bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trauma Assessment Clinic: A virtual fracture clinic model that delivers on its PROMise!
Authors: O’ Reilly Marc , Wallace Emma , Merghani Khalid , Conlon Breda , Breathnach Oisin , Sheehan Eoin 
Published: March 2022

Background The use of virtual fracture clinics across the United Kingdom and Ireland is growing and have been shown in an increasing number of studies to be safe, cost-effective and associated with good functional outcomes and patient satisfaction rates for certain fracture types. Initially pioneered at Glasgow Royal Infirmary, many centres have adopted similar templates, or variations of, and the overall aim of this study was to assess functional outcomes and injury recovery satisfaction rates of patients discharged directly following review in a specific virtual fracture clinic model known as the Trauma Assessment Clinic (TAC). Methods A prospective observational study was carried out of paediatric (aged <17 years) and adult (aged >17 years) patients, with the five most commonly observed fracture types, who were discharged directly following review at the TAC in a single hospital centre over a 12 month period from January to December 2018. Primary and secondary outcomes were assessed via telephone administered questionnaires and patient reported outcome measures (PROMs). Results A total of 198 patients were included in the study (n = 98 paediatric and n = 100 adult). Overall, 192 (97%) patients or parents/guardians of patients stated that they either strongly agreed (n = 148, 74.9%) or agreed (n = 44, 22.1%) that they were satisfied with their own or their child's recovery from their injury at a median follow-up of 9 months post direct discharge from the TAC. Adult patients had an EQ-5D-5L index median value of 1 (range 0-1), an EQ-VAS median of 87 (range 0-100), a QuickDASH median score of 0 (range 0-100) and a median LEFS of 80 (range 0–80). Conclusion The virtual management of trauma patients via the TAC model is a safe and patient-centred approach to treating certain injuries and fracture patterns. This study reports excellent patient reported outcome measures and patient injury recovery satisfaction rates. The use of current available technology in tandem with up-to-date best clinical practice and guidelines play a central role in this novel care pathway.
Near-Infrared Fluorescence Image-Guided Surgery in Esophageal and Gastric Cancer Operations
Authors: Ekman Marcin , Girnyi Sergii , Marano Luigi , Roviello Franco , Chand Manish , Diana Michele , Polom Karol 
Published: March 2022

Background Near-infrared fluorescence image-guided surgery helps surgeons to see beyond the classical eye vision. Over the last few years, we have witnessed a revolution which has begun in the field of image-guided surgery. Purpose, and Research design Fluorescence technology using indocyanine green (ICG) has shown promising results in many organs, and in this review article, we wanted to discuss the 6 main domains where fluorescence image-guided surgery is currently used for esophageal and gastric cancer surgery. Study sample and data collection Visualization of lymphatic vessels, tumor localization, fluorescence angiography for anastomotic evaluation, thoracic duct visualization, tracheal blood flow analysis, and sentinel node biopsy are discussed. Conclusions It seems that this technology has already found its place in surgery. However, new possibilities and research avenues in this area will probably make it even more important in the near future.
Delaying an infliximab infusion by more than 3 days is associated with a significant reduction in trough levels but not with clinical worsening
Authors: Ben-Shatach Zohar , Ziv-Baran Tomer , Fudim Ella , Yavzori Miri , Picard Orit , Levartovsky Asaf , Selinger Limor , Weiss Batia , Kopylov Uri , Eliakim Rami , Ungar Bella 
Published: March 2022

