bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts
Authors: Nicholson David N. , Himmelstein Daniel S. , Greene Casey S. 
Published: October 2022

Abstract
Background
Knowledge graphs support biomedical research efforts by providing contextual information for biomedical entities, constructing networks, and supporting the interpretation of high-throughput analyses. These databases are populated via manual curation, which is challenging to scale with an exponentially rising publication rate. Data programming is a paradigm that circumvents this arduous manual process by combining databases with simple rules and heuristics written as label functions, which are programs designed to annotate textual data automatically. Unfortunately, writing a useful label function requires substantial error analysis and is a nontrivial task that takes multiple days per function. This bottleneck makes populating a knowledge graph with multiple nodes and edge types practically infeasible. Thus, we sought to accelerate the label function creation process by evaluating how label functions can be re-used across multiple edge types.

Results
We obtained entity-tagged abstracts and subsetted these entities to only contain compounds, genes, and disease mentions. We extracted sentences containing co-mentions of certain biomedical entities contained in a previously described knowledge graph, Hetionet v1. We trained a baseline model that used database-only label functions and then used a sampling approach to measure how well adding edge-specific or edge-mismatch label function combinations improved over our baseline. Next, we trained a discriminator model to detect sentences that indicated a biomedical relationship and then estimated the number of edge types that could be recalled and added to Hetionet v1. We found that adding edge-mismatch label functions rarely improved relationship extraction, while control edge-specific label functions did. There were two exceptions to this trend, Compound-binds-Gene and Gene-interacts-Gene, which both indicated physical relationships and showed signs of transferability. Across the scenarios tested, discriminative model performance strongly depends on generated annotations. Using the best discriminative model for each edge type, we recalled close to 30% of established edges within Hetionet v1.

Conclusions
Our results show that this framework can incorporate novel edges into our source knowledge graph. However, results with label function transfer were mixed. Only label functions describing very similar edge types supported improved performance when transferred. We expect that the continued development of this strategy may provide essential building blocks to populating biomedical knowledge graphs with discoveries, ensuring that these resources include cutting-edge results.
The effect of backpack load on intersegmental motions of the foot and plantar pressure in individuals with mild flatfoot
Authors: Kyung Min Gyu , Bak Ppu Ri , Lim Jong Wook , Lee Dong‐Oh , Park Gil Young , Lee Dong Yeon 
Published: October 2022

AbstractBackgroundThe feet play an essential role in shock absorption, and foot posture is closely related to gait. The compensatory mechanism under heavy‐load conditions in individuals with mild flatfoot is poorly understood. In the authors' country, individuals with mild flatfoot are drafted as active‐duty soldiers and participate in military rucking wearing heavy backpacks. This study investigated the effect of backpack load on gait and foot plantar pressure and possible differences in participants with mild flatfoot. The average weight of the backpack during military rucking (approximately 20 kg), was simulated in this study.MethodsThis study prospectively enrolled 30 healthy young males, divided into a control group (CON, n = 15) and a mild low‐arched group (MLA, n = 15), based on the presence of flatfoot. Segmental foot kinematics were evaluated using a three‐dimensional multi‐segment foot model, and gait data of the temporal and spatial parameters were obtained. The dynamic plantar pressure was simultaneously measured using a pedobarography platform with gait trials. The protocol was repeated with all participants wearing 20 kg backpacks. Comparisons between the baseline and loaded states, as well as comparison between groups, were conducted.ResultsAlthough the cadence, gait speed, and stride length decreased in the loaded condition, step time and proportion of the stance phase increased in both groups. Although the MLA group showed more supinated and abducted positions of the forefoot and more pronated positions of the hindfoot than the CON group, the change in intersegmental foot and ankle motion in each group after backpack loading was minimal. However, the former showed a larger step width and a greater increase in contact area in the midfoot region, while the latter demonstrated a greater increase in peak pressure.ConclusionsIndividuals with mild flatfoot demonstrated significantly different gait curve patterns (waveforms) compared to the controls. In the loaded condition, the CON and MLA groups may have adopted different strategies to maintain balance during gait. We suggest that although individuals with asymptomatic mild flatfoot are drafted as active‐duty soldiers, they should be thoroughly investigated under loaded conditions, and orthoses may be helpful.
Hospital change to mixed lipid emulsion from soybean oil-based lipid emulsion for parenteral nutrition in hospitalized and critically ill adults improves outcomes: a pre–post-comparative study
Authors: Haines Krista L. , Ohnuma Tetsu , Trujillo Charles , Osamudiamen Obanor , Krishnamoorthy Vijay , Raghunathan Karthik , Wischmeyer Paul E. 
Published: October 2022

