bluuebunny/crossref_metadata_2025_split huggingface dataset:
Randomized Trial of Group Postpartum Care Model Improves Knowledge and Clinical Outcomes
Authors: Adams Yenupini Joyce , Agbenyo John Stephen , Lau Elizabeth , Young Jessica , Haas David 
Published: February 2025

Abstract

Background
In sub-Saharan Africa, the risk of obstetric complications remains high throughout the postpartum period.

Objective
We developed and tested a novel, integrated model of group postpartum care titled Focused-Postpartum Care (Focused-PPC) to improve outcomes. In this paper, we report clinical outcomes of participants in the intervention arm and differences in knowledge of post-birth warning signs among those in the intervention and control arms.

Methods
Focused-PPC encompassed recommended clinical assessments, targeted education, and peer support up to 1 year after birth. Focused-PPC was implemented as a parallel randomized controlled trial involving 192 postpartum women across four health centers in Tamale, Ghana, from February 2022 to August 2023. Eligible participants 18 years or older with a live birth were randomly assigned to either the Focused-PPC intervention arm or the control arm at a 1:1 allocation and were not blinded to their allocation. At each health center, 48 participants were allocated to either an intervention or control arm. Focused-PPC groups in the intervention arm consisted of eight participants per group. Participants in the intervention arm received the Focused-PPC integrated group model of care. Participants in the control arm received the standard of postnatal care already administered at each health center.

Results
Baseline analysis included 96 participants from the control arm and 91 participants from the intervention arm. We found that vital signs and clinical outcomes were relatively stable; however, incidences of hypertension substantially decreased among participants in the intervention arm. By 3 months post-birth, most participants in the intervention arm were able to identify all post-birth warning signs and retain this knowledge compared to the control arm. Those in the intervention arm were also knowledgeable of more warning signs at each time point compared to the control arm.

Discussion
An integrated, evidence-based approach to postpartum care, such as Focused-PPC, has potential to increase knowledge and improve clinical outcomes among mothers in Ghana.
Opioid-free Laparoscopic Appendectomy: Quality Improvement Project
Authors: Mitchell Kelsey , Hoffman Hilary , Liston David E. , Hamilton Jeffrey , Low Daniel K. 
Published: February 2025

Introduction:
This quality improvement project has tracked postoperative measures for more than 5 years as we implement an opioid-free laparoscopic appendectomy protocol.

Methods:
We used statistical process control charts to analyze real-world data captured from the medical record. Outcome measures included postanesthesia care unit (PACU) length of stay (LOS), 24-hour maximum pain scores, PACU intravenous opioid medication administration, hospital LOS, and postoperative day 1 morphine milliequivalent requirement. We monitored this family of measures in all appendectomy patients as our team adopted the opioid-free protocol; in addition, we rationally subgrouped patients into the opioid-receiving group versus the opioid-free group.

Results:
A total of 2,483 pediatric laparoscopic appendectomies were performed between January 1, 2017, and June 30, 2023. Starting in 2017, we encouraged anesthesia providers to follow an opioid-free protocol for laparoscopic appendectomy. By October 2019, a ~50% adoption rate of intraoperative opioid-free anesthetic management had occurred. In total, 1,486 patients received opioids and 997 patients did not (opioid-free). No special cause variation was observed for the measured outcomes, including maximum 24-hour pain scores or PACU rescue opioid administration. We did notice reduced hospital LOS in addition to a reduced postoperative day 1 morphine milliequivalent requirement in the opioid-free group.

Conclusions:
This quality improvement project implemented an opioid-free laparoscopic appendectomy protocol for pediatric patients without adversely affecting pain scores, rate of PACU rescue opioids, or hospital LOS.
Comparative Outcome Study of Gynecomastia Surgery and Gender-Affirming Mastectomy With 100% Nipple Preservation
Authors: Swanson Eric 
Published: February 2025

Background
Gynecomastia and gender-affirming top surgery share similarities in objectives. Traditionally, a subcutaneous mastectomy using a semicircular incision has been recommended for most gynecomastia patients. In recent years, mastectomies and nipple grafting have become the most popular treatment for gender-affirming top surgery. Nipple grafting is very debilitating to this unique body part, which also provides erogenous sensation. This study was undertaken to compare methods, complications, and outcomes using an approach that preserves nipples in 100% of patients.

Methods
A retrospective study was conducted, comparing all gynecomastia patients and gender-affirming top surgery patients treated by the author over the period 2016–2024. Most (92%) gynecomastia patients were treated with liposuction in combination with a semicircular incision and subcutaneous mastectomy. Twelve top surgery patients (71%) were also treated with this method. Two gynecomastia patients and 5 top surgery patients with pendulous breasts underwent vertical mammaplasties incorporating a medial pedicle. A telephone survey was also administered.

