bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-atherosclerotic acute cardiac syndromes: spontaneous coronary artery dissection and Takotsubo syndrome. Comparison of long-term clinical outcomes
Authors: Salamanca Jorge , García-Guimaraes Marcos , Sabaté Manel , Sanz-Ruiz Ricardo , Macaya Fernando , Roura Gerard , Jimenez-Kockar Marcelo , Nogales Juan Manuel , Tizón-Marcos Helena , Velazquez Maite , Veiga Gabriela , Gamarra Alvaro , Aguilar Rio , Jiménez-Borreguero Luis Jesús , Díez-Villanueva Pablo , Bastante Teresa , Núñez-Gil Iván , Alfonso Fernando 
Published: November 2023

Background
Spontaneous coronary artery dissection (SCAD) and Takotsubo syndrome (TTS) constitute two common causes of nonatherosclerotic acute cardiac syndrome particularly frequent in women. Currently, there is no information comparing long-term clinical outcomes in unselected patients with these conditions.

Methods
We compared the baseline characteristics, in-hospital outcomes, and the 12-month and long-term clinical outcomes of two large prospective registries on SCAD and TTS.

Results
A total of 289 SCAD and 150 TTS patients were included; 89% were women. TTS patients were older with a higher prevalence of cardiovascular risk factors. Precipitating triggers were more frequent in TTS patients, while emotional triggers and depressive disorders were more common in the SCAD group. Left ventricular ejection fraction was lower in TTS patients, but SCAD patients showed higher cardiac biomarkers. In-hospital events (43.3% vs. 5.2%, P<0.01) occurred more frequently in TTS patients. TTS patients also presented more frequent major adverse events at 12-month (14.7% vs. 7.1%, HR 5.3, 95% CI: 2.4–11.7, P<0.01) and long-term (median 36 vs. 31 months, P=0.41) follow-up (25.8% vs. 9.6%, HR 4.5, 95% CI: 2.5–8.2, P<0.01). Atrial fibrillation was also more frequent in TTS patients. Moreover, TTS patients presented a higher 12-month and long-term mortality (5.6% vs. 0.7%, P=0.01; and 12.6% vs. 0.7%, P<0.01) mainly driven by noncardiovascular deaths.

Conclusion
Compared to SCAD, TTS patients are older and present more cardiovascular risk factors but less frequent depressive disorder or emotional triggers. TTS patients have a worse in-hospital, mid-term, and long-term prognosis with higher noncardiac mortality than SCAD patients.
Novel therapies for pediatric acute lymphoblastic leukemia
Authors: Graff Zachary , Burke Michael J. , Gossai Nathan 
Published: November 2023

Purpose of review
This review summarizes the current novel therapy landscape in pediatric acute lymphoblastic leukemia (ALL), with a focus on key clinical trials which will shape the future direction of care for these children.

Recent findings
Recent landmark immunotherapy trials in B-ALL have demonstrated significant benefit for children, adolescents, and young adults with relapsed/refractory high-risk leukemia. Due to these successes, current trials are asking the question as to whether immunotherapy can be successfully incorporated upfront. Additionally, therapies targeting novel antigens or molecular pathways are being developed, providing new options for children previously thought to have incurable leukemia.

Summary
As survival for ALL has relatively plateaued with maximizing intensity through conventional chemotherapy, continued preclinical and clinical study of novel immunotherapeutic and targeted agents is crucial to further improve outcomes in childhood leukemia.
Controlling infections in hospitalized pretransplant candidates
Authors: Lacy Marian G. , Filippov Evgenii , Nematollahi Saman 
Published: November 2023

Purpose of review
Infections in hospitalized patients awaiting solid organ transplantation can pose complicated diagnostic and therapeutic challenges. Goals of management include stabilizing the patient, treating or controlling infections, and decreasing the risk of reactivation of infection after transplant.

Recent findings
Groups such as The Organ Procurement and Transplantation Network, American Society of Transplantation Infectious Diseases Community of Practice and the European Society of Clinical Microbiology and Infectious Diseases have updated their guidelines on screening and treatment of infection in transplant candidates. There are also recent developments in therapeutic options for tuberculosis, COVID-19, Clostridioides difficile colitis, bloodstream infections, and other common infections.