Abstract
Introduction
Early data suggest use of a mixed lipid emulsion (LE) with a soybean oil reduction strategy in parenteral nutrition (PN) may improve clinical outcomes. Duke University Hospital made a full switch to a Soybean oil/MCT/Olive/Fish Oil lipid (4-OLE) from pure soybean oil-based LE (Intralipid, Baxter Inc) in May 2017. Since 4-OLE has limited evidence related to its effects on clinical outcome parameters in US hospitals, evidence for clinical benefits of switching to 4-OLE is needed. Therefore, we examined the clinical utility of a hospital-wide switch to 4-OLE and its effect on patient outcomes.

Methods
We conducted a single-center retrospective cohort study among adult patients (> 18 years) requiring PN from 2016 to 2019. Our primary exposure was treatment period (1-year pre-4-OLE switch versus 2-year post). We used multivariable regression models to examine our primary outcomes, the association of treatment period with hospital length of stay (LOS), and secondary outcomes liver function, infections, and ICU LOS. Analyses were stratified into critically ill and entire adult cohort.

Results
We identified 1200 adults hospitalized patients. 28% of PN patients (n = 341) were treated pre-4-OLE switch and 72% post-4-OLE (n = 859). In the adult cohort, 4-OLE was associated with shorter hospital LOS (IRR 0.97, 95% CI 0.95–0.99, p = 0.039). The ICU cohort included 447 subjects, of which 25% (n = 110) were treated pre-4-OLE switch and 75% (n = 337) were post-switch. ICU patients receiving 4-OLE were associated with shorter hospital LOS (IRR 0.91, 95% CI 0.87–0.93, p < 0.0001), as well as a shorter ICU LOS (IRR 0.90, 95% CI 0.82–0.99, p = 0.036). 4-OLE ICU patients also had a significantly lower delta total bilirubin (− 1.6, 95% CI − 2.8 to − 0.2, p = 0.021) and reduced urinary tract infection (UTI) rates (OR 0.50, 95% CI 0.26–0.96, p = 0.038). There were no associations in AST, ALT, or total bilirubin in ICU and all adult patients.

Conclusion
4-OLE was successfully implemented and reduced soybean oil LE exposure in a large academic hospital setting. The introduction of 4-OLE was associated with reduced LOS, UTI rates, and mitigated hepatic dysfunction in critically ill patients. Overall, these findings prove a switch to a soybean oil-LE sparing strategy using 4-OLE is feasible and safe and is associated with improved clinical outcomes in adult PN patients.
Pharmacological counseling in hepatotoxicity induced by macitentan and selexipag: a case report
Authors: Lattanzio Mariangela , Ferrari Marco , Martini Stefano , Ceriani Francesca , Imporzani Andrea , Marino Franca , De Ponti Roberto , Cosentino Marco 
Published: October 2022

Abstract
Background
Pulmonary arterial hypertension is a progressive, debilitating condition characterized by increased resistance in the pulmonary arterial circulation. Current treatments for pulmonary arterial hypertension include endothelin receptor antagonists such as bosentan, sitaxentan, ambrisentan, macitentan, and oral prostacyclin receptor agonists such as selexipag. Endothelin receptor antagonists have been associated with liver injury, while hepatotoxicity was not reported for selexipag. Although genetic variability has been indisputably associated with variability in drug response, no study has been designed until now to assess its effects on the pharmacokinetics of endothelin receptor antagonists or selexipag.

