bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycoengineering with neuraminic acid analogs to label lipooligosaccharides and detect native sialyltransferase activity in gram-negative bacteria
Authors: Alvarado-Melendez Erianna I , de Jong Hanna , Hartman Jet E M , Ong Jun Yang , Wösten Marc M S M , Wennekes Tom 
Published: September 2024

Abstract
Lipooligosaccharides are the most abundant cell surface glycoconjugates on the outer membrane of Gram-negative bacteria. They play important roles in host–microbe interactions. Certain Gram-negative pathogenic bacteria cap their lipooligosaccharides with the sialic acid, N-acetylneuraminic acid (Neu5Ac), to mimic host glycans that among others protects these bacteria from recognition by the hosts immune system. This process of molecular mimicry is not fully understood and remains under investigated. To explore the functional role of sialic acid-capped lipooligosaccharides at the molecular level, it is important to have tools readily available for the detection and manipulation of both Neu5Ac on glycoconjugates and the involved sialyltransferases, preferably in live bacteria. We and others have shown that the native sialyltransferases of some Gram-negative bacteria can incorporate extracellular unnatural sialic acid nucleotides onto their lipooligosaccharides. We here report on the expanded use of native bacterial sialyltransferases to incorporate neuraminic acids analogs with a reporter group into the lipooligosaccharides of a variety of Gram-negative bacteria. We show that this approach offers a quick strategy to screen bacteria for the expression of functional sialyltransferases and the ability to use exogenous CMP-Neu5Ac to decorate their glycoconjugates. For selected bacteria we also show this strategy complements two other glycoengineering techniques, Metabolic Oligosaccharide Engineering and Selective Exo-Enzymatic Labeling, and that together they provide tools to modify, label, detect and visualize sialylation of bacterial lipooligosaccharides.
Beyond the Needle: Understanding Tissue Marker Migration in Breast MRI-Guided Biopsies
Authors: Golan Orit , Lazar Sapir , Menes Tehillah S , Kessner Rivka , Shalmon Tamar , Neeman Rina , Mercer Diego , Amitai Yoav 
Published: September 2024

Abstract

Objective
To evaluate the frequency and factors associated with clip migration in MRI-guided breast biopsies.

Methods
This study was approved by our Institutional Review Board and was compliant with HIPAA. We retrospectively evaluated all MRI-guided biopsies performed between January 2013 and December 2020 in our institution for clip migration. Only patients with follow-up breast MRI showing the clip were included in the study. Migration was defined as movement of the clip of 10 mm or more from the target lesion. Migration frequency and directions were recorded. Factors associated with clip migration were analyzed using statistical tests as appropriate.

Results
A total of 291 biopsies in 268 women were included in the study with 31 migration events recorded (11%; 95% CI, 7%-15%). All migrations occurred along the biopsy tract; 97% (30/31) of them displaced distal to the needle entry site. More than 50% regional fat (around the target lesion) was the strongest factor associated with migration, seen in 21/141 women (15%), compared to 10/150 (7%) with 50% or less local fat (P = .023). Global fatty breast was more loosely associated with migration, showing borderline significance (P = .06). Other factors did not correlate with clip migration, including lesion size, depth, or location; pathology result; breast thickness; or biopsy approach.

Conclusion
Although clip migration after breast MRI-guided biopsy is an uncommon event, it occurs more often when the target lesion is surrounded by fat, with the clip usually displaced away from the needle entry site.
Racial and socioeconomic disparities in non–small cell lung cancer molecular diagnostics uptake
Authors: Tuminello Stephanie , Turner Wiley M , Untalan Matthew , Ivic-Pavlicic Tara , Flores Raja , Taioli Emanuela 
Published: September 2024

Abstract

Background
Precision therapies, such as targeted and immunotherapies, have substantially changed the landscape of late-stage non–small cell lung cancer (NSCLC). Yet, utilization of these therapies is disproportionate across strata defined by race and socioeconomic status, possibly because of disparities in molecular diagnostic testing (or biomarker testing), which is a prerequisite to treatment.

Methods
We extracted a cohort of NSCLC patients from the Surveillance, Epidemiology, and End Results–Medicare linked data. The primary outcome was receipt of a molecular diagnostic test, based on claims data. The primary predictors were race and socioeconomic status. Likelihood of receiving a molecular diagnostic test and overall survival were investigated using logistic and Cox proportional hazards regression, adjusted for sex, age, residence, histology, marital status, and comorbidity.