Summary
Ideally, antimicrobial therapy should be complete prior to transplantation. In situations in which completion of therapy prior to transplant is not feasible, therapy may need to be prolonged or modified. In most situations, infections can be managed similarly to the general population, although some infections, particularly fungal and mycobacterial, require a different management approach. We review disease- and organ-specific management.
Fetal growth assessed via ultrasound in relation to maternal HIV infection status and antiretroviral regimens
Authors: Williams Paige L. , Karalius Brad , Patel Kunjal , Aschengrau Ann , Chakhtoura Nahida , Enriquez Naomi , Moye Jack , Garvie Patricia A. , Monte Dina , Seage George R. , Zorrilla Carmen , Mussi-Pinhata Marisa M. ,   for the HIV ZIP Study
Published: November 2023

Objective:
To evaluate effects of maternal HIV and antiretroviral treatment (ART) on intrauterine fetal growth.

Design:
Prospective cohort studies of HIV and ZIKA infection among women living with HIV (WLHIV) and women not living with HIV (WNLHIV) conducted in Brazil and the US from 2016 to 2020.

Methods:
We evaluated fetal growth via repeated ultrasounds and calculated z scores for fetal growth measures using Intergrowth-21st standards among women with singleton pregnancies. Adjusted linear mixed models were fit for each fetal growth z score by HIV status. Among WLHIV, we compared fetal growth z scores by the most common maternal ART regimens, stratified by timing of ART initiation.

Results:
We included 166 WLHIV and 705 WNLHIV; none had Zika infection. The z scores were similar for WLHIV and WNLHIV for femur length (latest third trimester median = 1.08) and estimated fetal weight (median ≈0.60); adjusted mean differences in fetal weight z scores by HIV status were less than 0.1 throughout gestation. Other fetal growth measurements were lower for WLHIV than WNLHIV early in gestation but increased more rapidly over gestation. Among WLHIV not on ART at conception, adjusted mean z scores were generally similar across regimens initiated during pregnancy but somewhat lower for atazanavir-based regimens for biparietal diameter compared with efavirenz-based or raltegravir-based regimens. Among WLHIV on ART at conception, mean z scores were similar across ART regimens.

Conclusion:
Within our cohorts, fetal growth was lower in WLHIV than WNLHIV early in gestation but similar by the end of gestation, which is reassuring. Among WLHIV, fetal growth measures were generally similar across ART regimens evaluated.
The Effects of Progressive Resistance Strength Training on Pain, Mobility and Activities of Daily Living among Knee Osteoarthritis Patients: A randomized controlled trial
Authors: Rafiq Muhammad Tariq , Hamid Mohamad Shariff A , Hafiz Eliza , Chaudhary Farid Ahmad , Khan Muhammad Irfan 
Published: November 2023

ABSTRACTObjectiveThe objective of this study was to investigate the effects of progressive resistance strength training of lower limb rehabilitation protocol (LLRP) on pain, activities of daily living (ADL) and mobility among knee OA patients who are overweight or obese.Materials and MethodsFifty-six overweight or obese knee OA patients were included and randomly assigned to a Rehabilitation Protocol Group (RPG) or Control Group (CG). The patients in the RPG performed the progressive resistance strength training of LLRP and followed the instructions of daily care (IDC) for duration of twelve weeks at home. The patients in the CG followed the IDC (conventional treatment) only. Outcome measures were assessed at baseline and after the interventions in both groups by comparing the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score for pain, Timed Up and Go (TUG) test score for mobility and Katz Index of Independence scores for ADL.ResultsThe patients in the RPG reported significant improvements in WOMAC score for pain (p = 0.001), Katz Index of Independence scores for ADL (p = 0.003) and TUG test score for mobility (p = 0.004). The patients in the CG also reported significant improvements in WOMAC score for pain (p = 0.002) and ADL (p = 0.052), but not in mobility score (p = 0.065). The improvement in the pain and ADL scores was greater in the patients of RPG than the CG with p-value of 0.001 and 0.000 respectively.ConclusionThe progressive resistance strength training of LLRP is effective in terms of reducing pain, improving mobility and ADL among knee OA patients who are overweight or obese.
Membranous Nephropathy: Muti-omics Mendelian randomization and colocalization analysis
Authors: Su Zhihang , Liu Wen , Yin Zheng , Wu Di , Cheng Yuan , Wan Qijun 
Published: November 2023