Results
Fifty-three patients were evaluated, including 36 gynecomastia patients and 17 top surgery patients. The complication rate was 21%. Three patients (6%) developed hematomas. Five patients (9%) underwent revisions. No patient experienced complications of the nipple/areola complex. All surveyed patients reported that nipple preservation was important. Two patients (11%) reported reduced nipple sensation after surgery. No patient reported scar dissatisfaction. Fifteen patients (83%) were comfortable exposing their chest after surgery, compared with 1 patient (6%) before surgery.

Discussion
Today, a major disparity exists in treatment recommendations, with almost all gynecomastia patients being offered nipple-preserving methods and the majority of top surgery patients undergoing mastectomies with nipple grafting, or even without grafting. In view of the importance of nipple sensation, and the success of an alternative approach, surgical priorities should be realigned to preserve nipple/areola complexes.

Conclusions
Nipple preservation is offered to all patients. Subcutaneous mastectomies are often sufficient, and limit scarring. Vertical mammaplasties with a medial pedicle are effective in patients with pendulous breasts. Liposuction is offered as a second-stage procedure, although many patients are satisfied with some residual breast fullness. The need for secondary surgery of the nipple/areola complex and scar revisions is minimized.
GraphMatch: Knowledge Graphs for Allogeneic Stem Cell Matching
Authors: Kunau Timothy M. 
Published: February 2025

AbstractAllogeneic bone marrow and umbilical cord stem cell transplants often provide the best hope for curing many patients with leukemia, lymphoma, and over 70 other diseases. Matching patients to unrelated donors requires flexible and timely searches as matching criteria change. Matching systems should scale to accommodate the diversity in patient and donor typing resolution and the growing number of donors.We developed GraphMatch (GM), a scalable graph database solution for storing and searching variable-resolution HLA genotype markers. As a test set, we expanded the World Marrow Donor Association (WMDA) validation set based on the IPD-IMGT/HLA Database version 2.16 to create a synthetic production data set of 1 million patients and 10 million donors.Single-patient identity search times range from 218.5 milliseconds per patient for 2 million donors to 1201.4 milliseconds per patient for 10 million donors. Search performance timing remained linear with the number of edges, even at a production scale.In general, GM demonstrates the usefulness of graph databases as a flexible platform for scalable matching solutions.
Massive Chromosome Fission and Speciation in Asian River Chub: Integrating Kinetochore Reproduction Theory with Transposable Element Dynamics
Authors: Tai Jui-Hung , Wang Tzi-Yuan , Ma Gwo-Chin , Wu Yu-Wei , Yu Tsung-Han , Wang Chen-Fan , Liao Te-Yu , Huang Shih-Pin , Wang Feng-Yu , Terai Yohey , Wu Tsung-Han , Hsu Chun-Hua , Yu Hon-Tsen , Shao Kwang-Tsao , Chaw Shu-Miaw , Wang Hurng-Yi 
Published: February 2025

ABSTRACTChromosome rearrangements significantly influence speciation, but the role of chromosome fission is paradoxical due to its link with unbalanced segregation. The kinetochore reproduction theory suggests that fissions from kinetochore duplication should allow normal segregation, though empirical support remains scarce. In the Opsariichthyini tribe (Asian river chub), chromosome number vary from 2N=48 in most genera to 76-78 inOpsariichthysdue to 15 fission events.Opsariichthysharbors over 15 species, substantially surpassing the typical three to four species in other genera. This exceptional diversity, coupled with dramatic chromosome fission, makes the Opsariichthyini as an ideal model for studying speciation driven by chromosome fission. We sequenced and annotated genomes from five representative species, finding that significant transposable element (TE) accumulation in centromeres likely contributes to centromeric DNA expansion. This, in turn, may have facilitated neokinetochore formation, potentially leading to chromosome fissions. The fissioned chromosomes showed lower migration rates and higher genetic divergence between species than their intact counterparts, highlighting their role as reproductive barriers that promote speciation. Our findings offer unprecedented support for the kinetochore reproduction theory and elucidate the complex interplay between TE activities, genomic structure, and speciation.
Examining Perinatal Regionalization in Practice: A Network Analysis of Maternal Transport in Georgia
Authors: Li Jingyu , Radke Stephanie M. , Steimle Lauren N. 
Published: February 2025

