bluuebunny/crossref_metadata_2025_split huggingface dataset:
A second view on the evolution of flight in stick and leaf insects (Phasmatodea)
Authors: Bank Sarah , Bradler Sven 
Published: May 2022

Abstract
Background
The re-evolution of complex characters is generally considered impossible, yet, studies of recent years have provided several examples of phenotypic reversals shown to violate Dollo’s law. Along these lines, the regain of wings in stick and leaf insects (Phasmatodea) was hypothesised to have occurred several times independently after an ancestral loss, a scenario controversially discussed among evolutionary biologists due to overestimation of the potential for trait reacquisition as well as to the lack of taxonomic data.

Results
We revisited the recovery of wings by reconstructing a phylogeny based on a comprehensive taxon sample of over 500 representative phasmatodean species to infer the evolutionary history of wings. We additionally explored the presence of ocelli, the photoreceptive organs used for flight stabilisation in winged insects, which might provide further information for interpreting flight evolution. Our findings support an ancestral loss of wings and that the ancestors of most major lineages were wingless. While the evolution of ocelli was estimated to be dependent on the presence of (fully-developed) wings, ocelli are nevertheless absent in the majority of all examined winged species and only appear in the members of few subordinate clades, albeit winged and volant taxa are found in every euphasmatodean lineage.

Conclusion
In this study, we explored the evolutionary history of wings in Phasmatodea and demonstrate that the disjunct distribution of ocelli substantiates the hypothesis on their regain and thus on trait reacquisition in general. Evidence from the fossil record as well as future studies focussing on the underlying genetic mechanisms are needed to validate our findings and to further assess the evolutionary process of phenotypic reversals.
Taxonomic position, antibiotic resistance and virulence factor production by Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections
Authors: Fluit Ad C. , Bayjanov Jumamurat R. , Aguilar María Díez , Cantón Rafael , Elborn Stuart , Tunney Michael M. , Scharringa Jelle , Benaissa-Trouw Barry J. , Ekkelenkamp Miquel B. 
Published: May 2022

Abstract
Background
The potential pathogenic role of Stenotrophomonas maltophilia in lung disease and in particular in cystic fibrosis is unclear. To develop further understanding of the biology of this taxa, the taxonomic position, antibiotic resistance and virulence factors of S. maltophilia isolates from patients with chronic lung disease were studied.

Results
A total of 111 isolates recovered between 2003 and 2016 from respiratory samples from patients in five different countries were included. Based on a cut-off of 95%, analysis of average nucleotide identity by BLAST (ANIb) showed that the 111 isolates identified as S. maltophilia by Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) belonged to S. maltophilia (n = 65), S. pavanii (n = 6) and 13 putative novel species (n = 40), which each included 1–5 isolates; these groupings coincided with the results of the 16S rDNA analysis, and the L1 and L2 ß-lactamase Neighbor-Joining phylogeny. Chromosomally encoded aminoglycoside resistance was identified in all S. maltophilia and S. pavani isolates, while acquired antibiotic resistance genes were present in only a few isolates. Nevertheless, phenotypic resistance levels against commonly used antibiotics, determined by standard broth microbroth dilution, were high. Although putative virulence genes were present in all isolates, the percentage of positive isolates varied. The Xps II secretion system responsible for the secretion of the StmPr1–3 proteases was mainly limited to isolates identified as S. maltophilia based on ANIb, but no correlation with phenotypic expression of protease activity was found. The RPF two-component quorum sensing system involved in virulence and antibiotic resistance expression has two main variants with one variant lacking 190 amino acids in the sensing region.