AbstractBackgroundThe currently available medications for treating membranous nephropathy (MN) still have unsatisfactory efficacy in inhibiting disease recurrence, slowing down its progression, and even halting the development of end-stage renal disease. There is still a need to develop novel drugs targeting MN.MethodsWe utilized summary statistics of MN from the Kiryluk Lab and obtained plasma proteins from Zheng et al., Decode, and UKBioBank and gene data from eQTLgen and GTEX. We performed a two-sample Bidirectional mediation Mendelian randomization analysis, SMR analysis, HEIDI test, Bayesian colocalization, phenotype scanning, external validation, mediation analysis, drug bank analysis, and protein-protein interaction network.ResultsThe Mendelian randomization analysis uncovered 8 distinct proteins associated with MN after False Discovery Rate multiple correction. Proteins associated with an increased risk of MN in plasma include ABO [(Histo-Blood Group Abo System Transferase) (WR OR = 1.116, 95%CI:1.047-1.190, FDR=0.090, PPH4 = 0.795)], VWF [(Von Willebrand Factor) (WR OR = 1.412, 95%CI:1.157-1.725, FDR=0.018, PPH4 = 0.816)] and CD209 [(Cd209 Antigen) (WR OR = 1.187, 95%CI:1.074-1.312, FDR=0.090, PPH4 = 0.795)], and proteins that have a protective effect on MN: HRG [(Histidine-Rich Glycoprotein) (WR OR = 1.814, 95%CI:1.345-2.445, FDR=0.018, PPH4 = 0.797)], CD27 [(Cd27 Antigen) (WR OR = 0.785, 95%CI:0.681-0.904, FDR=0.018, PPH4 = 0.797)], LRPPRC [(Leucine-Rich Ppr Motif-Containing Protein, Mitochondrial) (WR OR = 0.790, 95%CI:0.688-0.907, FDR=0.090, PPH4 = 0.797)], TIMP4 [(Cd27 Antigen) (WR OR = 0.666, 95%CI:0.527-0.840, FDR=0.090PPH4 = 0.833)] and MAP2K4 [(Metalloproteinase Inhibitor 4) (WR OR = 0.815, 95%CI:0.723-0.919, FDR=0.090, PPH4 = 0.797)]. None of these proteins exhibited a reverse causal relationship. Bayesian colocalization analysis provided evidence that all of them share variants with MN. In external validation, ABO, CD27, HRG, MAP2K4, TIMP4, and VWF showed significant mediation results. We identified type 1 diabetes, trunk fat, and asthma as having intermediate effects in these pathways. We discovered several genes that are causally related to MN.ConclusionsOur comprehensive analysis indicates a causal effect of ABO, CD209, CD27, HRG, LRPPRC, MAP2K4, and TIMP4 at the genetically determined circulating levels on the risk of MN. These proteins have the potential to be a promising therapeutic target for the treatment of MN. We identified type 1 diabetes, trunk fat, and asthma as having intermediate effects in these pathways. We discovered several genes that are causally related to MN.
COPD with elevated sputum group 2 innate lymphoid cells is characterized by severe disease
Authors: Flayer Cameron H. , Linderholm Angela L. , Ge Moyar Q. , Juarez Maya , Franzi Lisa , Tham Tina , Teuber Melissa , Liao Shu-Yi , Schivo Michael , Kuhn Brooks , Zeki Amir , Haczku Angela 
Published: November 2023

ABSTRACTRationalePulmonary innate immune cells play a central role in the initiation and perpetuation of chronic obstructive pulmonary disease (COPD), however the precise mechanisms that orchestrate the development and severity of COPD are poorly understood.ObjectivesWe hypothesized that the recently described family of innate lymphoid cells (ILCs) play an important role in COPD.MethodsSubjects with COPD and healthy controls were clinically evaluated, and their sputum samples were assessed by flow cytometry. A mouse model of spontaneous COPD [genetically deficient in surfactant protein-D (SP-D-/-)] and ozone (O3) exposure were used to examine the mechanism by which lack of functional SP-D may skew ILC2s to produce IL-17A in combination with IL-5 and IL-13, leading to a mixed inflammatory profile and more severe disease.Measurements and Main ResultsCOPD was characterized by poor spirometry, sputum inflammation, and the emergence of sputum GATA3+ILCs (ILC2s), but not T-bet+ILCs (ILC1s) nor RORγt+ILCs (ILC3s). COPD subjects with elevated sputum ILC2s (the ILC2highgroup) had worse spirometry and sputum neutrophilia and eosinophilia than healthy and ILC2lowsubjects. This was associated with the presence of dual-positive IL-5+IL-17A+and IL-13+IL-17A+ILCs and nonfunctional SP-D in the sputum in ILC2highsubjects. SP-D-/-mice showed spontaneous airway neutrophilia. Lack of SP-D in the mouse lung licensed ILC2s to produce IL-17A, which was dose-dependently inhibited by recombinant SP-D. SP-D-/-mice showed enhanced susceptibility to O3-induced airway neutrophilia, which was associated with the emergence of inflammatory IL-13+IL-17A+ILCs.ConclusionsWe report that the presence of sputum ILC2s predicts the severity of COPD, and unravel a novel pathway of IL-17A plasticity in lung ILC2s, prevented by the immunomodulatory protein SP-D.
A simple correction to adjust for sampling biases in phylogeographic discrete trait analysis
Authors: Jorgensen David , Pons-Salort Margarita , Grassly Nicholas C 
Published: November 2023