Results
Of the 28 511 NSCLC patients, 11 209 (39.3%) received molecular diagnostic testing. Compared with White patients, fewer Black patients received a molecular diagnostic test (40.4% vs 27.9%; P &lt; .001). After adjustment, Black patients (adjusted odds ratio [OR] = 0.64, 95% confidence interval [CI] = 0.58 to 0.71) and those living in areas with greater poverty (adjusted OR = 0.85, 95% CI = 0.80 to 0.89) had statistically significant decreased likelihood of molecular diagnostic testing. Patients who did receive testing had a statistically significant decreased risk of death (adjusted hazard ratio [HR] = 0.74, 95% CI = 0.72 to 0.76). These results held in the stratified analysis of stage IV NSCLC patients.

Conclusion
Disparities exist in comprehensive molecular diagnostics, which is critical for clinical decision making. Addressing barriers to molecular testing could help close gaps in cancer care and improve patient outcomes.
Is news really news? The effects of selective disclosure regulations
Authors: Kitchens Brent , Parham Robert , Yung Chris 
Published: September 2024

Abstract
Before regulations were enacted to prevent such practices, information leaked through selective disclosure was incorporated into markets prior to the public release of news. “News days” did not deliver news to markets; now they do. We provide novel evidence of changes in returns and turnover behavior around the enactment of regulations barring selective disclosure practices in the United States and the EU. We conversely document lack of such changes in Australia and Japan, which did not implement similar measures. We conclude that selective disclosure resolves Roll’s R2 puzzle.
The Common Structure of the Major Psychoses: More Similarities Than Differences in the Network Structures of Schizophrenia, Schizoaffective Disorder, and Psychotic Bipolar Disorder
Authors: Shao Wen , Simmonds-Buckley Melanie , Zavlis Orestis , Bentall Richard P 
Published: September 2024

Abstract

Background and Hypothesis
There has been a century-long debate about whether the major psychoses (eg, bipolar disorder, schizophrenia, and schizoaffective disorder) are one disorder with various manifestations or different disease entities. Traditional approaches using dimensional models have not provided decisive findings. Here, we address this question by examining the network constellation of affective and psychotic syndromes.

Design
Comparable symptom data of 1882 patients with psychotic bipolar disorder, schizoaffective disorders, and schizophrenia were extracted from three datasets: B-SNIP 1, B-SNIP2, and PARDIP. Twenty-six items from the Positive and Negative Syndrome Scale, YMRS, and the Montgomery-Asberg Depression Rating Scale were selected for the analysis using a principled approach to eliminate overlapping/redundant items. Gaussian graphical models were estimated and assessed for stability, and their communities were identified using bootstrapped exploratory graph analysis. The structures and global densities of the networks were compared with network comparison tests.

Results
The network structures were highly similar (r &gt;. 80) across diagnostic groups. For all diagnoses, manic symptoms were more connected with positive symptoms while depressive symptoms were more linked with negative symptoms. The depressive and negative symptoms were the strongest indicators of depressive and psychotic communities. Theoretically interesting variability in network edge weights between symptoms was found relating to thought disorder and pessimistic thinking.

Conclusions
The same broad structure of psychopathology underlies the symptom expressions of bipolar disorder, schizoaffective disorder, and schizophrenia. Future studies should build on the present finding by comparing specific inter-relations between symptoms in the different diagnostic groups using methods capable of detecting causality.
Effect of freeze–thaw treatments with different conditions on frost fatigue in three diffuse-porous trees
Authors: Ma Bolong , Lv Qingzi , Zhang Ruihan , Zhang Junyao , Wang Yue , Cai Jing 
Published: September 2024