Background: Higher infliximab trough levels (TLs) correlate with better clinical, inflammatory, and endoscopic outcomes among inflammatory bowel disease (IBD) patients. Although standard scheduled infliximab therapy regimen consists of infusions at pre-defined time-points (weeks 0, 2, 6, and every 8 weeks), short-period deviations from therapeutic schedule are common in ‘real life’, but the pharmacokinetic impact of these deviations has not been explored. In this study, we aim to determine whether short-period deviations from infusion schedule affect infliximab-TL. Methods: A retrospective analysis of all IBD patients receiving infliximab maintenance therapy every 8 weeks was conducted in a tertiary medical center. Patients with anti-drug antibodies, deliberate interval shortening and <3 sequential maintenance sera available were excluded. Associations between time since last infusion and TL were studied. Statistical analysis was performed using generalized estimating equations. Results: Out of over 10,000 sera, 2088 sera of 302 maintenance period stable infliximab-therapy-patients met inclusion criteria (median TL 4.1 μg/mL, interquartile range (IQR) 2.3–6.5 μg/mL). A delay beyond 3 days in infusion schedule (n > 59 days since last infusion) was found to significantly affect TL (mean difference in TL 0.9 μg/mL, 95% confidence interval (CI): 0.03–1.9 μg/mL, p < 0.04). Furthermore, among patients with delayed infusions, 80% had TL below 5 μg/mL, in comparison to 55% of patients who were not late (odds ratio (OR): 2.81, CI: 2.02–3.92, p < 0.0001). Conclusion: Real-life delays of ⩽3 days from infusion protocol can probably be allowed. Delays >3 days culminate in measurable decrease of TL, although effect on clinical outcome is unclear. This needs to be taken into account when interpreting drug-level test results. Summary: A total of 2088 sera of 302 maintenance period inflammatory bowel disease (IBD) patients treated with infliximab were analyzed, to assess effect of small deviations from infusion schedule on TLs. A significant decline in patients’ trough level (TL) was noted as early as 3 days after scheduled infusion.
Failed induction of labor and associated factors in Adama Hospital Medical College, Oromia Regional State, Ethiopia
Authors: Demssie Enku Afework , Deybasso Haji Aman , Tulu Tewodros Mengistu , Abebe Dawit , Kure Mohammed Abdurke , Teji Roba Kedir 
Published: March 2022

Background: Failed induction of labor continues to be a public health challenge throughout the world. This failed induction of labor is associated with a higher rate of maternal and fetal morbidity because it increases the unwanted effect of emergency cesarean section. It is also associated with an increased risk of numerous adverse maternal and perinatal outcomes such as uterine rupture, nonreassuring fetal heart rate tracing, postpartum hemorrhage, stillbirth, and severe birth asphyxia. Thus, this study was aimed to assess the failed induction of labor and associated factors in the Adama Hospital Medical College, Oromia Regional State, Ethiopia. Methods: A facility-based cross-sectional study was conducted from 1 to 30 December 2020 in Adama Hospital Medical College, Ethiopia. A total of 379 women who underwent labor induction in the Adama Hospital Medical College from December 2019 to November 2020 were enrolled in the study. The participants’ charts were selected using a simple random sampling technique. Data were collected using a pretested and validated structured questionnaire. Descriptive statistics were carried out using frequency tables, proportions, and summary measures. Predictors were assessed using a multivariable logistic regression analysis model and reported using adjusted odds ratio with 95% confidence interval. Statistical significance was considered at a p value <0.05. Results: Of 379 induced labor included in the study, the proportion of failed induction was found to be 29.6% (95% confidence interval (25.2, 34.3)). Prelabor rupture of the membrane was found to be the most common indication for induction of labor (46.4%) followed by a hypertensive disorder of pregnancy (21.6%). In the final model of multivariable analysis, predictors such as: nulliparity (adjusted odds ratio = 2.32, 95% confidence interval (1.08, 5.02)), unfavorable cervical status (adjusted odds ratio = 3.46, 95% confidence interval (1.51, 7.94)), prelabor rupture of membrane (adjusted odds ratio = 2.60, 95% confidence interval (1.14, 5.91)), hypertensive disorder of pregnancy (adjusted odds ratio = 3.01;95% confidence interval (1.61, 558)), preinduction membrane status (adjusted odds ratio = 3.63; 95% confidence interval (1.48, 8.86)), and birth weight of greater than 4000 g (adjusted odds ratio = 4.33; 95% confidence interval (1.44, 13.02)) were statistically associated with failed induction of labor. Conclusion: The prevalence of failed induction of labor was relatively high in this study area because more than a quarter of mothers who underwent induction of labor had failed induction. This calls for all stakeholders to adhere to locally available induction protocols and guidelines. In addition, pre-induction conditions must be a top priority to improve the outcome of induction of labor.
Proposal of sialyl Lewis x/a as prognostic biomarkers in clear cell renal cell carcinoma: A study on a cohort of 117 patients submitted to curative surgery
Authors: Tanio Makoto , Fukiage Yusuke , Muramoto Akifumi , Yokoyama Osamu , Kobayashi Motohiro 
Published: March 2022

