bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depletion of key gut bacteria predicts disrupted bile acid metabolism in inflammatory bowel disease
Authors: Peterson Daniel , Weidenmaier Christopher , Timberlake Sonia , Gura Sadovsky Rotem 
Published: December 2024

ABSTRACT

The gut microbiome plays a key role in bile acid (BA) metabolism, where a diversity of metabolic products contribute to human health and disease. In particular, Inflammatory Bowel Disease (IBD) is characterized by a low concentration of secondary bile acids (SBAs), whose transformation from primary bile acids (PBAs) is an essential function performed solely by gut bacteria. BA-transformation activity mediated by the bile acid inducible (bai) operon has been functionally characterized in the genus
Clostridium
, and homologous bai gene sequences have been found in metagenome-assembled genomes (MAGs) belonging to other taxa in the human gut, but it is unclear which species of bai-carrying bacteria perform physiologically significant amounts of bile acid transformation in healthy and sick individuals. Here, we analyzed hundreds of stool samples with paired metagenomic and metabolomic data from IBD patients and controls and found that the abundance of the bai operon in metagenomic samples was highly predictive of that sample’s high- or low-SBA metabolic state. We further found that bai genes from the
Clostridium
species best characterized as BA transformers were more prevalent in IBD patients than in non-IBD controls, while bai genes from uncharacterized taxa known only from MAGs were much more physiologically relevant in non-IBD samples. These un-isolated clades of BA-transforming bacteria merit further research; as beyond their prevalence in the human population, we found some cases in which they engrafted in IBD patients who had undergone fecal microbiota transplantation and experienced a clinical response.

IMPORTANCE
In this paper, we identify specific bacteria that perform an important metabolic function in the human gut and demonstrate that in the guts of a large subset of patients with IBD, these bacteria are missing and the function is defective. This is a rare example where the correlation between the absence of specific bacteria and the dysfunction of metabolism is directly observed, not in mice nor in the lab, but in physiologic microbial communities in the human gut. Our results point to a path for studying how a small but important set of bacteria is affected by conditions in the IBD gut and perhaps to the development of interventions to mitigate the loss of these bacteria in IBD.
Researchers’ agency and the boundaries of global mental health: perspectives from and about Latin America
Authors: Montenegro Cristian , Abarca-Brown Gabriel , Flores Elaine C , Susser Ezra , Rivera Eliut , Paniagua-Ávila Alejandra , Florence Ana Carolina , Mascayano Franco 
Published: December 2024

The decolonise global health movement has critically reassessed the field’s historical and political underpinnings, urging researchers to recognise biases and power imbalances through reflexivity and action. Genuine change is seen as the outcome of the researcher’s self-awareness, often leaving the underlying structures of global health—and global mental health (GMH)—in the background. Here, we problematise how expectations around agency and change have been mobilised in discussions around decolonisation, highlighting the gradual and contingent nature of international collaboration in GMH.We present three international research initiatives based in or focused on South America: RedeAmericas, the Platform for Social Research on Mental Health in Latin America and the HEalthcaRe wOrkErS project. Instead of comparing the three initiatives directly we identify and discuss common elements among them that challenge and redefine the boundaries of GMH by leveraging local leadership, creating hybrid expert profiles and implementing principles of equity and epistemic justice. Particular attention is given to the fragmentary translation of these principles into the project’s concrete activities.The interplay of agency and the structural confines of GMH is examined in each initiative, expanding the notion of ‘boundaries’ in the field beyond geographical or institutional demarcations. Using the notion of milieu, we call for a more nuanced understanding of the field as simultaneously shaping and being shaped by the tentative collaborative infrastructures developed by researchers. We advocate for a reconceptualisation of GMH that is as diverse and complex as the issues it seeks to address.
Pain determinants and quality of life in Guillain-Barre syndrome: a prospective cohort study
Authors: Papri Nowshin , Mohammed Asif , Rahman Md. Mantaka , Hasan Imran , Azam Rufydha , Saha Tamal , Shaon Farzana Tamanna Ummey , Jahan Israt , Hayat Shoma , Ara Gulshan , Islam Badrul , Islam Zhahirul 
Published: December 2024