Abstract
In addition to inducing xylem embolism, freeze–thaw events can cause frost fatigue phenomena. Freezing temperature, freezing times, number of freeze–thaw cycles and frost drought can affect the level of freeze–thaw-induced embolism, but it is unknown whether there is an effect on frost fatigue. We assessed whether these frost-related factors changed frost fatigue in the three diffuse-porous species by simulating freeze–thaw treatments under different conditions. We also proposed a new metric, embolism area, in place of embolism resistance, to more accurately quantify the shift of the vulnerability curve after experiencing freeze–thaw-induced embolism and refilling. Frost fatigue caused vulnerability curves of all species to change from S-shaped to double S-shaped or even R-shaped curves. When exposed to a freeze–thaw event, Acer truncatum showed strong resistance to frost fatigue; in contrast, Populus (I-101 × 84 K) and Liriodendron chinense were more vulnerable. Changing freezing temperature and times did not impact the response to frost fatigue in the three species, but a greater number of freeze–thaw cycles and more severe frost drought significantly exacerbated their fatigue degree. Considering that frost fatigue may be a widespread phenomenon among temperate diffuse-porous species, more work is needed in the future to reveal the mechanisms of frost fatigue.
Morphological diversification with emphasis on the structural and homology patterns of male genitalia in genus Limnebius (Leach 1815; Hydraenidae: Coleoptera)
Authors: Rudoy Andrey , Meng Ling-Zeng 
Published: September 2024

Abstract
Limnebius exhibits uniform external appearance but variable male genitalia: from differently curved rod shapes in the subgenus Bilimneus to up to seven longitudinally separated folds or appendages in Limnebius s.s.. Among nonsexual traits, two subgenera diverge only in the wing. The aedeagal complexity in Limnebius s.s. is associated with the secondary sexual structures on the abdomen and metatibia; larger body size, which forms two clusters; and male-biased sexual dimorphism. To cluster the subdivisions with phylogenetically unresolved relationships, we examined the coincidence of the traits in both sexes, based on the premise of the independent and monophyletic origin of histologically unsimilar elements. The folds and additional appendages on the median lobe, abdominal paired rows of setae, and protuberances show that the L. parvulus and L. nitidus groups have maximum aedeagal complexity in the L. parvulus and L. nitiduloides subgroups, respectively. The L. parvulus group exhibits a gradual increase in the number of elements of the aedeagi. The histology of connections of the parameres and additional appendages to the median lobe, along with that of the flagellum opening, reveal the subgroups’ relationship in the L. nitidus group, as well as a decrease in the complexity of the male genitalia in their recent branches.
Therapeutic DNA Vaccine TargetingMycobacterium tuberculosisPersisters Shortens Curative Tuberculosis Treatment
Authors: Karanika Styliani , Wang Tianyin , Yilma Addis , Castillo Jennie Ruelas , Gordy James T. , Bailey Hannah , Quijada Darla , Fessler Kaitlyn , Tasneen Rokeya , Rouse Salcido Elisa M. , Harris Harley T. , Bates Rowan E. , Ton Heemee , Meza Jacob , Li Yangchen , Taylor Alannah D. , Zheng Jean J. , Zhang Jiaqi , Peske J David , Karantanos Theodoros , Maxwell Amanda R. , Nuermberger Eric , Markham Richard B. , Karakousis Petros C. 
Published: September 2024

AbstractMycobacterium tuberculosis (Mtb) is one of the leading infectious causes of death worldwide. There is no available licensed therapeutic vaccine that shortens active tuberculosis (TB) disease drug treatment and prevents relapse, despite the World Health Organization’s calls. Here, we show that an intranasal DNA vaccine containing a fusion of the stringent responserelMtbgene with the gene encoding the immature dendritic cell-targeting chemokine, MIP-3α/CCL20, shortens the duration of curative TB treatment in immunocompetent mice. Compared to the first-line regimen for drug-susceptible TB alone, our novel adjunctive vaccine induced greater RelMtb-specific T-cell responses associated with optimal TB control in spleen, blood, lungs, mediastinal lymph nodes, and bronchoalveolar lavage (BAL) fluid. These responses were sustained, if not augmented, over time. It also triggered more effective dendritic cell recruitment, activation, and colocalization with T cells, implying enhanced crosstalk between innate and adaptive immunity. Moreover, it potentiated a 6-month TB drug-resistant regimen, rendering it effective across treatment regimens, and also showed promising results in CD4+ knockout mice, perhaps due to enhanced Rel-specific CD8+ T-cell responses. Notably, our novel fusion vaccine was also immunogenic in nonhuman primates, the gold standard animal model for TB vaccine studies, eliciting antigen-specific T-cell responses in blood and BAL fluid analogous to those observed in protected mice. Our findings have critical implications for therapeutic TB vaccine clinical development in immunocompetent and immunocompromised populations and may serve as a model for defining immunological correlates of therapeutic vaccine-induced protection.One sentence summaryA TB vaccine shortens curative drug treatment in mice by eliciting strong TB-protective immune responses and induces similar responses in macaques.
Placental Network Differences Among Obstetric Syndromes Identified With An Integrated Multiomics Approach
Authors: Piekos Samantha N , Barak Oren , Baumgartner Andrew , Chu Tianjiao , Parks W Tony , Hadlock Jennifer , Hood Leroy , Price Nathan D , Sadovsky Yoel 
Published: September 2024