Case presentation
We report the case of a 58-year-old female Caucasian patient with a dramatic increase in plasma levels of transaminases after treatment with macitentan and selexipag, drugs whose risk of causing liver injury has so far been considered limited. After therapy discontinuation, plasma levels of transaminases returned to baseline, thus suggesting a role of these drugs in the observed hepatotoxicity. After pharmacological counseling, we decided to introduce ambrisentan for the patient’s treatment. After 7 months of treatment, no liver injury has been reported. To evaluate the role of genetic factors in the observed hepatotoxicity, we genotyped the patient for single-nucleotide polymorphisms previously associated with macitentan, ambrisentan, or selexipag metabolism. We found a genetic profile associated with a poor metabolizer (PM) phenotype for CYP2C8 and CYP2C9, key enzymes for elimination of both macitentan and selexipag. The reported results suggest that an allelic profile associated with low activity for CYP2C8 and CYP2C9 enzyme could be a potential risk factor for macitentan and selexipag-induced liver injury and could provide a possible marker for early identification of subjects at higher risk of developing hepatotoxicity.

Conclusions
A multidisciplinary approach based on clinical evaluation, as well as pharmacological counseling and evaluation of the patient’s genetic profile, might be useful for identification of patients with a high chance of drug-induced liver injury, avoiding unnecessary risks in therapy selection and prescription.
SKDStream: a dynamic clustering algorithm on time-decaying data stream
Authors: Liu Hui , Wu Aihua , Wei Mingkang , Chang Chin-Chen 
Published: October 2022

AbstractData stream is a type of data that continue to grow over time. For example, network security data stream will constantly be generated in the field of data security, and encrypted data stream will be generated in the privacy protection scenario. Clustering is a basic task in the analysis of data stream. In addition to the large amount of data and limited computer memory, there are the following challenges in time-decaying data stream clustering: (1) How to quickly process time-varying data stream and how to quickly save vaild data. (2) How to maintain and update clusters and track their evolution in real time. Based on the fact that the existing data stream algorithms do not provide a good strategy to the above problems, this paper proposes a dynamic clustering algorithm named SKDStream. The algorithm divides the entire data space into distinct minimal bound hypercubes, which are maintained and indexed by a newly defined structure, SKDTree, that aggregates and updates clusters in real time without requiring large primary storage. Clusters are composed of dense hypercubes. Experiments on synthetic datasets and real datasets show that the response time of the algorithm is similar to that of existing dataflow algorithms, but the quality of the generated clusters is relatively stable over time. Furthermore, the SKDStream algorithm is able to track the evolution of the number of clusters, centers, and density in real time, and compared to D-stream, SKDStream is efficient and effective in clustering.
Diagnostic assessment of novice EFL learners’ discourse competence in academic writing: a case study
Authors: Wang Yumin , Xie Qin 
Published: October 2022

AbstractDiscourse competence is an essential component of communicative competence and central to the mastery of academic writing. This article reports a three-tiered diagnostic assessment of two English as a foreign language (EFL) student writers’ discourse competence in terms of textual features, composing strategies, and knowledge about academic writing. Drawing on extensive analyses of their writing samples, writer logs, and semi-structured interviews, we identified their discourse-level weaknesses and examined their writing strategies and academic writing knowledge status to ascertain their relationships with the observed weaknesses. Global coherence, which conveys the macros-level structure of the whole discourse, was found to be a shared problem of the two students. An investigation into their writing processes found that both students were deadline fighters whose poor time management seemed to account for the problems in their texts. Both spent too much time researching content knowledge but did not reserve sufficient time for writing and revision. Having limited knowledge of the disciplinary content and the required genre type and lacking adequate writing strategies were three salient blocks that impeded their composition of disciplinary essays. Based on the above, we propose a three-stage instructional procedure to facilitate novice EFL learners’ development of discourse competence in English academic writing.
Attitude and perception of pharmacists and healthcare professionals about the criteria used in drug formulary selection in the United Arab Emirates
Authors: Al‑Hemyari Sabaa Saleh , Mohamed Noor Dzul Azri , El‑Dahiyat Faris 
Published: October 2022

Abstract
Background
There is lack of both resources and expertise explains the limited extent to which pharmacoeconomic evidence is used in formulary decision-making.

