contribute to controlling health and disease. We recently found that unique DC–Treg crosstalk plays a role in several conditions. First, Treg cells are expanded in ultraviolet B (UVB)-exposed skin by interacting with DCs, and the UVB-expanded Treg cells have a healing function. Second, manipulating DC–Treg crosstalk can induce effective acquired immune responses against severe acute respiratory syndrome coronavirus 2 antigens without adjuvants. Third, Treg cells with a special feature interact with DCs in the tumor microenvironment of human head and neck cancer, which may contribute to the prognosis. Understanding the underlying mechanisms of DC–Treg crosstalk may provide a novel strategy to control health and disease.
The Dynamic Effects of UN SEA Reporting on the Actions of Peacekeeping Contributing Countries
Authors: Torres-Beltran Angie , Mailhot Cameron 
Published: July 2024

Abstracts
What effect does sexual exploitation and abuse (SEA) reporting by the United Nations (UN) have on the actions of peacekeeping missions’ troop and police contributing countries (TPCCs)? While past scholarship has studied the effect of naming and shaming for states’ human rights records, we examine the relationship between the UN’s reporting on human rights abuses committed by its Member States’ personnel and their policy and personnel responses. Focusing on SEA reporting within peacekeeping missions, we theorize the ways in which the UN’s reporting of SEA may lead to two distinct responses: TPCCs may issue legal frameworks to demonstrate compliance and address SEA, or they may withdraw from peacekeeping missions by reducing their personnel commitments. Using an original, cross-national dataset of UN reporting on SEA allegations and the patterns of framework issuance and personnel commitments among TPCCs (2010–2020), we find that TPCCs with SEA reports are more likely to issue legal frameworks and to reduce personnel contributions than their nonreported counterparts, and that this relationship is particularly strong following the first instance of reporting. With targeted TPCCs demonstrating both greater policy compliance and personnel withdrawal, our findings highlight the dynamic impact that UN reporting for SEA can have on the actions of TPCCs.
Revealing the effect of X-ray or proton brain irradiation on systemic inflammation and leukocyte subpopulation interplay in rodents
Authors: Pham Thao-Nguyen , Coupey Julie , Rousseau Marc , Thariat Juliette , Valable Samuel 
Published: July 2024

Abstract
The absolute lymphocyte count (ALC), lymphocyte-to-monocyte ratio (LMR), and neutrophil-to-lymphocyte ratio (NLR) offer convenient means to assess systemic inflammation post-cancer treatment, which influences treatment outcomes. Understanding these biomarker variations and leukocyte subpopulation interplay is crucial for optimizing radiotherapy. Herein, leukocyte subpopulations (T-CD4+, T-CD8+, B cells, NK cells, neutrophils, monocytes) during and after brain irradiation (using X-rays or protons) in tumor-free mice were used to compute ALC, LMR, and NLR, on which radiation parameter influence was assessed by principal component analysis (PCA). NLR kinetics was further examined using modeling. Leukocyte subpopulation interplays and their response to radiation parameters were examined using PCA and correlation analysis. Under X-rays, ALC and LMR decreased, with ALC recovered to baseline after irradiation, but not LMR. Both X-rays and protons increased the NLR during irradiation, recovering in protons but not X-rays. Both irradiation volume and dose rate had a pronounced effect on the NLR. Leukocyte subpopulation interplay was observed under X-rays and protons, normalizing in the proton group by day 28. Lymphopenia was observed in all lymphocyte subpopulations under X-ray irradiation but not protons. The recovery patterns varied among the subpopulations. Neutrophil counts increased during irradiation, with the recovery of protons, but not X-rays, by day 28. Interplays between NK cells and myeloid subpopulations were evident under X-rays but not protons. Importantly, no interplay was detected between myeloid cells and T/B cells, indicating that LMR and NLR variations were primarily due to independent responses to brain irradiation. A tumor-free experimental mouse model was used to study the effects of brain radiotherapy on systemic immunity. When administering fractionated irradiation with a total dose of 20 Gy using a vertical beam to either the whole brain or hemi-brain, proton irradiation had fewer adverse impacts on the immune system compared to X-rays in tumor-free rodents.
Measuring the ejecta velocities of type Ia supernovae from the pan-STARRS1 medium deep survey
Authors: Pan Y -C , Jheng Y -S , Jones D O , Lee I -Y , Foley R J , Chornock R , Scolnic D M , Berger E , Challis P M , Drout M , Huber M E , Kirshner R P , Kotak R , Lunnan R , Narayan G , Rest A , Rodney S , Smartt S 
Published: July 2024

ABSTRACT
There is growing evidence that Type Ia supernovae (SNe Ia) may originate from multiple explosion channels. Previous studies have indicated that the ejecta velocity of SNe Ia is one powerful tool to discriminate between different channels. In this work, we study ∼400 confirmed SNe Ia discovered by the Pan-STARRS1 Medium Deep Survey (PS1-MDS), and obtain a sample of ∼50 SNe Ia that have near-peak $\mathrm{Si}\, {\small II}\, \lambda 6355$ velocity ($v_{\mathrm{Si}\, {\small II}}$) measurements. We investigate the relationships between $v_{\mathrm{Si}\, {\small II}}$ and various parameters, including SN light-curve width, colour, host galaxy properties, and redshift. No significant trends are identified between $v_{\mathrm{Si}\, {\small II}}$ and light-curve parameters. Regarding the host-galaxy properties, we see a significant trend that high-velocity (HV) SNe Ia ($v_{\mathrm{Si}\, {\small II}}\gtrsim 12000$  km s$^{-1}$) tend to reside in more massive galaxies compared to normal velocity (NV) SNe Ia ($v_{\mathrm{Si}\, {\small II}}\lt 12000$  km s$^{-1}$) when combining both the PS1-MDS data set and those from previous low-z studies. While we do not see a significant trend between $v_{\mathrm{Si}\, {\small II}}$ and redshift, HV SNe Ia appear to be more prevalent in low-z samples than in high-z samples. We discuss several possibilities that could potentially contribute to this trend. Furthermore, we investigate the potential bias on SN Ia distances and find no significant difference in Hubble residuals between HV and NV subgroups.
Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies
Authors: Reyna-Blanco Carlos S , Caduff Madleina , Galimberti Marco , Leuenberger Christoph , Wegmann Daniel 
Published: July 2024