AbstractThe placenta is essential for a healthy pregnancy, and placental pathology can endanger both maternal and fetal health. Placental function is affected by dynamic, complex, and interconnected molecular, cellular, and environmental events; therefore, we need a systems biology approach to study disease in normal physiological placenta function. We use placental multiomics (short and bulk transcriptomics, untargeted metabolomics, and targeted proteomics) paired with clinical data and placental histopathology reports from 321 placentas across multiple obstetric conditions: fetal growth restriction (FGR), FGR with pregnancy-related hypertension (FGR+HDP), preeclampsia (PE), and spontaneous preterm delivery (PTD). We first performed cellular deconvolution to estimate cell type numbers from bulk transcriptomes: FGR+HDP placentas were the most different from control placentas driven by a higher estimated number of extravillous trophoblast (p<0.0001). Next, we evaluated the impact of fetal sex and gestational age on analyte levels, adjusting for these confounders. We then generated obstetric condition-specific correlation networks and identified communities of related analytes associated with physiology and disease. We demonstrated how network connectivity and its disruption in disease can be used to identify signatures unique to a clinical outcome. We examined a community defined in control placentas for which the most connected node was miR-365a-3p in contrast to the corresponding community in FGR+HDP placentas for which the most connected node was hypoxia-induced miR-210-3p. From this community, we identified a signature containing mRNA transcripts implicated in placental dysfunction (e.g. FLT1, FSTL3, HTRA4, LEP, and PHYHIP). This signature distinguishes between FGR+HDP placentas and placentas of differing clinical outcomes in high-dimensional space. These findings illustrate the power of systems biology-driven interomics network analysis in a single tissue type, laying the groundwork for future multi-tissue studies.
Community-wide interactions sustain life in geothermal spring habitats
Authors: Stephens Timothy G. , Van Etten Julia , McDermott Timothy , Christian William , Chaverra Martha , Gurney James , Lee Yongsung , Kim Hocheol , Cho Chung Hyun , Chovancek Erik , Westhoff Philipp , Otte Antonia , Northen Trent R. , Bowen Benjamin P. , Louie Katherine B. , Barry Kerrie , Grigoriev Igor V. , Mock Thomas , Liu Shao-Lun , Miyagishima Shin-ya , Yoshinaga Masafumi , Weber Andreas P.M. , Yoon Hwan Su , Bhattacharya Debashish 
Published: September 2024

AbstractWe investigated an alga-dominated geothermal spring community in Yellowstone National Park, USA. Our goal was to determine how cells cope with abiotic stressors during diurnal sampling that spanned over two orders of magnitude in solar irradiance. We report a community level response to toxic metal resistance and energy cycling that spans the three domains of life. Arsenic detoxification is accomplishedviacomplementary gene expression by different lineages. Photosynthesis is dominated byCyanidioschyzon, with the mixotroph,Galdieria, relegated to nighttime heterotrophy. Many key functions, including the cell cycle, are strongly regulated by diurnal light fluctuations. These results demonstrate that biotic interactions are highly structured in extreme habitats. We suggest this was also the case on the early Earth when geothermal springs were cradles of microbial life, prior to the origin of eukaryotes.
Session duration affects the magnitude of post-exercise hypervolemia but not the erythropoietin response to acute high-intensity interval exercise
Authors: Tripp Thomas R. , Caswell Allison M. , Edgett Brittany A. , MacInnis Martin J. 
Published: September 2024