Objectives
The present study aims to assess attitude and perceptions toward the criteria used to select formulary drugs among UAE healthcare organizations.

Methods
A descriptive cross-sectional study was conducted amongst the licensed physicians in all specialties, all pharmacists and other healthcare professionals with a minimum of 3 month experience those registered with Ministry of health and prevention and those working in the private sector in the UAE. Participants are sent an email containing a validated web-based electronic link to access the questionnaire. The questionnaire composed of two sections is used to assess the healthcare professionals’ attitude and perceptions regarding the criteria used to select formulary drugs. Data analysis were done using SPSS Version 24.

Results
A total of 866 respondents participated in the study and completed the whole questionnaire. The average attitude score about the criteria used in drug formulary selection was 84.5% with a 95% confidence interval (CI) of [83.9%, 85.4%]. Of the total participants, 27 (3.1%) had poor attitude about the criteria used in drug formulary selection, 240 (27.7%) had moderate attitude and 599 (69.2%) had good attitude. The results of statistical modeling showed that education level, area of expertise and age were jointly highly associated with attitude about the criteria used in drug formulary selection.

Conclusions
The study revealed that pharmacists and Healthcare professionals had a good attitude about the criteria used in drug formulary selection in the United Arab Emirates. This study purposed to provide Emirate pharmacy and therapeutics policy makers with a clear criterion of best practice related to methodological recommendations to help in increasing the utilization and implementation of pharmacoeconomic evidence in the drug formulary selection process.
Subinertial frequency variations in the axis of the Tsugaru Warm Current east of the Tsugaru Strait
Authors: Kaneko Hitoshi , Tanaka Takahiro , Abe Hiroto , Wakita Masahide , Sasaki Ken’ichi , Miyazawa Yasumasa , Okunishi Takeshi , Watanabe Shuichi , Tatamisashi Shoko , Sato Yoshiaki 
Published: October 2022

AbstractThe eastern part of the Tsugaru Strait (located at ~ 41.5° N) is a remarkable region of the coastal flow system around Japan due to the Tsugaru Warm Current (TgWC), an intensive eastward current that flows over its complex topography and exhibits marked tidal variation. The TgWC has a jetlike structure and demonstrates drastic seasonal changes in its path and vertical current structure. Using a high-resolution dataset obtained from a high-frequency radar system (HFR) and a coastal data assimilation experiment (JCOPE-T DA), we focused on the frontal variation, which is shorter than the seasonal timescale, along the axis of the TgWC in relation to the meanders of the jet. We found variations in the axis with multiple timescales between 1 and 14 days, especially in summer and autumn. The ~ 14-day variation, a remarkable occurrence on the west side of the eastern Tsugaru Strait, was consistent with the tidal variation in the strait. The zonal scale of the axis meander estimated by the HFR matched a scale several times larger than the internal deformation radius, especially in summer and autumn. JCOPE-T DA outputs showed that the crest of such a meander at greater depths progresses in relation to that at the surface. The outputs also suggested instabilities, indicating potential and kinetic energy conversion from the mean to the eddy field. The propagation speed of the several-day variation in the axis estimated from the HFR data was consistent with that of the two-layer baroclinic instability. The several-day variation also showed relatively high coherence with wind variation from summer to autumn, during which time the seasonal wind over the strait switched from easterly to westerly. These variations with multiple timescales imply an effect on north–south water mass mixing in the eastern part of the strait, including rapid acidification in the strait and intensification of stratification.
Child marriage and health disparities in adulthood: the differential risk of untreated hypertension among young adult women in India
Authors: Datta Biplab Kumar , Haider Mohammad Rifat 
Published: October 2022