BackgroundPain is a serious manifestation in both the acute and chronic stages of Guillain-Barre syndrome (GBS). We evaluated the frequency, characteristics and associated factors of pain and its impact on quality of life (QoL) among patients with GBS.MethodsWe enrolled 644 patients with GBS from prospective cohort studies in Bangladesh conducted between 2010 and 2024. Data were collected at enrolment and at standard follow-up time points up to 26 weeks. Pain intensity was measured by a pain numeric rating scale. Group differences were tested using the χ² or Fisher’s exact test, longitudinal changes were analysed with repeated-measures analysis of variance and correlations were analysed with Spearman’s rank test.ResultsThe median age of the patients was 31 years, with 70% men. During enrolment, 71% of patients reported pain, which persisted among 38% at week 13 and 26% at week 26. Pain was significantly associated with disease severity, muscle weakness and treatment with intravenous immunoglobulin in both the acute and chronic stages. Patients with acute pain had a higher proportion of axonal GBS (p=0.000) than those without pain. Chronic pain was associated with higher age (p=0.006), male sex (p=0.000), preceding diarrhoea (p=0.033) and dysautonomia (p=0.000). Higher pain intensity was reported among women (p=0.027), patients with higher age (p=0.029) and severe form of GBS (p=0.038) compared with counter groups. Acute pain was significantly associated with the ‘self-care’ (p=0.023), ‘usual activities’ (p=0.049) and ‘anxiety/depression’ (p=0.048) domains of QoL, whereas chronic pain was associated with the ‘anxiety/depression’ (p=0.005) domain.ConclusionsPain presented as a serious symptom negatively affecting the QoL in GBS. Systematic evaluation of pain is recommended to ensure a personalised treatment approach for GBS.
Inequalities in COVID-19 impact on preschool mental health in India: key moderators of adverse outcome
Authors: Sharp Helen , Wright Nicky , Bozicevic Laura , Supraja Thirumalai Ananthanpillai , Pickles Andrew , Hill Jonathan , Chandra Prabha S. 
Published: December 2024

IntroductionWorldwide research suggests that the COVID-19 pandemic had little to no overall effect on preschool children’s mental health, but that the impact is variable depending on pre-existing and COVID-19-related inequalities. Evidence from low- and middle-income country settings is sparse, yet effects may be more variable due to greater inequalities. We provide the first empirical evidence for the impact of the pandemic on emotional and behavioural problems in Indian preschool children, after accounting for normative age-related change, and test whether the impact varied depending on COVID-19-related inequalities.MethodsFamilies participating in an Indian-based prospective longitudinal birth cohort (Bangalore Child Health and Development Study) provided data at age 2 years (before COVID-19) and again during COVID-19 (n=528). Mothers reported child emotional and behavioural problems and a range of COVID-19-related adverse experiences.ResultsThere was a small overall pandemic effect on emotional (rate ratio (RR)=1.31, p=0.040), but not behavioural problems, after adjusting for age-related change. However, compared with the lowest risk level, emotional and behavioural problems rose higher compared with whole sample age-expected rates in families who reported the highest levels of perceived negative impact of COVID-19-related adversities (moderation p<0.001, RR=2.43 and p<0.001, RR=1.32), COVID-19 life events (p<0.001, RR=3.28, and p<0.001, RR=1.26) and time the child spent playing alone (p<0.001, RR=2.49). Emotional problems rose higher with high perceived COVID-19 maternal stress (p=0.013, RR=1.57) and with increased child mobile phone use (p<0.001, RR 1.48). Secondary analyses controlling for variation in age trends within moderator subgroups revealed these to be rarely significant. Where significant and accounted for, having more children living at home emerged as protective, whereas living below the poverty line emerged as a risk for adverse pandemic impact on child mental health.ConclusionA small overall increase in preschool mental health problems was evident. However, this masked substantial worsening of such problems in families with elevated COVID-19 adversities in India. These findings can inform the targeting of policy and practice initiatives to better mitigate adverse longer-term mental health outcomes arising from the pandemic response.
Initial experience of parenchyma-sparing liver resection with systematic selective hepatic vein reconstruction for colorectal metastases
Authors: Trehub Yevhenii , Fretland Åsmund Avdem , Zelinskyi Artem , Kharkov Dzmitrii , Babashev Oleksii , Chieverdiuk Dmytro , Shchebetun Artem , Khyzhniak Kyrylo , Pavlovskii Maksym , Strokan Andrii , Zemskov Sergii 
Published: December 2024

