bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secondary hypogammaglobulinemia: diagnosis and management of a pediatric condition of clinical importance
Authors: DiGiacomo Daniel , Barmettler Sara 
Published: September 2024

Purpose of review
Secondary hypogammaglobulinemia, or low serum immunoglobulins, is associated with a variety of medications or medical conditions and may be symptomatic and lead to increased infectious risk. There is limited data regarding the study of acquired, or secondary, hypogammaglobulinemia (SHG) in pediatrics. The data to date has suffered from methodologic issues including retrospective study design, lack of baseline immunoglobulin measurements, and limited longitudinal follow-up.

Recent findings
There is emerging research on the impact of B-cell depleting therapies, specifically rituximab and chimeric antigen T-cells, along with other autoimmune and malignant disease states, in the development of SHG in pediatric patients. This review will also summarize other relevant pediatric conditions related to SHG.

Summary
The clinical relevance of SHG in pediatrics is increasingly appreciated. Improved understanding of the specific etiologies, risk factors, and natural history of SHG have informed screening and management recommendations.
Local Public Health Strategies for Addressing Social Determinants of Health—Analysis of Recent Community Health Improvement Plans
Authors: Johnson Karl , Oruganti Nidhi , Cilenti Dorothy , Wiesman John , Jensen Todd , Hassmiller Kristen 
Published: September 2024

Context:
The Public Health 3.0 (PH3.0) framework encourages local health departments (LHDs) to address the social determinants of health (SDOHs) that impact health equity.

Objective:
This study sought to understand how often LHDs are working to address SDOH, which SDOHs are most often being addressed, as well as the mix of strategies that have been proposed to address this work.

Design:
We reviewed recent Community Health Improvement Plans (CHIPs) to analyze the current involvement of LHDs in addressing SDOH.

Setting:
CHIPs published from 2020.

Participants:
Accredited LHDs from across the United States (n = 80).

Main Outcome Measures:
We developed a qualitative guidebook to characterize CHIP strategies based on the SDOH domain they addressed and the strategic mechanism they proposed.

Results:
Across our entire sample, CHIPs were roughly 1.5 times more likely to address Health Care Access than Food Insecurity and Access to Healthy Food (65%), Neighborhood Infrastructure (61%), or Affordable Housing (65%), and they were 3 to 4 times more likely to address Health Care Access than Safe Housing (23%), Education Access and Quality (31%), or Economic Stability (24%). Across all major domains, a few concerned policy changes and a handful focused on improving systems or developing the built environment. Most strategies focused on service provision through events or the education of the public and professionals on health-related topics.

Conclusions:
The results of this study demonstrate that not all SDOHs are addressed equally by LHDs within their CHIPs. There is significant variation in how SDOHs are addressed along at 2 dimensions: first, in the likelihood that a CHIP addresses the domain and, second, in the mechanism by which each domain is addressed. Practically, the list of strategies we documented from the 80 CHIPs included in our sample may serve as the basis for strategies that other communities may wish to consider when addressing SDOH.
Macular Optical Coherence Tomography Findings in Patients With Syphilitic Optic Neuropathy—A Case Series and Systematic Review
Authors: Sverdlichenko Irina , McDonald Heather M. , Xie Jim Shen Chu , Margolin Edward A. 
Published: September 2024

Background:
Syphilis is a sexually or congenitally acquired infectious disease that can affect multiple organs systems, including the eye. When left undiagnosed and untreated, it can lead to significant morbidity and mortality. Syphilitic optic neuropathy can be difficult to diagnose because it can mimic many other nonsyphilitic causes of optic nerve involvement, leading to delay in treatment. Diagnosing ocular syphilis may be facilitated by assessing for specific outer retina abnormalities on macular optical coherence tomography (OCT).