Objective: Metastatic recurrence has been reported to occur in 20–30% of patients with clear cell renal cell carcinoma (ccRCC). Although the prognosis of these patients is poor, no marker has been established to predict metastatic potential and/or prognosis. Therefore, we investigated membrane expression of sialyl Lewis x (sLex) and sialyl Lewis a (sLea), which is generally considered to be associated with cancer metastasis. Materials and methods: We enrolled 117 patients who underwent curative surgery for RCC and were pathologically diagnosed as ccRCC. Immunohistochemistry for sLex and sLea was performed to evaluate the signal intensity on the cell membrane. We statistically analysed whether membrane expression of sLex/sLea is correlated with clinicopathological parameters and prognosis. Results: Of the 117 patients, 72 were classified as sLex-positive and 44 as sLea-positive. The sLex-positive group had significantly shorter progression-free survival (PFS) and overall survival (OS) than the negative group. Similarly, the sLea-positive group had significantly shorter PFS than the negative group, and it showed a trend towards a reduction of OS, although it did not reach statistical significance, a fact that could be due to the small sample size. Conclusion: Both sLex and sLea could be possible future prognostic indicators in ccRCC. Level of evidence: Level 3
STEADI Self-Report Measures Independently Predict Fall Risk
Authors: Ritchey Katherine , Olney Amanda , Chen Sunny , Phelan Elizabeth A. 
Published: March 2022

Falls are a significant contributor to disability and death among older adults. Despite practice guidelines to increase falls screening in healthcare settings, preventive care for falls continues to be infrequently delivered. Simplifying screening by relying on self-report of balance, gait, or strength concerns, alone may increase the frequency of falls screening. We assessed the diagnostic accuracy of self-report measures of gait, strength, and balance from the Centers for Disease Control and Prevention’s Stopping Elderly Accidents, Deaths, and Injuries (STEADI) for identification of fall risk. The criterion standard for fall risk was the Timed Up-and-Go (TUG). Assessments were conducted with 95 adults aged 65 years or older in an outpatient osteoporosis clinic between May 2015 and September 2016. Receiver operating characteristic curve analysis found that two self-report questions (“I feel unsteady with walking” and “I need my arms to stand from a chair”) had high discriminatory ability (AUC 0.906; 95% CI 0.870–0.942) to identify those at high fall risk; additional questions did not substantially improve discrimination. These findings suggest that two self-report questions identify those at risk of falling who would benefit from interventions (e.g., physical therapy). Performance testing as part of routine falls screening of older persons in the outpatient setting may be unnecessary.
Deficiency of SARS-CoV-2 T-cell responses after vaccination in long-term allo-HSCT survivors translates into abated humoral immunity
Authors: Einarsdottir Sigrun , Martner Anna , Waldenström Jesper , Nicklasson Malin , Ringlander Johan , Arabpour Mohammad , Törnell Andreas , Wiktorin Hanna Grauers , Nilsson Staffan , Bittar Rudy , Nilsson Malin , Lisak Mikael , Veje Malin , Friman Vanda , Al-Dury Samer , Bergström Tomas , Ljungman Per , Brune Mats , Hellstrand Kristoffer , Lagging Martin 
Published: March 2022

