bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of Stress Urinary Incontinence: Does Race Matter?
Authors: Boyd Brittni , Guaderrama Noelani , Zhuang Zimin , Tovar Stephanie , Whitcomb Emily 
Published: May 2024

Importance
The importance of this study was to examine treatment patterns and surgical complications for stress urinary incontinence (SUI).

Objectives
The aim of this study was to describe the treatment of SUI and associated complications in a racially and ethnically diverse population.

Study Design
This was a retrospective cohort study of patients with a new diagnosis of SUI. We identified patients who received treatment with a pessary, pelvic floor physical therapy, or surgery. Surgical complications were abstracted. Logistic regression was used to examine the association between race/ethnicity and treatment, as well as surgical complications.

Results
A total of 67,187 patients with a new diagnosis of SUI were included. The population was predominately Hispanic (47.5%) followed by White, Asian, Black, Native Hawaiian/Pacific Islander, and American Indian/Alaska Native. Comparing no treatment to any treatment, all racial/ethnic groups, except American Indian/Alaska Native, had decreased odds of receiving treatment compared with White women. Hispanic and Native Hawaiian/Pacific Islander women had increased odds of referral for pelvic floor physical therapy compared with White women. All racial/ethnic groups, except for American Indian/Alaska Native women, had decreased odds of receiving a sling procedure compared with White women. When these racial/ethnic minority groups did receive treatment, it was more likely to be conservative treatment compared with White women. There were no significant differences in individual surgical complications.

Conclusions
Racial minority women were 20–50% less likely to undergo a sling procedure, commonly posited as the gold standard surgical treatment. Racial minority women were 40–100% more likely to receive conservative management and 20–50% less likely to receive any treatment compared with White women.
Factors Associated With Persistent Bothersome Urinary Symptoms and Leakage After Pregnancy
Authors: Bhandari Randhawa Sonia , Rizkallah Andrea , Nelson David B. , Duryea Elaine L. , Spong Catherine Y. , Pruszynski Jessica E. , Rahn David D. 
Published: May 2024

Importance
Urinary incontinence is a common postpartum morbidity that negatively affects quality of life.

Objective
This study aimed to identify factors associated with persistent (ie, 12 months postpartum) bothersome urinary symptoms, including stress urinary incontinence (SUI) and urgency urinary incontinence (UUI), and explore their association with mental health in medically underserved communities.

Study Design
This was a cross-sectional analysis of a prospective study of individuals enrolled into “extending Maternal Care After Pregnancy,” a program providing 12 months of postpartum care to individuals with health disparities. Patients were screened at 12 months for urinary dysfunction, anxiety, and depression using the Urinary Distress Index-6, Generalized Anxiety Disorder-7, and Edinburgh Postnatal Depression Scale, respectively. Bivariate and multivariable logistic regression analyses were performed for at-least-somewhat-bothersome SUI versus no-SUI, UUI versus no-UUI, and for bothersome versus asymptomatic urinary symptoms, using demographic and peripartum and postpartum variables as associated factors.

Results
Four hundred nineteen patients provided data at median 12 months postpartum. Patients were 77% Hispanic White and 22% non-Hispanic Black. After multivariable analysis, SUI (n = 136, 32.5%) was significantly associated with increasing body mass index at the time of delivery and greater depression screening scores. Fetal birthweight, mode of delivery, degree of laceration, and breastfeeding status were not associated. Urgency urinary incontinence (n = 69, 16.5%) was significantly associated with increasing parity and higher anxiety screening scores. Similarly, participants with urinary symptom bother had significantly greater parity and higher anxiety screening scores.