Methods:
This was a case series and case-based systematic review. For the case series, a retrospective chart review was conducted of all patients who presented to a tertiary university–affiliated neuro-ophthalmology practice over 6 months with undifferentiated optic neuropathy and were eventually diagnosed with syphilitic optic neuropathy. For the systematic review, OVID MEDLINE, EMBASE, and COCHRANE CENTRAL databases were searched to identify all cases of syphilitic optic neuropathy with macular OCT. The primary research outcome was the prevalence of cases with outer retinal abnormalities on OCT.

Results:
Four cases were identified that were eligible for inclusion. The ages ranged from 27 to 62 years old, and 2 of the patients were female. On examination, vision ranged from Snellen 20/50 to hand motion; all patients had optic neuropathy, and macular OCT revealed chorioretinitis characterized by retinal pigment epithelium (RPE) excrescences. The patients subsequently underwent uveitis workup and were diagnosed with syphilis. They were treated with intravenous penicillin and showed improvement in outer retina appearance on follow-up. The systematic review consisted of 24 cases and 35 eyes with syphilitic optic neuropathy and reported macular OCT findings. Eighty-three percent (20/24) were males, and the mean age was 47.7 years (SD: 49.2). The mean visual acuity at presentation was Snellen 20/57. On fundoscopy, 25.7% (9/35) of eyes had vitritis, whereas 22.8% (8/35) had placoid chorioretinal lesions. On OCT, 45.7% (16/35) of eyes had abnormal outer retina findings, most commonly disruption of the ellipsoid zone (EZ) and/or RPE excrescences. All patients were treated with penicillin or ceftriaxone, and final mean visual acuity was Snellen 20/29.

Conclusions:
All 4 patients identified in the case series, and nearly half of patients with syphilitic optic neuropathy described in the literature had concurrent-specific outer retina abnormalities (disruption of EZ and/or placoid chorioretinitis in the form of RPE excrescences) seen on macular OCT. We recommend that clinicians obtain macular OCT for all patients presenting with undifferentiated optic neuropathy.
Mast cells promote pathology and susceptibility in tuberculosis
Authors: Gupta Ananya , Taneja Vibha , Rangel Moreno Javier , Abhimanyu  , Ahmed Mushtaq , Naqvi Nilofer , Chauhan Kuldeep S. , de León Daniela Trejo-Ponce , Ramírez-Martínez Gustavo , Jiménez-Alvarez Luis , Luna-Rivero Cesar , Zuniga Joaquin , Kaushal Deepak , Khader Shabaana A. 
Published: September 2024

AbstractTuberculosis (TB), caused by the bacteriumMycobacterium tuberculosis(Mtb), infects approximately one-fourth of the world’s population. While most infected individuals are asymptomatic, latent TB infection (LTBI) can progress to cause pulmonary TB (PTB). We recently reported an increased accumulation of mast cells (MCs) in lungs of macaques with PTB, compared with LTBI in macaques. MCs respond in vitro toMtbexposure via degranulation and by inducing proinflammatory cytokines. In the current study, we show the dominant production of chymase by MCs in granulomas of humans and macaques with PTB. Using scRNA seq analysis, we show that MCs found in LTBI and healthy lungs in macaques are enriched in genes involved in tumor necrosis factor alpha, cholesterol and transforming growth factor beta signaling. In contrast, MCs clusters found in PTB express transcriptional signatures associated with interferon gamma, oxidative phosphorylation, and MYC signaling. Additionally, MC deficiency in the mouse model showed improved control ofMtbinfection that coincided with reduced accumulation of lung myeloid cells and diminished inflammation at chronic stages. Thus, these collective results provide novel evidence for the pathological contribution of MCs duringMtbinfection and may represent a novel target for host directive therapy for TB.
Lysyl Oxidases are Necessary for Myometrial Contractility and On-Time Parturition in Mice
Authors: Ouellette Alexis , Do Christina , Cohn-Guthrie Sydney , Lam Ying-Wai , Mahendroo Mala , Nallasamy Shanmugasundaram 
Published: September 2024