ObjectivesThis study aims to assess the feasibility and short-term and intermediate-term technical success rate of the concept of systematic selective hepatic vein (HV) reconstruction for parenchyma-sparing hepatectomies (PSHs) in patients with colorectal liver metastases (CRLM) in accordance with stage 2a of the IDEAL framework.DesignThe prospective case series of patients deemed eligible and operated on according to the concept.SettingAll patients were treated by a single surgical team in three hospitals in Ukraine from June 2022 to November 2023.ParticipantsThe study included nine cases of resectable CRLM with at least one lesion located in the hepatocaval confluence with HV(s) invasion, for whom reconstruction of the HV(s) allowed for additional parenchyma preservation, being an alternative to major or extended hepatectomy.InterventionsLiver resections with different types of HVs reconstruction (primary closure, patching, end-to-end anastomosis with or without grafting) were performed after a thorough evaluation of the future liver remnant volume, volume of potentially additionally preserved parenchyma and possibility of future repeat hepatectomies.Main outcome measuresPostoperative morbidity, short-term and long-term patency of the reconstructed vessels, and the volume of additionally preserved parenchyma were the focus.ResultsSegmental resection was performed in four cases, two with graft interposition. Patch reconstruction was performed for three HVs and two inferior vena cava resections. Two cases required primary closure. No mortality was observed, while the major morbidity rate was 33%. The short-term and long-term patency of the reconstructed HVs was 88.9% and 66.7%, respectively. HV reconstructions allowed the preservation of additional parenchyma (mean 495.4 mL, 95% CI 350.2 to 640.7). A decision-making algorithm to be used within the described approach is proposed.ConclusionsSelective HV reconstruction is a feasible approach for PSH for CRLM. Further studies are needed to compare this approach to convenient major hepatectomies.
Predicting the likelihood ofBRCA1/2germline pathogenic variants in unselected patients with breast cancer: analysis of more than 10,000 individuals
Authors: Sun Jie , Yao Lu , Chen Jiuan , Hu Li , Zhang Juan , Xu Ye , Xie Yuntao 
Published: December 2024

BackgroundModels for accurately predicting the likelihood ofBRCA1/2germline pathogenic variants (PVs) based on a large cohort of unselected patients with breast cancer are limited.MethodsA logistic regression model to predict theBRCA1/2carrier probability, named PKCBRCA, was established and validated based on 10 167 unselected Chinese patients with breast cancer treated in Peking University Cancer Hospital between October 2003 and August 2020. All patients were tested forBRCA1/2germline variants. The discrimination and calibration of the model were assessed.ResultsA total of 601 (5.9%) patients carriedBRCA1/2germline PVs in the entire cohort of 10 167 unselected patients with breast cancer. The cohort was separated into a training set (n=6331; 387 (6.1%)BRCA1/2carriers) and a validation set (n=3836; 214 (5.6%)BRCA1/2carriers). Five variables strongly associated withBRCA1/2carrier probability were incorporated in the establishment of PKCBRCA including age of diagnosis, bilateral breast cancer, family history of breast or ovarian cancer, hormone receptor and ERBB2. PKCBRCA showed a good ability to discriminate both in the training set (area under the receiver operating characteristic curve (AUC)=0.77) and in the validation set (AUC=0.77).ConclusionOur model provides a useful tool for accurately assessing theBRCA1/2carrier probability for unselected patients with breast cancer.
Community of trauma care partnering with stakeholders to improve injury outcomes: survey analysis and panel development
Authors: Appelbaum Rachel D , Newcomb Anna B , Price Michelle A , Joseph Katherine , Moreno Ashley N , Hennessy Morgan , Fortin Princess , Bixby Pam J , Prentiss Sue , McConnell-Hill Alexandra , Flayter Rochelle , Dicker Rochelle A , Kozar Rosemary A , Haut Elliott R , Stein Deborah M 
Published: December 2024