Conclusions
At 12 months postpartum, bothersome urinary symptoms and incontinence were quite common. Since these are treatable, postpartum screening for urinary complaints—and associated anxiety and depression—is essential, as is assisting patients in achieving a healthy weight.
Preprocessing Choices for P3 Analyses with Mobile EEG: A Systematic Literature Review and Interactive Exploration
Authors: Jacobsen Nadine S. J. , Kristanto Daniel , Welp Suong , Inceler Yusuf Cosku , Debener Stefan 
Published: May 2024

AbstractPreprocessing is necessary to extract meaningful results from electroencephalography (EEG) data. With many possible preprocessing choices, their impact on outcomes is fundamental. While previous studies have explored the effects of preprocessing on stationary EEG data, this research delves into mobile EEG, where complex processing is necessary to address motion artifacts. Specifically, we describe the preprocessing choices studies reported for analyzing the P3 event-related potential (ERP) during walking and standing. A systematic review of 258 studies of the P3 during walking, identified 27 studies meeting the inclusion criteria. Two independent coders extracted preprocessing choices reported in each study. Analysis of preprocessing choices revealed commonalities and differences, such as the widespread use of offline filters but limited application of line noise correction (3 of 27 studies). Notably, 59% of studies involved manual processing steps, and 56% omitted reporting critical parameters for at least one step. All studies employed unique preprocessing strategies. These findings align with stationary EEG preprocessing results, emphasizing the necessity for standardized reporting in mobile EEG research. We implemented an interactive visualization tool (Shiny app) to aid the exploration of the preprocessing landscape. The app allows users to structure the literature regarding different processing steps, enter planned processing methods, and compare them with the literature. The app could be utilized to examine how these choices impact P3 results and understand the robustness of various processing options. We hope to increase awareness regarding the potential influence of preprocessing decisions and advocate for comprehensive reporting standards to foster reproducibility in mobile EEG research.
In vitroefficacy andin vivotoxicity and retention of targeted nanoformulated carboplatin in a sustained release carrier for treatment of osteosarcoma
Authors: Day Kevin , Risselada Marije , Sokolsky-Papkov Marina 
Published: May 2024

AbstractObjectiveevaluate 1) if targeting of platinum magnetic nanoclusters will promote uptake in osteosarcoma cellsin vitro, 2) targeting will improve uptake and delivery in murine OSAin vivocompared to free carboplatin, 3) incorporation into a sustained release carrier (SRC) will prolong local retentionin vivo.MethodsComplex stability and peptide loading was assessed. Drug release was tested at pH 7.4 and 5.5 and cellular uptake and cytotoxity determined for canine, human and mouse osteosarcoma. Subcutaneous murine osteosarcoma was induced and optimal dose and time until tumor growth were established. Tumor bearing mice were equally distributed between 8 treatment (0.5mg carboplatin/mouse) and 1 control group and sacrificed at 8 predetermined time points between 1 hour and 8 days. Blood, tumor site and organs were harvested for tissue ferron and platinum content analysis (ICP-MS).ResultsCarboplatin was preferentially released at pH5.5. Targeting increased cellular uptake for carboplatin 15.2-fold, and decreased IC50at 24h and 48h. At 2 weeks, a SC injection of 1-1.56live cells/mouse reliably resulted in a palpable tumor. Plasma platinum peaked prior to 6 hours while plasma ferron peaked at 24-48 hours. Intratumoral delivery did not lead to a sustained local presence while local delivery in a SRC after surgery did.ConclusionsTargeting of MNC-carboplatin is possible with an increased osteosarcoma cell uptakein vitro.In vivometastatic uptake could not be assessed due to lack of metastases, but local delivery in a SRC yielded high local, and low systemic platinum concentrations in mice.
Weather explains inter-annual variability, but not the temporal decline, in insect biomass
Authors: Duchenne François , Fontaine Colin 
Published: May 2024