ABSTRACTThe extracellular matrix (ECM) plays a pivotal role in the maintenance of tissue mechanical homeostasis. Collagens and elastic fibers are the most predominant fibrous ECM proteins providing tissue mechanical function through covalent cross-linking which is mediated by the lysyl oxidase family of enzymes. In this study, the function of lysyl oxidases in maintaining the integrity of the extracellular matrix in the myometrium and its impact on parturition-timing was investigated. Gene and protein expression analyses demonstrate that a sub-set of the lysyl oxidase family of enzymes are highly induced in pregnant myometrium. Inhibition of the activity of the lysyl oxidase family of enzymes through β-aminopropionitrile (BAPN) delays parturition in mice, in part, due to myometrial dysfunction. In BAPN treated mice, the expression of genes encoding contraction associated proteins such as connexin 43, oxytocin receptor and prostaglandin synthase 2 is significantly reduced in the myometrium compared to the untreated control mice. Proteomic analysis revealed that the composition of the ECM is altered in response to BAPN treatment which demonstrates that the inhibition of the activity of lysyl oxidases disrupted the integrity of the myometrial ECM. Our findings demonstrate that the lysyl oxidases-mediated ECM function is necessary for the myometrium to transition from a quiescent to a contractile phenotype at term for on-time parturition.
The personal space and the collective behavior of crowd disasters
Authors: Lugo Igor , Alatriste-Contreras Martha G. 
Published: September 2024

AbstractThe personal space in dense crowd situations is commonly underestimated. However, the self-awareness of it can prevent and handle risk situations. The aim of this study was to explore theoretically the use of the personal space as a key concept for designing simple computational models related to collective behaviors and crushing events. We used an agent-based model related to transitional rules associated with the Shelling’s spatial proximity model of segregation. Based on an explorative data analysis and model validation, we found that the dynamics of crowd events showed significant statistical regularities between dense situations and the individual perception of the personal space. These results suggests that crushing events in dense crowd situations are highly probable and that the density levels are the key for delaying the presence of such disasters.
Developing heterospecific Sterile Insect Technique for pest control: insights from the spotted wing flyDrosophila suzukii
Authors: Cerasti Flavia , Cristofaro Massimo , Mastrantonio Valentina , Scifo Jessica , Verna Adriano , Canestrelli Daniele , Porretta Daniele 
Published: September 2024

AbstractBACKGROUNDReproductive interference (i.e., sexual interaction between males of one species and females of another species that reduce the fitness of one or both the interacting individuals) is an important species interaction significantly affecting population dynamics and persistence. However, its exploitation in pest control remains overlooked. Here, we investigated the possible integration of reproductive interference into the Sterile Insect Technique (SIT) to develop a heterospecific SIT (h-SIT). Under this approach, contrary to the classic SIT, sterile heterospecific males from closely related, non-pest species are released to compete with the pest population for mates. At this aim, we focused on the invasive pest speciesDrosophila suzukiiand usedD. melanogasteras the control species. First, we investigated the effect of irradiation onD. melanogastersterility and longevity. Then, we tested the mating performance of irradiated males and their ability to reduce theD. suzukiifitness.RESULTSWe found by microcosm experiments that: i) irradiation induced high levels ofD. melanogastermale sterility without reducing longevity; ii) irradiatedD. melanogastermales courtD. suzukiifemales as much asD. suzukiimales and they couple, mate and fecund heterospecific females; iii) irradiatedD. melanogastermales significantly reduce the offspring ofD. suzukiifemales under two different species ratios.CONCLUSIONSOur results provide the first foundation to develop a heterospecific Sterile Insect Technique againstD. suzukiiand fuel to test this approach against other groups of pest species.
Presence of distinct operant phenotypes and transient withdrawal-induced escalation of operant ethanol intake in female rats
Authors: Pitock Joseph R , Wheeler Shannon R , Ayala Arleen Perez , Hou Shikun , Soto Nathaly Arce , Glover Elizabeth J 
Published: September 2024