AbstractObjectiveThe primary objective was to use network analysis to characterize maternal transport patterns in the state of Georgia and compare them with the state’s designated perinatal regions (DPRs).Study DesignUsing 2017-2022 birth records in Georgia, we constructed network graphs of maternal transport routes among obstetric facilities. We used multivariate logistic regression to identify factors associated with inter-DPR transports. We applied a community-detection algorithm to cluster facilities and compared the clusters to Georgia’s DPRs.ResultsAmong 774 639 deliveries, 2 757 (0.36%) involved transports among obstetric facilities. 8 facility clusters were identified and strongly aligned with DPRs (p < 0.001). Inter-DRP transports tended to occur between neighboring DPRs and between facilities belonging to the same healthcare system (p < 0.001).ConclusionNetwork analysis reveals patterns of maternal transports among obstetric facilities. States can improve the design of perinatal regionalization systems by formalizing existing partnership among obstetric facilities.
Predicting age-related determinants of heterogeneous outcomes to COVID-19 mRNA vaccines through mathematical modelling
Authors: Deng Xiaoyan , Farhang-Sardroodi Suzan , Craig Morgan 
Published: February 2025

ABSTRACTOlder adults tend to exhibit weaker vaccine-elicited responses to mRNA COVID-19 immunization than younger people. This is a public health concern, as older individuals are more likely to experience severe COVID-19. To better understand the mechanisms of this age-related disparity, we developed a mathematical model of the post-vaccination humoral immune response. Through calibration to clinical data from 32 healthcare workers (HCWs) and 27 seniors who received the primary vaccine series (two priming doses and one booster), our model predicted that repeated vaccinations consistently enhanced antibody responses in both groups. While seniors were estimated to experience an accelerated decay in T follicular helper cells compared to HCWs, a larger booster dose effectively compensated for this weakened antibody response. Furthermore, we linked antibody and neutralization levels and used this relationship to predict post-vaccination neutralization, thus serving as a proxy for vaccine efficacy. By studying various combinations of mixed doses sizes in the primary vaccination series, our model predicted that administering a full-dose booster significantly enhances immunization outcomes, irrespective of the initial vaccine dose size. Further, a biannual half booster strategy was found to be more effective than one with an annual full booster, especially for seniors. Overall, our findings highlight the importance of tailoring vaccination strategies to different age groups to provide robust and long-lasting immunity against SARS-CoV-2 infections.
Quantitative Fluorescence Imaging of Porphyrin Phospholipid Photobleaching and Light Activated Liposomal Doxorubicin Release Using Wide-field and Laparoscopic SFDI in an Ovarian Cancer Model
Authors: Ahmmed Rasel , Kluiszo Elias , Aygun-Sunar Semra , Willadsen Matthew , Kutscher Hilliard L , Lovell Jonathan F. , Sunar Ulas 
Published: February 2025

AbstractChemophototherapy (CPT) is an emerging cancer treatment that leverages the synergistic effects of photodynamic therapy (PDT) and chemotherapy. This approach utilizes photosensitizers like Porphyrin Phospholipid (PoP) and Doxorubicin (Dox) to enable phototriggered drug release and targeted tumor destruction. In this study, we present the development and validation of a wide-field laparoscopic spatial frequency domain imaging (SFDI) system, designed to improve intraoperative quantitative fluorescence imaging and monitoring of PoP photobleaching, a PDT-driven effect for tumor destruction, and light-activated Dox release, which facilitates targeted chemotherapeutic drug delivery in an ovarian cancer model. Compared to previous flexible endoscopic imaging methods, our laparoscopic SFDI system offers enhanced spatial coverage, enabling accurate wide-field optical property quantification in minimally invasive surgical settings. Using this system, we performed quantitative fluorescence imaging in vivo to obtain absolute concentrations of PoP and Dox fluorescence, correcting for tissue absorption and scattering effects. This capability allows for precise assessment of PoP photobleaching and Dox release kinetics with improved spatial resolution. Fluorescence imaging revealed a significant reduction in PoP concentration in tumor regions post-illumination, demonstrating the PDT-mediated photobleaching effect and successful light-triggered drug release activation for chemo-induced tumor destruction. The ability to differentiate PoP and Dox fluorescence in a laparoscopic system underscores its potential for real-time intraoperative monitoring of CPT efficacy. These findings establish wide-field laparoscopic SFDI as a promising tool for guiding minimally invasive photodynamic therapy and targeted drug delivery in clinical settings.
Communication pathway analysis within protein-nucleic acid complexes
Authors: Bheemireddy Sneha , González-Alemán Roy , Bignon Emmanuelle , Karami Yasaman 
Published: February 2025