Abstract
Background
Hypertension is a major risk factor of cardiovascular diseases, which is the leading cause of premature mortality worldwide. While untreated hypertension heightens the risk of mortality and morbidity among hypertensive individuals, access to hypertension care in low-and-middle income countries has ties with various socioeconomic inequalities. Child brides represent a marginalized group of population who experience various socioeconomic disadvantages. This study investigates whether there exists any disparity in receiving treatment for hypertension between child brides at young adult age and their same-age peers who were married as adults.

Methods
We obtained data on 22,140 currently married hypertensive women aged 20 to 34 years from the 2015–16 wave of National Family Health Survey (NFHS-4) of India. We estimated multilevel univariate and multivariable logistic regressions to obtain the odds in favor of not receiving treatment for hypertension. We compared the odds for child brides with those of their peers who were married as adults.

Results
Among the study participants, 72.6% did not receive any treatment for hypertension. While the share was 70.6% among women who were married as adults, it was 4.3 percentage points higher (P < 0.001) among the child brides. Results from the multilevel logistic regressions reveal that adjusted odds of having untreated hypertension for child brides were 1.12 times (95% confidence interval, 1.00–1.25) that of those who were married as adults.

Conclusions
Our findings show that hypertensive women who were married as children are at greater risk of not receiving hypertension care at young adult age. Therefore, young women who got married in their childhood should be targeted for regular screening and proper referral and treatment to avoid further detrimental effects of elevated blood pressure.
Integrative analyses of genes related to liver ischemia reperfusion injury
Authors: Wang Hang-Pin , Chen Chu-Hong , Wei Ben-Kai , Miao Ying-Lei , Huang Han-Fei , Zeng Zhong 
Published: October 2022

Abstract
Background
Liver ischemia reperfusion injury (LIRI) is not only a common injury during liver transplantation and major hepatic surgery, but also one of the primary factors that affect the outcome of postoperative diseases. However, there are still no reliable ways to tackle the problem. Our study aimed to find some characteristic genes associated with immune infiltration that affect LIRI, which can provide some insights for future research in the future. Therefore, it is essential for the treatment of LIRI, the elucidation of the mechanisms of LIRI, and exploring the potential biomarkers. Efficient microarray and bioinformatics analyses can promote the understanding of the molecular mechanisms of disease occurrence and development.

Method
Data from GSE151648 were downloaded from GEO data sets, and we performed a comprehensive analysis of the differential expression, biological functions and interactions of LIRI-associated genes. Then we performed Gene ontology (GO) analysis and Kyotoencydlopedia of genes and genomes (KEGG) enrichment analysis of DEGs. At last, we performed a protein-protein interaction network to screen out hub genes.

Results
A total of 161 differentially expressed genes (DEGs) were identified. GO analysis results revealed that the changes in the modules were mostly enriched in the neutrophil degranulation, neutrophil activation involved in immune response, and neutrophil mediated immunity. KEGG enrichment analysis of DEGs demonstrated that LIRI mainly involved the cytokine-cytokine receptor interaction. Our data indicated that macrophages and neutrophils are closely related to LIRI. 9 hub genes were screened out in the protein-protein interaction network.

Conclusions
In summary, our data indicated that neutrophil degranulation, neutrophil activation involved in immune response, neutrophil mediated immunity and cytokine-cytokine receptor interaction may play a key role in LIRI, HRH1, LRP2, P2RY6, PKD1L1, SLC8A3 and TNFRSF8, which were identified as potential biomarkers in the occurrence and development of LIRI. However, further studies are needed to validate these findings and explore the molecular mechanism of these biomarkers in LIRI.