AbstractOperant self-administration is frequently used to investigate the neurobiological mechanisms underlying alcohol seeking and drinking and to test the efficacy of drugs under development for the treatment of alcohol use disorder (AUD). Although widely used by the research community, there is a paucity of operant ethanol self-administration studies that include female subjects. The current study characterizes home cage drinking and operant ethanol self-administration in female Sprague Dawley, Long Evans, and Wistar rats. Rats underwent three weeks of intermittent-access two-bottle choice home cage drinking before being trained to lever press for ethanol in standard operant chambers equipped with contact lickometers. After capturing baseline operant performance, rats were chronically exposed to control or ethanol liquid diet using the Lieber-DeCarli method. Operant ethanol self-administration was re-evaluated after chronic liquid diet exposure to determine whether female rats exhibit similar withdrawal-induced escalation of ethanol intake as is regularly observed in male rats. Our findings reveal the presence of three distinct operant phenotypes (Drinker, Responder, Nonresponder), the prevalence of which within each strain is strikingly similar to our previous observations in males. Within a given phenotype, rats of each strain performed similarly during operant testing. Ethanol intake during home cage drinking was unable to predict future operant phenotype. Relative to controls, Drinkers chronically exposed to ethanol liquid diet exhibited a significant, but transient, escalation in consummatory, but not appetitive, responding during acute withdrawal. Collectively, these data closely parallel many of our previous observations in males while also highlighting potential sex differences in drinking strategies following dependence. The presence of the Responder phenotype reinforces the importance of using direct measures of ethanol consumption. Our findings provide new insight into similarities and differences in operant ethanol self-administration between males and females and emphasize the importance of including females in future studies of ethanol drinking and dependence.
Understanding Ecological Systems Using Knowledge Graphs: An Application to Highly Pathogenic Avian Influenza
Authors: Robertson Hailey , Han Barbara A. , Castellanos Adrian A. , Rosado David , Stott Guppy , Zimmerman Ryan , Drake John M. , Graeden Ellie 
Published: September 2024

AbstractEcological systems are complex. Representing heterogeneous knowledge about ecological systems is a pervasive challenge because data are generated from many subdisciplines, exist in disparate sources, and only capture a subset of important interactions underpinning system structure, resilience, and dynamics. Knowledge graphs have been successfully applied to organize heterogeneous data systematically and to predict new linkages representing unobserved relationships in complex systems. Though not previously applied broadly in ecology, knowledge graphs have much to offer in an era of global change when system dynamics are responding to rapid changes across multiple scales simultaneously. We developed a knowledge graph to demonstrate the method’s utility for ecological problems focused on highly pathogenic avian influenza (HPAI), a highly transmissible virus with a broad animal host range, wide geographic distribution, and rapid evolution with pandemic potential. We describe the development of a graph to include a wide range of data related to HPAI including pathogen-host associations, animal species distributions, and human population demographics, using a semantic ontology that defines relationships within the data and between datasets. We use the graph to perform a set of proof-of-concept analyses validating the method and identifying new relationships and features of HPAI ecology, underscoring the generalizable value of knowledge graphs to ecology including their utility in revealing previously known relationships between entities and generating testable hypotheses in support of a deeper mechanistic understanding of ecological systems.
The Importance of Nonsense Errors: Estimating the Rate and Implications of Drop-Off Errors during Protein Synthesis
Authors: Cope Alexander L. , Pak Denizhan , Gilchrist Michael A. 
Published: September 2024

AbstractThe process of mRNA translation is both energetically costly and relatively error-prone compared to transcription and replication. Nonsense errors during mRNA translation occur when a ribosome drops off a transcript before reaching a stop codon, resulting in energetic investment in an incomplete and likely non-functional protein. Nonsense errors impose a potentially significant energy burden on the cell, making it critical to quantify their frequency and energetic cost. Here, we present a model of ribosome movement for estimating protein production, elongation, and nonsense error rates from high-throughput ribosome profiling data. Applying this model to an exemplary ribosome profiling dataset inS. cerevisiae, we find that nonsense error rates vary between codons, in conflict with the general assumption of uniform rates across sense codons. Using our parameter estimates, we find multiple lines of evidence that selection against nonsense errors is a prominent force shaping coding-sequence evolution, including that nonsense errors place an energetic burden on cells comparable to ribosome pausing. Our results indicate greater consideration should be given to the impact of nonsense errors in shaping coding-sequence evolution.
DendroTweaks: An interactive approach for unraveling dendritic dynamics
Authors: Makarov Roman , Chavlis Spyridon , Poirazi Panayiota 
Published: September 2024