AbstractIn a recent publication, Mülleret al. (2023) re-analysed, in light of new data, the dataset of the highly cited paper of Hallmannet al. (2017) showing a strong decline in insect biomass in Germany between 1989 and 2016. In their re-analysis, Mülleret al. completed Hallmannet al’s model with a focus on modelling the effects of weather conditions on insect biomass. They also included temporal changes in habitat as additional predictors, using the same variables as Hallmannet al., which although not entirely satisfactory due to the scarcity of historical habitat data, represent the best available data. While they trained their model on the Hallmannet al.’s dataset, Mülleret al. validated it with an independent dataset. These upgraded analyses are a nice demonstration of the strong impact of climatic conditions on annual insect biomass. However, Mülleret al. conclusion that “temporal variation in weather conditions explained most of the temporal changes in insect biomass whereas temporal changes in habitat conditions played only a minor role” was overstated. Here we argue that their methodological approach was unsuitable to draw such conclusion, because of omitted variable bias. We show that more appropriate analyses produce a pattern opposite to the main conclusion of Mülleret al.: there is a significant temporal decline in insect biomass not explained by weather conditions.
Enhancing Biosecurity with Watermarked Protein Design
Authors: Chen Yanshuo , Hu Zhengmian , Wu Yihan , Chen Ruibo , Jin Yongrui , Chen Wei , Huang Heng 
Published: May 2024

AbstractThe biosecurity issue arises as the capability of deep learning-based protein design has rapidly increased in recent years. To address this problem, we propose a new general framework for adding watermarks to protein sequences designed by various sampling-based deep learning models. Compared to currently proposed protein design regulation procedures, watermarks ensure robust traceability and maintain the privacy of protein sequences. Moreover, using our framework does not decrease the performance or accessibility of the protein design tools.
Hemispheric specialization of functions are tuned by conduction velocities of neuronal propagation in large-scale brain networks
Authors: Kumar Neeraj , Roy Dipanjan , Banerjee Arpan 
Published: May 2024

AbstractWe propose a tuning-by-delay hypothesis to explain the hemispheric specialization of function that has intrigued psychologists, philosophers, neurologists and neuroscientists for decades. In the auditory domain, speech and melody processing are understood to be lateralized in the left and the right hemispheric brain areas, respectively. Thus, analogous to the notion of pleiotropy where one gene can influence two or three unrelated traits, there exists a shared structural connectome encompassing both hemispheres underlying speech and melody processing, which however gets segregated along left vs right hemispheres, respectively. Here, we demonstrate how empirical observations of hemispheric specialization of speech and melody are shaped by the computational time-scales of information integration in cortical networks. First, we demonstrate that context-specific causal outflow of information emerging from primary auditory cortices (PAC) drives the hemispheric specialization of speech and melody processing when human volunteers listened toa cappellasongs placed within a delayed match to sample task while electroencephalogram (EEG) were recorded. Second, together with participant specific whole-brain connectome model guided by diffusion weighted imaging, we predicted individual specific lateralization indices of inflow in cortical sources - after rigorous source time series reconstruction of EEG spectra. High levels of accuracy in the prediction of laterality indices in the extended large-scale auditory related regions can be achieved after optimizing conduction speeds of information propagation over a neuro-oscillatory network - a novel way to interpret about the neural mechanisms. We demonstrate that parametric modulation of conduction speeds that effectively controls the transmission delays - a key metric for understanding information processing and control of any biological network. Thus, the transmission delay in turn, acts as the switch and triggered by the spectro-temporal complexity of the task context to select the geometry of lateralization.
Human Organoid Tumor Transplantation Identifies Functional Glioblastoma - Microenvironmental Communication Mediated by PTPRZ1
Authors: Ge Weihong , Kan Ryan L. , Yilgor Can , Fazzari Elisa , Nano Patricia R. , Azizad Daria J. , Li Matthew , Ito Joyce Y. , Tse Christopher , Tum Hong A. , Scholes Jessica , Patel Kunal S. , Nathanson David A. , Bhaduri Aparna 
Published: May 2024