BackgroundIn June 2021, the Injury Research Engagement Project (I-REP) was established. In 2022, we preformed focus group analysis with patients/caregiver and researchers that resulted in themes in preferences, motivations, and best practices to increase participation in trauma research. The importance of trust and well-established relationships was common across all groups. In this study, we aimed to further evaluate preferences regarding research procedures and outcomes, and develop a panel for sustained patient engagement.MethodsWe performed a multiphase, mixed methods study to elicit trauma stakeholders’ perspectives regarding aspects of research. Previously published phase 1 involved focus group analysis. Phase 2 vignette-based surveys and phase 3 panel formation are described here. One survey was completed by patients/caregivers, and the second by trauma researchers. We compared the responses using independent t-tests. This was followed by a webinar and development of an I-REP panel of patients/caregivers.Results60 patients/caregivers and 114 researchers participated in the online surveys, with completion rates of 68% and 69%, respectively. The majority of patients/caregivers were >45 years, female (66.7%), and >3 years out from their or their family member’s injury (68.6%). The majority of the researchers were >35 years and male (56.2%). Participants were asked to gauge their perceptions of different research scenarios. The analysis identified themes emerging across groups. Several survey findings differed from phase 1, including motivations to participate (payment) and consent preferences (timing, approach). Racial and ethnic demographics of the participants were not collected.ConclusionsEngaging trauma stakeholders results in research more relevant to patients’ needs and priorities. Qualitative engagement methods that intentionally include a more diverse population and determining the appropriate format for specific questions may lead to results that are be more generalizable. The educational webinar was well received, and several participants opted to serve as I-REP panelists to collaborate with trauma researchers moving forward.Level of evidenceIV.
Adversarial Network Optimization under Bandit Feedback: Maximizing Utility in Non-Stationary Multi-Hop Networks
Authors: Dai Yan , Huang Longbo 
Published: December 2024

Stochastic Network Optimization (SNO) concerns scheduling in stochastic queueing systems and has been widely studied in network theory. Classical SNO algorithms require network conditions to be stationary w.r.t. time, which fails to capture the non-stationary components in increasingly many real-world scenarios. Moreover, most existing algorithms in network optimization assume perfect knowledge of network conditions before decision, which again rules out applications where unpredictability in network conditions presents.
Motivated by these issues, this paper considers Adversarial Network Optimization (ANO) under bandit feedback. Specifically, we consider the task of i) maximizing some unknown and time-varying utility function associated with scheduler's actions, where ii) the underlying network topology is a non-stationary multi-hop network whose conditions change arbitrarily with time, and iii) only bandit feedback (the effect of actually deployed actions) is revealed after decision-making. We propose the UMO2 algorithm, which does not require any pre-decision knowledge or counterfactual feedback, ensures network stability, and also matches the utility maximization performance of any "mildly varying" reference policy up to a polynomially decaying gap. To our knowledge, no previous algorithm can handle multi-hop networks or achieve utility maximization guarantees in ANO problems with bandit feedback, whereas ours is able to do both.
Technically, our method builds upon a novel integration of online learning techniques into the Lyapunov drift-plus-penalty method. Specifically, we propose meticulous analytical techniques to jointly balance online learning and Lyapunov arguments, which is used to handle the complex inter-dependency among queues in multi-hop networks. To tackle the learning obstacles due to potentially unbounded queue sizes and negative queue differences, we design a new online linear optimization algorithm that automatically adapts to the unknown (potentially negative) loss magnitudes. Finally, we also propose a bandit convex optimization algorithm with novel queue-dependent learning rate scheduling that suites drastically varying queue lengths in utility maximization. Our new insights and techniques in online learning can also be of independent interest.
Beaver: A High-Performance and Crash-Consistent File System Cache via PM-DRAM Collaborative Memory Tiering
Authors: Pan Qinglin , Qi Ji , He Jiatai , Zhang Heng , Yu Jiageng , Wu Yanjun 
Published: December 2024