AbstractRecipients of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for hematological diseases are at risk of severe disease and death from COVID-19. To determine the safety and immunogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines, samples from 50 infection-naive allo-HSCT recipients (median, 92 months from transplantation, range, 7-340 months) and 39 healthy controls were analyzed for serum immunoglobulin G (IgG) against the receptor binding domain (RBD) within spike 1 (S1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; anti–RBD-S1 IgG) and for SARS-CoV-2–specific T-cell immunity, reflected by induction of T-cell–derived interferon-γ in whole blood stimulated ex vivo with 15-mer SI-spanning peptides with 11 amino acid overlap S1-spanning peptides. The rate of seroconversion was not significantly lower in allo-transplanted patients than in controls with 24% (12/50) and 6% (3/50) of patients remaining seronegative after the first and second vaccination, respectively. However, 58% of transplanted patients lacked T-cell responses against S1 peptides after 1 vaccination compared with 19% of controls (odds ratio [OR] 0.17; P = .009, Fisher’s exact test) with a similar trend after the second vaccination where 28% of patients were devoid of detectable specific T-cell immunity, compared with 6% of controls (OR 0.18; P = .02, Fisher’s exact test). Importantly, lack of T-cell reactivity to S1 peptides after vaccination heralded substandard levels (&lt;100 BAU/mL) of anti–RBD-S1 IgG 5 to 6 months after the second vaccine dose (OR 8.2; P = .007, Fisher’s exact test). We conclude that although allo-HSCT recipients achieve serum anti–RBD-S1 IgG against SARS-CoV-2 after 2 vaccinations, a deficiency of SARS-CoV-2–specific T-cell immunity may subsequently translate into insufficient humoral responses.
Molecular landscape of IDH-mutant astrocytoma and oligodendroglioma grade 2 indicate tumor purity as an underlying genomic factor
Authors: Zhao Binghao , Xia Yu , Yang Fengchun , Wang Yaning , Wang Yuekun , Wang Yadong , Dai Congxin , Wang Yu , Ma Wenbin 
Published: March 2022

Abstract
Background
IDH-mutant astrocytoma and oligodendroglioma have an indolent natural history and are recognized as distinct entities of neoplasms. There is little knowledge on the molecular differences between IDH-mutant astrocytoma and oligodendroglioma grade 2. Therefore, we investigated the multiomics and clinical data regarding these two types of tumors.

Method
In silico analyses were performed around mRNA, somatic mutations, copy number alternations (CNAs), DNA methylation, microRNA (miRNA), epigenetics, immune microenvironment characterization and clinical features of the two types of gliomas. A diagnostic model incorporating tumor purity was further established using machine learning algorithms, and the predictive value was evaluated by receiver operative characteristic curves.

Results
Both types of gliomas shared chromosomal instability, and astrocytomas exhibited increased total CNAs compared to oligodendrogliomas. Oligodendrogliomas displayed distinct chromosome 4 (chr 4) loss, and subtyping of chr 7 gain/chr 4 loss (+ 7/− 4) presented the worst survival (P = 0.004) and progression-free interval (PFI) (P < 0.001). In DNA damage signatures, oligodendroglioma had a higher subclonal genome fraction (P < 0.001) and tumor purity (P = 0.001), and astrocytoma had a higher aneuploidy score (P < 0.001). Furthermore, astrocytomas exhibited inflamed immune cell infiltration, activated T cells and a potential response to immune checkpoint inhibitors (ICIs), while oligodendrogliomas were more homogeneous with increased tumor purity and decreased aggression. The tumor purity-involved diagnostic model exhibited great accuracy in identifying astrocytoma and oligodendroglioma.