AbstractDiscrete trait analysis (DTA) methods are widely used to infer patterns of movement between discrete geographic locations from genetic sequence data as they are simple and fast to implement. With the increasing interest in phylogeography for pathogen genomic epidemiology, accounting for and understanding the limitations of the methods used is becoming increasingly important. Applying DTA to location makes several strong simplifying assumptions, including the assumption of equal sampling probability across locations. This may lead to biased estimates of migration rates and ancestral locations where sampling rates vary. Here we investigate these biases using simulated migration and transmission data. We propose a simple correction to DTA for unequal sampling probability across locations when sampling rates are known or can be estimated. This correction to the migration rate matrix can be applied only to phylogenetic branches leading to sampled tips or to the whole phylogeny. We assess the performance of this correction using simulated data for a range of endemic transmission scenarios with varied sampling and migration rates. In a simple, two-location, case the correction performs significantly better than a standard DTA method in three of the four sampling rate distributions investigated. Applying the correction across only the tips of the phylogeny and over the full depth of the tree gives similar results, with the correction only at the tips performing marginally better in this simple two-location simulation. As migration is a key driver of infectious disease spread, improving estimates of migration with simple phylogenetic methods is a valuable development in infectious disease phylogeography.
iMab Antibody Binds Single-Stranded Cytosine-Rich Sequences and Unfolds DNA i-Motifs
Authors: Boissieras Joseph , Bonnet Hugues , Susanto Maria Fidelia , Gomez Dennis , Granzhan Anton , Defrancq Eric , Dejeu Jérôme 
Published: November 2023

ABSTRACTi-Motifs (iMs) are non-canonical, four-stranded secondary structures formed by stacking of hemi-protonated CH+·C base pairs in cytosine-rich DNA sequences, predominantly at pH < 7. The presence of iM structures in cells was a matter of debate until the recent development of iM-specific antibody, iMab, that was instrumental for several studies that suggested the existence of iMs in live cells and their putative biological roles. We assessed the interaction of iMab with cytosine-rich oligonucleotides by biolayer interferometry (BLI), pull-down assay and bulk-FRET experiments. Our results suggest that binding of iMab to DNA oligonucleotides is governed by the presence of runs of at least two consecutive cytosines and is generally increased in acidic conditions, irrespectively of the capacity of the sequence to adopt, or not, an iM structure. Moreover, the results of the bulk-FRET assay indicate that interaction with iMab results in unfolding of iM structures even in acidic conditions (pH 5.8 or 6.5), similarly to what has been observed with hnRNP K, well-studied single- stranded DNA binding protein. Taken together, our results suggest that iMab actually binds to blocks of 2–3 cytosines in single-stranded DNA, and call for more careful interpretation of results obtained with this antibody.
Aalbo1200: global genetic differentiation and variability of the mosquitoAedes albopictus
Authors: Crawford Jacob E. , Beebe Nigel , Bonizzoni Mariangela , Caputo Beniamino , Carter Brendan H. , Chen Chun-Hong , Cosme Luciano V. , De Marco Carlo Maria , Torre Alessandra della , Estallo Elizabet , Guo Xiang , Liu Wei-Liang , Maringer Kevin , Mains Jimmy , Maynard Andrew , Mogi Motoyoshi , Livdahl Todd , Rose Noah , Scarafia Patricia Y. , Severson Dave , Stein Marina , Surendran Sinnathamby N. , Tuno Nobuko , Wahid Isra , Wang Xiaoming , Xu Jiannong , Yan Guiyan , Yee Don , Armbruster Peter A. , Coccone Adalgisa , White Bradley J. 
Published: November 2023

AbstractThe mosquitoAedes albopictustransmits human viruses including dengue and chikungunya and is an extremely successful invasive species expanding into new regions of the world. New tools are needed to complement existing tools to help monitor and control this species. Genomic resources are improving for this species including genome reference sequences, and whole genome sequencing data will help to catalog genetic diversity in this species and further enable genetic analysis. We collected populations ofAe. albopictusfrom throughout its distribution and generated whole genome sequencing data from population samples. These data will be used to address a number of basic and applied questions for this species. Here, we show genetic differentiation patterns among the tropical and temperate forms, as well as finer scale genetic clustering at the regional and population scale. These data and results will be a valuable resource for further study and tool development for this species.
BACTERIAL DIVERSITY IN ESTUARINE SEDIMENTS IN BRAZILIAN COASTAL: A FOCUS IN BACTERIAL RESISTANCE
Authors: dos Santos Itana Almeida , de Santana Carolina Oliveira , Cruz André Freire , de Oliveira Eddy José Francisco 
Published: November 2023