AbstractInter-residue communication forms a vast and intricate network that underpins essential biological processes such as catalysis, gene expression, and cell signaling. Allostery, a crucial phenomenon where distant regions of a macromolecule are energetically coupled to elicit functional responses, operates through these intricate communication networks within macromolecular complexes. Despite the pivotal role of nucleic acids in these networks, their contributions to allostery remain largely overlooked. To address this gap, we developed ComPASS, a large-scale computational method designed to study communication networks in protein-protein and protein-nucleic acid complexes. Recognizing the significance of dynamics in the communication of macromolecules, our approach leverages molecular dynamics (MD) simulation data to extract inter-residue key properties, including dynamical correlations, interactions, and distances. These properties are integrated to construct a weighted communication network that comprehensively represents dependencies among amino acids and nucleotides. Using ComPASS, we uncovered distinct mechanisms of signal transmission in diverse macromolecular systems. In Cysteinyl-tRNA synthetase, the central domain was found to mediate the coordination between substrate recognition and enzymatic activity, ensuring functional precision. In the LacI repressor, allosteric communication occurs through interface pathways within the dimer, effectively linking ligand sensing to DNA binding. For the Type IIF restriction endonuclease Bse634I, structural communication across dimer and tetramer interfaces was crucial for specific DNA recognition. In the liver X receptor, a key helical region was identified as a bridge connecting ligand-binding events to DNA interactions. Finally, our analysis with ComPASS aligned with previous literature, confirmed the role of H2A L1 loops in mediating communication across histone interfaces and coordinating interactions between structural domains in nucleosome complexes. ComPASS is available as an open-source tool, maintained athttps://github.com/yasamankarami/compass. By offering an integrated framework for studying communication networks, ComPASS advances our understanding of conformational dynamics, particularly within protein-nucleic acid complexes.
MARTi: a real-time analysis and visualisation tool for nanopore metagenomics
Authors: Peel Ned , Martin Samuel , Heavens Darren , Yu Douglas W , Clark Matthew D , Leggett Richard M 
Published: February 2025

AbstractThe emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and bio-surveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools.We present MARTi (Metagenomic Analysis in Real-Time), an innovative open-source software designed for the real-time analysis, visualisation, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customise parameters and utilise their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification.MARTi’s architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi’s performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.
Climate-driven warming disrupts the symbiosis of bobtail squidEuprymna scolopesand the luminous bacteriumVibrio fischeri
Authors: Otjacques E. , Jatico B. , Marques T.A. , Xavier J.C. , Ruby E. , McFall-Ngai M. , Rosa R. 
Published: February 2025

AbstractUnder the current climate crisis, marine heatwaves (MHW) are expected to intensify and become more frequent in the future, leading to adverse effects on marine life. Here, we aimed to investigate the impact of environmental warming on the symbiotic relationship between the Hawaiian bobtail squid (Euprymna scolopes) and the bioluminescent bacteriumVibrio fischeri. We exposed eggs ofE. scolopesto three different temperatures during the embryogenesis, namely: i) 25 °C (yearly average), ii) 27 °C (average summer), or iii) 30 °C (category IV MHW), followed by a colonisation assay under the same conditions. Decreased hatching success and reduced developmental time were observed across warmer conditions compared to 25 °C. Moreover, exposure to the category IV MHW led to a significant decrease in survival after 48 hours. With increasing temperature, bobtail squids required more bacteria in the surrounding seawater for successful colonisation. When colonised, the regression of the light organ’s appendages was not dependent on temperature, but the opposite was found in non-colonised bobtail squids. Furthermore, the capacity to maintain the symbiosis diminished significantly with temperature. Finally, the capacity for crypt 3 formation in the squid’s light organ, which is crucial for enhancing resilience under stress, also declined with warming conditions. This study emphasises the critical need to study the dynamics of microbial symbiosis under the projected conditions for the ocean of tomorrow.
Accuracy of the Lotka-Volterra Model fails in strongly coupled microbial consumer-resource systems
Authors: Mustri Michael , Duan Quqiming , Pawar Samraat 
Published: February 2025

AbstractThe generalized Lotka-Volterra (GLV) model is a cornerstone in theoretical ecology for modeling the dynamics emerging from pairwise species interactions within complex ecological communities. The GLV is also increasingly being used to infer species interactions and predict dynamics from empirical data on microbial communities in particular. However, despite its widespread use, the accuracy of the GLV’s pairwise interaction structure in capturing the unseen dynamics of microbial consumer-resource interactions—arising from resource competition and metabolite exchanges—remains unclear. Here, we rigorously quantify how well the GLV can represent the dynamics of a general mathematical model that encapsulates key consumer-resource processes in microbial communities. We find that the GLV significantly misrepresents the feasibility, stability, and reactivity of microbial communities above a threshold, biologically feasible level of consumer-resource coupling because it omits higher-order nonlinear interactions. We show that the probability of the GLV making inaccurate predictions can be quantified by a simple, empirically accessible measure of timescale separation between consumers and resources. These insights advance understanding of the temporal dynamics in resource-mediated microbial interactions and provide a method to gauge the GLV’s reliability under various empirical and theoretical scenarios.