The in-memory cache layer is crucial in building a file system. Crash-consistency is highly desirable for applications running on the file system, ensuring that data is written in an all-or-none fashion during unexpected system failures or crashes. However, existing works fail to achieve both high read and write performance in constructing a crash-consistent cache layer.
In this paper, we propose Beaver, a new in-memory file system cache that achieves both crash-consistency and high read/write performance. Beaver exploits a read/write distinguishable memory hierarchy involving both PM and DRAM. Beaver uses the PM to serve write operations for crash-consistency and high write performance, and uses the DRAM to serve read operations for high read performance. We also introduce a kprefetcher to asynchronously move data from PM to DRAM off the critical path of write operations. We extensively evaluated Beaver with the latest file system cache using real-world applications and popular benchmarks. Application evaluation results show that Beaver outperformed other file system caches by up to 16.1% and 11.0% on RocksDB and MinIO, respectively. Beaver's source code is available at https://github.com/PanQL/Beaver.
Beyond Data Points: Regionalizing Crowdsourced Latency Measurements
Authors: Sharma Taveesh , Schmitt Paul , Bronzino Francesco , Feamster Nick , Marwell Nicole P. 
Published: December 2024

Despite significant investments in access network infrastructure, universal access to high-quality Internet connectivity remains a challenge. Policymakers often rely on large-scale, crowdsourced measurement datasets to assess the distribution of access network performance across geographic areas. These decisions typically rest on the assumption that Internet performance is uniformly distributed within predefined social boundaries, such as zip codes, census tracts, or neighborhood units. However, this assumption may not be valid for two reasons: (1) crowdsourced measurements often exhibit non-uniform sampling densities within geographic areas; and (2) predefined social boundaries may not align with the actual boundaries of Internet infrastructure.
In this paper, we present a spatial analysis on crowdsourced datasets for constructing stable boundaries for sampling Internet performance. We hypothesize that greater stability in sampling boundaries will reflect the true nature of Internet performance disparities than misleading patterns observed as a result of data sampling variations. We apply and evaluate a series of statistical techniques to: (1) aggregate Internet performance over geographic regions; (2) overlay interpolated maps with various sampling unit choices; and (3) spatially cluster boundary units to identify contiguous areas with similar performance characteristics. We assess the effectiveness of the techniques we apply by comparing the similarity of the resulting boundaries for monthly samples drawn from the dataset. Our evaluation shows that the combination of techniques we apply achieves higher similarity compared to directly calculating central measures of network metrics over census tracts or neighborhood boundaries. These findings underscore the important role of spatial modeling in accurately assessing and optimizing the distribution of Internet performance, which can better inform policy, network operations, and long-term planning decisions.
Guided Bone Regeneration in the Posterior Mandible Using a Resorbable Metal Magnesium Membrane and Fixation Screws: A Case Report
Authors: Franke Thomas , Korzinskas Tadas 
Published: December 2024

Background: Due to bone loss, implant placement in the posterior mandible is often impossible without prior augentative procedures. The reconstruction of bone defects with horizontal and vertical components using particulated bone grafts requires the placement of a mechanically stable structure for stabilization of the grafting material. Although titanium‐reinforced membranes and titanium meshes have been shown to be effective in this indication, the necessity of their removal, often in a separate surgical procedure, is seen as a disadvantage. Since the introduction of a new resorbable magnesium metal membrane and fixation screw, a mechanically stable and resorbable system might provide an alternative option for guided bone regeneration (GBR) in the posterior mandible.Case Presentation: A 61‐year‐old patient was presented with large edentulous areas in all posterior regions and requested fixed dentures in Areas 34–36. Tooth 33 was extracted and treated with an immediate implantation of a ceramic implant, whereas Positions 34–36 were treated with a two‐stage approach. The site was augmented horizontally, with a slight vertical component using autologous and allogenic bone and a new completely resorbable magnesium metal membrane and fixation screw. During the initial healing period, the patient reported a tingling sensation at the site of the augmentation. This is an observation that is specific to the magnesium products and is potentially caused by the release of hydrogen gas as the metal degrades and is resorbed. Upon re‐entry at 3 months, it was clinically observed that there was a very dense and vascularized bone that was sufficient for placing two 5.5 × 10 mm ceramic dental implants.Conclusion: A completely resorbable magnesium membrane and fixation screw were able to support the bony regeneration in a large GBR situation in the posterior mandible. Due to the use of a new material for GBR, different clinical observations were made compared to the standard material choices.