ABSTRACTEstuaries are final depositional environments of sediments transported along rivers. Therefore, they give a generalized dimension about the human effluents released in water systems. The development of molecular techniques allowed the study of environmental DNA (eDNA), which can provide a real dimension about the functioning of the microbial communities of those environments and the impacts of human activities. In this context, antimicrobial resistance is an emerging problem, caused by irresponsible use of antimicrobial drugs in human and animal health, which has contributed to a selection of bacteria resistant to these drugs. The objective of this study is to identify the main phyla of bacteria and to detect the presence of Antibiotic Resistance Genes (ARGs) in different mangroves environments. We observed significant differences between ARGs quantity in each point. Samples collected on Guaibim-2 and Una had bigger diversity of ARGs, while Guaibim-1 had less AGRs diversity. The predominant phyla in all of the samples was Proteobacteria, Actinobacteria and Firmecutes. We detectedEnterococcus faecium, Acinetobacter sp, Klebsiella pneumoniae, Enterococcus faeciumandEnterobacter cloacae,listed bacteria for priority surveillance for World Health Organization on points Una and Guaibim-2.
A general framework for modeling pathogen transmission in co-roosting host communities
Authors: Simonis Molly C. , Becker Daniel J. 
Published: November 2023

AbstractCross-species transmission of pathogens can be facilitated by frequent contact among wildlife. Cross-species transmission is often driven by phylogenetic similarity between host species, but the role this plays when multiple host species co-roost is unknown. We developed a generalizable framework for understanding how cross-species transmission is driven by contact among co-roosting species spanning evolutionary similarities and the net impact on roost-level infection prevalence. We developed ordinary differential equation models describing population and infection dynamics between two and three co-roosting species. We parameterized models using co-roosting Neotropical bat systems, with interspecific transmission exponentially declining with phylogenetic distance. To assess the relative contribution of contact rates and phylogenetic similarity, we co-varied intraspecific transmission rates and phylogenetic distances while considering sensitivity to host and pathogen traits. While our models converged on similar equilibria under high intraspecific transmission or long durations of infection and immunity or latency, simulations with lower intraspecific transmission and shorter such periods revealed roost-level prevalence was greatest when hosts were most closely related. However, we identified regions of parameter space where roost-level prevalence also maximized when hosts were distantly related, driven by species-specific traits. Our generalizable models are adaptable to other co-roosting systems and informs our understanding of pathogen spillover.
Nephron progenitors rhythmically alternate between renewal and differentiation phases that synchronize with kidney branching morphogenesis
Authors: Davis Sachin N. , Grindel Samuel H. , Viola John M. , Liu Grace Y. , Liu Jiageng , Qian Grace , Porter Catherine M. , Hughes Alex J. 
Published: November 2023

AbstractThe mammalian kidney achieves massive parallelization of function by exponentially duplicating nephron-forming niches during development. Each niche caps a tip of the ureteric bud epithelium (the future urinary collecting duct tree) as it undergoes branching morphogenesis, while nephron progenitors within niches balance self-renewal and differentiation to early nephron cells. Nephron formation rate approximately matches branching rate over a large fraction of mouse gestation, yet the nature of this apparent pace-maker is unknown. Here we correlate spatial transcriptomics data with branching ‘life-cycle’ to discover rhythmically alternating signatures of nephron progenitor differentiation and renewal across Wnt, Hippo-Yap, retinoic acid (RA), and other pathways. We then find in human stem-cell derived nephron progenitor organoids that Wnt/β-catenin-induced differentiation is converted to a renewal signal when it temporally overlaps with YAP activation. Similar experiments using RA activation indicate a role in setting nephron progenitor exit from the naive state, the spatial extent of differentiation, and nephron segment bias. Together the data suggest that nephron progenitor interpretation of consistent Wnt/β-catenin differentiation signaling in the niche may be modified by rhythmic activity in ancillary pathways to set the pace of nephron formation. This would synchronize nephron formation with ureteric bud branching, which creates new sites for nephron condensation. Our data bring temporal resolution to the renewal vs. differentiation balance in the nephrogenic niche and inform new strategies to achieve self-sustaining nephron formation in synthetic human kidney tissues.