AbstractNeurons rely on the interplay between dendritic morphology and ion channels to transform synaptic inputs into a sequence of somatic spikes. Detailed biophysical models with active dendrites have been instrumental in exploring this interaction. However, such models can be challenging to understand and validate due to the large number of parameters involved. In this work, we introduceDendroTweaks— a toolbox designed to illuminate how morpho-electric properties map to dendritic events and how these dendritic events shape neuronal output.DendroTweaksfeatures a web-based graphical interface, where users can explore single-cell neuronal models and adjust their morphological and biophysical parameters with real-time visual feedback. In particular,DendroTweaksis tailored to interactive fine-tuning of subcellular properties, such as kinetics and distributions of ion channels, as well as the dynamics and allocation of synaptic inputs. It offers an automated approach for standardization and refinement of voltage-gated ion channel models to make them more comprehensible and reusable. The toolbox allows users to run various experimental protocols and record data from multiple dendritic and somatic locations, thereby enhancing model validation. Finally, it aims to deepen our understanding of which dendritic properties are essential for neuronal input-output transformation. Using this knowledge, one can simplify models through a built-in morphology reduction algorithm and export them for further use in faster, more interpretable networks. WithDendroTweaks, users can gain better control and understanding of their models, advancing research on dendritic input-output transformations and their role in network computations.
Three Subtypes of Autism Spectrum Disorder with Transcriptomic Signatures Derived from Morphometric Similarity Networks
Authors: Jiang Hongxiu , Rodriguez-Cruces Raul , Xie Ke , Kebets Valeria , Wang Yezhou , Weber Clara F. , He Ying , Kember Jonah , Poline Jean-Baptiste , Bzdok Danilo , Hong Seok-Jun , Bernhardt Boris , Chai Xiaoqian 
Published: September 2024

ABSTRACTAutism spectrum disorder (ASD) is a prevalent and highly heterogeneous neurodevelopmental disorder. Previous studies have attempted to identify ASD subgroups by analyzing isolated cortical structural features. However, these studies have not considered the relationship between multiple structural features, which provide information on the structural organization of the brain. Morphometric similarity network (MSN), a structural brain network contributed by multiple anatomical features (gray matter volume, mean cortical thickness, surface area, mean curvature, Gaussian curvature, curvature index, and fold index), strongly relates to cytoarchitectonic and genomic measures of histological similarity between cortical areas. We applied K-means clustering on MSN from 236 individuals with ASD and identified three subtypes. Subtype-1 showed relatively similar MSN values with typically developmental individuals (TD). Subtype-2 showed higher morphometric similarities in the lateral frontal and temporal cortical regions and lower in anterior prefrontal and occipital regions compared to TD. These patterns were the opposite in subtype-3. Behaviorally, subtype-3 had more severe verbal and social deficits compared to subtype-2. The weaker resting-state functional connectivity (rs-FC) between the language and salience networks was observed between subtype-2 and TD. Subtype-3 had stronger rs-FC between salience and default mode networks (DMN), between frontoparietal and visual networks, and between language and dorsal attention networks, while weaker rs-FC within DMN, within sensorimotor, and within salience networks. In addition, genes with expression patterns associated with regional MS changes in ASD subtypes were functionally enriched in neuron-specific biological processes related to nervous system development, synaptic signaling and chromatin organization. These genes were particularly enriched in GABAergic neurons, glutamatergic neurons, astrocytes and microglia. Taken together, our findings suggest the existence of different neuroanatomical subtypes based on multiple anatomical features in ASD with distinct transcriptomic signatures and functional connectome patterns.