AbstractGlioblastoma, the most aggressive and deadly form of primary brain cancer, is driven by both intrinsic cellular properties and external factors from the tumor microenvironment. Here, we leverage our novel human organoid tumor transplantation (HOTT) system to explore how extrinsic cues modulate glioblastoma cell type specification, heterogeneity, and migration. We show that HOTT recapitulates the core features of major patient tumor cell types and key aspects of peritumor cell types, while providing a human microenvironment that uniquely enables perturbations in both the patient tumor and its microenvironment. Our exploration of patient tumor – microenvironmental interactions in HOTT highlighted PTPRZ1, a receptor tyrosine phosphatase implicated in tumor migration, as a key player in intercellular communication. We observed that tumor knockdown of PTPRZ1 recapitulated previously described roles in migration and maintaining progenitor identity. Unexpectedly, environmental PTPRZ1 knockdown drove opposite migration and cell fate changes in the tumor, even when the tumor was not manipulated. This previously undiscovered mode of tumor-microenvironmental communication highlights the need to study human glioblastoma in the context of a human microenvironment such as HOTT.
Fasciclin 2 functions as an expression-level switch on EGFR to control organ shape and size inDrosophila
Authors: Garcia-Alonso Luis 
Published: May 2024

Fasciclin 2 (DrosophilaNCAM) is a homophilic Cell Adhesion Molecule expressed at moderate levels in the proliferating epithelial cells of imaginal discs, where it engages EGFR in a cell autonomous auto-stimulatory loop that promotes growth along larval development. In addition, Fasciclin 2 is expressed at high levels in the pre-differentiating cells of imaginal discs. Gain-of-function genetic analysis shows that Fasciclin 2 acts as a non-cell autonomous repressor of EGFR when high expression levels are induced during imaginal disc growth. Loss-of-function genetic analysis shows that this Fasciclin 2 functional facet is required at the end of larval development and it is mediated by interaction with IgCAMs CG15630 (Fipi) and CG33543 (Elff). Thus, Fasciclin 2 bears two complementary functional roles which correspond with different levels of expression. The combined results from loss- and gain-of-function analyses suggest a scenario where the Fasciclin 2/EGFR cell autonomous auto-stimulatory loop promotes cell proliferation until reaching a Fasciclin 2 expression threshold where its non-cell autonomous function stops growth. Thus, cellular integration of Fasciclin 2 autonomous and non-cell autonomous signaling from neighbor cells may be a key regulator component to orchestrate the rate of intercalary cell proliferation and the final size and shape of an organ.Author SummaryHow organ size and shape are controlled during development is a central and still unsolved problem in developmental biology. Growth control must be precise and local to account for the vast variation of organ shapes and sizes during evolution. Here I show that the expression of Fasciclin 2 (DrosophilaNCAM) controls whether to grow or not to grow by controlling EGFR activity in epithelial organs. Fasciclin 2 homophilic binding promotes cell autonomous activity of EGFR at low and medium levels of expression, which in turn causes a cell autonomous increase of Fasciclin 2 expression. In addition, at high expression levels, Fasciclin 2 function switches to a non-cell autonomous repressor of EGFR by interacting with its heterophilic partner IgCAMs Fipi and Elff. Thus, the two functional facets of Fasciclin 2, as cell autonomous activator and non-cell autonomous repressor of EGFR, constitute an expression-level switch for growth in the control of organ shape and size.
Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics
Authors: Dens Ceder , Adams Charlotte , Laukens Kris , Bittremieux Wout 
Published: May 2024

AbstractIn computational proteomics, machine learning (ML) has emerged as a vital tool for enhancing data analysis. Despite significant advancements, the diversity of ML model architectures and the complexity of proteomics data present substantial challenges in the effective development and evaluation of these tools. Here, we highlight the necessity for high-quality, comprehensive datasets to train ML models and advocate for the standardization of data to support robust model development. We emphasize the instrumental role of key datasets like ProteomeTools and MassIVE-KB in advancing ML applications in proteomics and discuss the implications of dataset size on model performance, highlighting that larger datasets typically yield more accurate models. To address data scarcity, we explore algorithmic strategies such as self-supervised pretraining and multi-task learning. Ultimately, we hope that this discussion can serve as a call to action for the proteomics community to collaborate on data standardization and collection efforts, which are crucial for the sustainable advancement and refinement of ML methodologies in the field.
Selective predation by ants against less-honeydew secreting aphids
Authors: Matsuura Takumi , Handa Chihiro , Takahashi Satobu , Itino Takao 
Published: May 2024