Conclusion
This study addresses the similarities and differences between IDH-mutant astrocytoma and oligodendroglioma grade 2 and facilitates a deeper understanding of their molecular features, immune microenvironment, tumor purity and prognosis. The diagnostic tool developed using machine learning may offer support for clinical decisions.
Development of resilience indicator traits based on daily step count data for dairy cattle breeding
Authors: Poppe Marieke , Mulder Han A. , van Pelt Mathijs L. , Mullaart Erik , Hogeveen Henk , Veerkamp Roel F. 
Published: March 2022

Abstract
Background
Resilient animals are minimally affected by disturbances, such as diseases and heat stress, and quickly recover. Daily activity data can potentially indicate resilience, because resilient animals likely keep variations due to disturbances that threat animal homeostasis at a low magnitude. We used daily step count of cows to define resilience indicators based on theory, exploratory analysis and literature, and then investigated if they can be used to genetically improve resilience by estimating heritability and repeatability, and genetic associations with other resilience-related traits, i.e. health traits, longevity, fertility, and body condition score (BCS).

Results
Two groups of resilience indicators were defined: indicators describing (1) mean step count at different lactation stages for individual cows, and (2) fluctuations in step count from individual step count curves. Heritability estimates were highest for resilience indicators describing mean step count, from 0.22 for the 2-week period pre-partum to 0.45 for the whole lactation. High mean step count was consistently, but weakly, genetically correlated with good health, fertility, and longevity, and high BCS. Heritability estimates of resilience indicators describing fluctuations ranged from 0.01 for number of step count drops to 0.15 for the mean of negative residuals from individual curves. Genetic correlations with health traits, longevity, fertility, and BCS were mostly weak, but were moderate and favorable for autocorrelation of residuals (− 0.33 to − 0.44) and number of step count drops (− 0.44 to − 0.56) with hoof health, fertility, and BCS. Resilience indicators describing variability of residuals and mean of negative residuals showed strong genetic correlations with mean step count (0.86 to 0.95, absolute), which suggests that adjustment for step count level is needed. After adjustment, ‘mean of negative residuals’ was highly genetically correlated with hoof health, fertility, and BCS.

Conclusions
Mean step count, autocorrelation and mean of negative residuals showed most potential as resilience indicators based on resilience theory, heritability, and genetic associations with health, fertility, and body condition score. Other resilience indicators were heritable, but had unfavorable genetic correlations with several health traits. This study is an important first step in the exploration of the use of activity data to breed more resilient livestock.
EnsembleFam: towards more accurate protein family prediction in the twilight zone
Authors: Kabir Mohammad Neamul , Wong Limsoon 
Published: March 2022

AbstractBackgroundCurrent protein family modeling methods like profile Hidden Markov Model (pHMM),k-mer based methods, and deep learning-based methods do not provide very accurate protein function prediction for proteins in the twilight zone, due to low sequence similarity to reference proteins with known functions.ResultsWe present a novel method EnsembleFam, aiming at better function prediction for proteins in the twilight zone. EnsembleFam extracts the core characteristics of a protein family using similarity and dissimilarity features calculated from sequence homology relations. EnsembleFam trains three separate Support Vector Machine (SVM) classifiers for each family using these features, and an ensemble prediction is made to classify novel proteins into these families. Extensive experiments are conducted using the Clusters of Orthologous Groups (COG) dataset and G Protein-Coupled Receptor (GPCR) dataset. EnsembleFam not only outperforms state-of-the-art methods on the overall dataset but also provides a much more accurate prediction for twilight zone proteins.ConclusionsEnsembleFam, a machine learning method to model protein families, can be used to better identify members with very low sequence homology. Using EnsembleFam protein functions can be predicted using just sequence information with better accuracy than state-of-the-art methods.
Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships
Authors: Xu Kewang , Lin Chenxue , Lee Shiou Yih , Mao Lingfeng , Meng Kaikai 
Published: March 2022

Abstract
Background
Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships.

Results
We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems.

Conclusion
Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.