Abstract
Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice
Authors: Tresky Roland , Miyamoto Yuta , Nagayoshi Yu , Yabuki Yasushi , Araki Kimi , Takahashi Yukie , Komohara Yoshihiro , Ge Huicong , Nishiguchi Kayo , Fukuda Takaichi , Kaneko Hitomi , Maeda Nobuko , Matsuura Jin , Iwasaki Shintaro , Sakakida Kourin , Shioda Norifumi , Wei Fan-Yan , Tomizawa Kazuhito , Chujo Takeshi 
Published: July 2024

Abstract
In higher eukaryotes, tRNA methyltransferase 10A (TRMT10A) is responsible for N1-methylguanosine modification at position nine of various cytoplasmic tRNAs. Pathogenic mutations in TRMT10A cause intellectual disability, microcephaly, diabetes, and short stature in humans, and generate cytotoxic tRNA fragments in cultured cells; however, it is not clear how TRMT10A supports codon translation or brain functions. Here, we generated Trmt10a null mice and showed that tRNAGln(CUG) and initiator methionine tRNA levels were universally decreased in various tissues; the same was true in a human cell line lacking TRMT10A. Ribosome profiling of mouse brain revealed that dysfunction of TRMT10A causes ribosome slowdown at the Gln(CAG) codon and increases translation of Atf4 due to higher frequency of leaky scanning of its upstream open reading frames. Broadly speaking, translation of a subset of mRNAs, especially those for neuronal structures, is perturbed in the mutant brain. Despite not showing discernable defects in the pancreas, liver, or kidney, Trmt10a null mice showed lower body weight and smaller hippocampal postsynaptic densities, which is associated with defective synaptic plasticity and memory. Taken together, our study provides mechanistic insight into the roles of TRMT10A in the brain, and exemplifies the importance of universal tRNA modification during translation of specific codons.
Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites
Authors: Chen Wenhan , Zeng Yi C , Achinger-Kawecka Joanna , Campbell Elyssa , Jones Alicia K , Stewart Alastair G , Khoury Amanda , Clark Susan J 
Published: July 2024

Abstract
CCCTC-binding factor (CTCF) is an insulator protein that binds to a highly conserved DNA motif and facilitates regulation of three-dimensional (3D) nuclear architecture and transcription. CTCF binding sites (CTCF-BSs) reside in non-coding DNA and are frequently mutated in cancer. Our previous study identified a small subclass of CTCF-BSs that are resistant to CTCF knock down, termed persistent CTCF binding sites (P-CTCF-BSs). P-CTCF-BSs show high binding conservation and potentially regulate cell-type constitutive 3D chromatin architecture. Here, using ICGC sequencing data we made the striking observation that P-CTCF-BSs display a highly elevated mutation rate in breast and prostate cancer when compared to all CTCF-BSs. To address whether P-CTCF-BS mutations are also enriched in other cell-types, we developed CTCF-INSITE—a tool utilising machine learning to predict persistence based on genetic and epigenetic features of experimentally-determined P-CTCF-BSs. Notably, predicted P-CTCF-BSs also show a significantly elevated mutational burden in all 12 cancer-types tested. Enrichment was even stronger for P-CTCF-BS mutations with predicted functional impact to CTCF binding and chromatin looping. Using in vitro binding assays we validated that P-CTCF-BS cancer mutations, predicted to be disruptive, indeed reduced CTCF binding. Together this study reveals a new subclass of cancer specific CTCF-BS DNA mutations and provides insights into their importance in genome organization in a pan-cancer setting.
Directed evolution of hyperactive integrases for site specific insertion of transgenes
Authors: Hew Brian E , Gupta Sabranth , Sato Ryuei , Waller David F , Stoytchev Ilko , Short James E , Sharek Lisa , Tran Christopher T , Badran Ahmed H , Owens Jesse B 
Published: July 2024

Abstract
The ability to deliver large transgenes to a single genomic sequence with high efficiency would accelerate biomedical interventions. Current methods suffer from low insertion efficiency and most rely on undesired double-strand DNA breaks. Serine integrases catalyze the insertion of large DNA cargos at attachment (att) sites. By targeting att sites to the genome using technologies such as prime editing, integrases can target safe loci while avoiding double-strand breaks. We developed a method of phage-assisted continuous evolution we call IntePACE, that we used to rapidly perform hundreds of rounds of mutagenesis to systematically improve activity of PhiC31 and Bxb1 serine integrases. Novel hyperactive mutants were generated by combining synergistic mutations resulting in integration of a multi-gene cargo at rates as high as 80% of target chromosomes. Hyperactive integrases inserted a 15.7 kb therapeutic DNA cargo containing von Willebrand Factor. This technology could accelerate gene delivery therapeutics and our directed evolution strategy can easily be adapted to improve novel integrases from nature.