AbstractMany ant-aphid interactions illustrate the concept of a mutually beneficial association between two organisms: aphids provide ants with honeydew; in return, ants defend aphids from enemies. However, ants also often prey on the aphids they attend, and we do not know if the predation pressure causes any adaptations on the side of aphids. The aphidStomaphis japonicahas an obligate mutualistic association withLasiusants. Here, we report evidence of selective predation of less-honeydew secretingStomaphisaphids by the tendingLasiusants. We show that 1. the aphids are severely preyed on by the ants – up to half of the aphids’ standing population per day. 2. the ants selectively prey on the aphids which do not deliver honeydew when attacked, and 3. the frequency of aphids’ honeydew secretion is heritable. These results suggest selective predation by ants against less-honeydew secreting aphids takes place and it is heritable.
Modulation of H3K4 trimethylation by KDM5A and MLLs impacts metabolic adaptability in prostate and cervical cancer cells
Authors: Kirtana R. , Manna Soumen , Patra Samir Kumar 
Published: May 2024

AbstractChemical modifications of chromatin modulate gene expression and induce essential metabolic plasticity for tumor growth. Accumulation of H3K4me3 in the promoter of a gene activates transcription by making the promoter accessible to the polymerases. Methylation of H3K4 is catalysed by MLLs and demethylation of H3K4me3 is catalysed by KDM5 family proteins. Herein, we investigated if genes encoding the enzymes involved in glucose metabolism are dependent on KDM5A and MLL1, and if targeting the H3K4me3 would help in modulating the resilience of cancer cells. We present that KDM5A modulates most of the metabolic genes in a demethylase dependent manner as assesses by H3K4me3 occupancy on G6PD and catalase promoters. Targeting its expression would indeed help in sensitizing cancer cells to ROS dependent apoptotic cell death. We elucidated the differences in the epigenetic regulation in cancerous cells originated from cervical and prostate tissues and used a normal skin keratinocyte for comparison. In cervical and prostate cancers - KDM5A activated glycolysis but downregulates other metabolic processes. In cervical cancer, which majorly depends on PPP, changes in KDM5A did not modulate the G6PD expression. Further, we have shown that curcumin treatment enhanced KDM5A expression and downregulated MLL2 in cancer cell lines but not in keratinocyte cells. Curcumin inhibited metabolic pathways and enhanced apoptosis in cancer cells without affecting keratinocyte cells by modulating KDM5A and MLL levels. This work also strengthens the basic concept that, epigenetic modulations of genes in a tissue precisely depends on signal and sites of modification(s).
Phylogenomics supports a single origin of terrestriality in Isopods
Authors: Thomas Thorpe Jessica A. 
Published: May 2024

ABSTRACTTerrestriality, the adaptation to life on land, is one of the key evolutionary transitions, having occurred numerous times across the tree of life. Within Arthropoda, there have been several independent transitions in hexapods, myriapods, arachnids and isopods. Isopoda is a morphologically diverse order within Crustacea, with species adapted to almost every environment on Earth. The order is divided into 11 suborders with the most speciose, Oniscidea, including terrestrial isopods such as woodlice and sea-slaters. Recent molecular phylogenetic studies have challenged traditional isopod morphological taxonomy, suggesting that several well-accepted suborders, including Oniscidea, may be non-monophyletic. This implies that terrestriality may have evolved more than once within Isopoda. Current molecular hypotheses, however, are based on limited sequence data. Here, I collate available transcriptome and genome datasets for 33 isopods and four peracarid crustaceans from public sources, generate assemblies, and use 960 single-copy orthologues to estimate isopod relationships and the timing of divergences with molecular dating. The resulting phylogenetic analyses support monophyly of terrestrial isopods and suggest that conflicting relationships based on nuclear ribosomal sequences may be caused by long-branch attraction. Dating analyses suggest a Carboniferous-Permian origin of isopod terrestriality, much more recently than other terrestrial arthropods.