ABSTRACTThe increase in plasma volume ∼24 hours post-exercise may act as an erythropoietic signal, but this mechanism’s responsiveness to different exercise prescription variables is poorly understood. The purpose of this study was to determine the impact of high-intensity interval exercise duration on plasma volume and related responses. On separate days, 16 healthy, recreationally active participants (n=8 males; n=8 females) performed four (4×4) or eight intervals (8×4) consisting of 4 min at 105% critical power with 3 min recovery. Venous blood samples collected before, immediately after, and 24 hours after each HIIT session were used to measure hemoglobin concentration and hematocrit to calculate plasma volume changes. Erythropoietic and plasma volume regulating hormone concentrations were measured using ELISA kits. Plasma volume decreased immediately after both protocols (4×4: −4.4±3.5%, p<0.05; 8×4: −4.4±3.6%, p<0.05) but was only significantly elevated above baseline 24 hours after the 8×4 protocol (4×4: +1.0±7.1%, p>0.05; 8×4: +5.6±4.6%, p<0.05). Erythropoietin concentration ([EPO]) was higher than baseline 24 hours after the HIIT protocols (4×4: Pre vs 24 h post: 6.5±3.1 vs. 7.1±3.3 mIU/mL; 8×4: 6.9±3.7 vs. 7.3±3.7 mIU/mL; main effect of time, p<0.05) with no difference between protocols (p>0.05). [Aldosterone] was elevated immediately post-exercise after both protocols (4×4: Pre vs 0 h post: 295±151 vs. 544±259 pg/mL; 8×4: 335±235 vs. 821±553 pg/mL), but the 8×4 protocol caused a larger increase (interaction effect, p<0.05). That post-exercise hypervolemia may be exercise duration-dependent but is not required for increases in circulating EPO has important implications for endurance training aiming to increase oxygen delivery to active tissues.NEWS AND NOTEWORTHYThis study is the first to show that both a common HIIT protocol length (4 x 4 min) and an extended HIIT protocol (8 x 4 min) similarly increased [erythropoietin] 24 h after exercise, despite only the extended protocol transiently increasing plasma volume. Previous works have investigated plasma volume regulation following different HIIT durations, but not explored links to erythropoietic signalling. This study’s findings have relevance for understanding the physiology of exercise-induced erythropoiesis.
Mouse Brain Extractor: Brain segmentation of mouse MRI using global positional encoding and SwinUNETR
Authors: Kim Yeun , Hrncir Haley , Meyer Cassandra E. , Tabbaa Manal , Moats Rex A. , Levitt Pat , Harris Neil G. , MacKenzie-Graham Allan , Shattuck David W. 
Published: September 2024

AbstractIn spite of the great progress that has been made towards automating brain extraction in human magnetic resonance imaging (MRI), challenges remain in the automation of this task for mouse models of brain disorders. Researchers often resort to editing brain segmentation results manually when automated methods fail to produce accurate delineations. However, manual corrections can be labor-intensive and introduce interrater variability. This motivated our development of a new deep-learning-based method for brain segmentation of mouse MRI, which we call Mouse Brain Extractor. We adapted the existing SwinUNETR architecture (Hatamizadeh et al., 2021) with the goal of making it more robust to scale variance. Our approach is to supply the network model with supplementary spatial information in the form of absolute positional encoding. We use a new scheme for positional encoding, which we call Global Positional Encoding (GPE). GPE is based on a shared coordinate frame that is relative to the entire input image. This differs from the positional encoding used in SwinUNETR, which solely employs relative pairwise image patch positions. GPE also differs from the conventional absolute positional encoding approach, which encodes position relative to a subimage rather than the entire image. We trained and tested our method on a heterogeneous dataset of N=223 mouse MRI, for which we generated a corresponding set of manually-edited brain masks. These data were acquired previously in other studies using several different scanners and imaging protocols and includedin vivoandex vivoimages of mice with heterogeneous brain structure due to different genotypes, strains, diseases, ages, and sexes. We evaluated our method’s results against those of seven existing rodent brain extraction methods and two state-of-the art deep-learning approaches, nnU-Net (Isensee et al., 2018) and SwinUNETR. Overall, our proposed method achieved average Dice scores on the order of 0.98 and average HD95 measures on the order of 100 µm when compared to the manually-labeled brain masks. In statistical analyses, our method significantly outperformed the conventional approaches and performed as well as or significantly better than the nnU-Net and SwinUNETR methods. These results suggest that Global Positional Encoding provides additional contextual information that enables our Mouse Brain Extractor to perform competitively on datasets containing multiple resolutions.