Conclusions
The putative novel Stenotrophomonas species recovered from patient samples and identified by MALDI-TOF/MS as S. maltophilia, differed from S. maltophilia in resistance and virulence genes, and therefore possibly in pathogenicity. Revision of the Stenotrophomonas taxonomy is needed in order to reliably identify strains within the genus and elucidate the role of the different species in disease.
Automated medical chart review for breast cancer outcomes research: a novel natural language processing extraction system
Authors: Chen Yifu , Hao Lucy , Zou Vito Z. , Hollander Zsuzsanna , Ng Raymond T. , Isaac Kathryn V. 
Published: May 2022

AbstractBackgroundManually extracted data points from health records are collated on an institutional, provincial, and national level to facilitate clinical research. However, the labour-intensive clinical chart review process puts an increasing burden on healthcare system budgets. Therefore, an automated information extraction system is needed to ensure the timeliness and scalability of research data.MethodsWe used a dataset of 100 synoptic operative and 100 pathology reports, evenly split into 50 reports in training and test sets for each report type. The training set guided our development of a Natural Language Processing (NLP) extraction pipeline system, which accepts scanned images of operative and pathology reports. The system uses a combination of rule-based and transfer learning methods to extract numeric encodings from text. We also developed visualization tools to compare the manual and automated extractions. The code for this paper was made available on GitHub.ResultsA test set of 50 operative and 50 pathology reports were used to evaluate the extraction accuracies of the NLP pipeline. Gold standard, defined as manual extraction by expert reviewers, yielded accuracies of 90.5% for operative reports and 96.0% for pathology reports, while the NLP system achieved overall 91.9% (operative) and 95.4% (pathology) accuracy. The pipeline successfully extracted outcomes data pertinent to breast cancer tumor characteristics (e.g. presence of invasive carcinoma, size, histologic type), prognostic factors (e.g. number of lymph nodes with micro-metastases and macro-metastases, pathologic stage), and treatment-related variables (e.g. margins, neo-adjuvant treatment, surgical indication) with high accuracy. Out of the 48 variables across operative and pathology codebooks, NLP yielded 43 variables with F-scores of at least 0.90; in comparison, a trained human annotator yielded 44 variables with F-scores of at least 0.90.ConclusionsThe NLP system achieves near-human-level accuracy in both operative and pathology reports using a minimal curated dataset. This system uniquely provides a robust solution for transparent, adaptable, and scalable automation of data extraction from patient health records. It may serve to advance breast cancer clinical research by facilitating collection of vast amounts of valuable health data at a population level.
Test–retest reliability of selected HBSC items in Vietnam: well-being, physical and sedentary activities, and eating behaviours
Authors: Kohoutek Jaroslav , Maráček Marek , Ng Kwok , Hamrik Zdenek 
Published: May 2022

Abstract
Background
Valid and reliable research tools to assess children’s and adolescent’s health-related behaviour are highly needed across the globe. Rapid economic development, globalization, and associated lifestyle challenges observed in most countries support the need for high-quality evidence in adolescents to target health-promoting policies and interventions. This study aims to examine the test–retest reliability of selected well-being, physical and screen-time related siting activities, and eating behaviour items of the Health Behaviour in School-Aged Children (HBSC) questionnaire in a sample of Vietnamese adolescents.

Methods
Data were collected in autumn 2018 in Vietnam (3-week interval). The sample consisted of 410 adolescents (41.0% of boys; mean age = 12.61; SD = 1.24).Test–retest reliability was evaluated using the single measure Intraclass Correlation Coefficients (ICC) and Cohen’s kappa statistic stratified by sex, grade and place of residence (urban or rural).

Results
The reliability analyses of the well-being items were poor to good ICC values (0.43–0.79) and moderate to large Cohen’s kappa values (0.33–0.77). The physical activity and eating behaviour items were moderate (ICC = 0.54–0.65; Cohen’s kappa = 0.38–0.57). The screen-time related siting activities items were moderate to large (ICC = 0.51–0.72; Cohen’s kappa = 0.42–0.53). There was more item stability among females than males. The social media item was not as stable for 6th graders (ICC = 0.45) compared with older adolescents (ICC 0.68–0.77).

Conclusions
The findings show that with regards to age, sex and place of residence, self-reported health, life satisfaction, physical and screen-time related siting activities, as well as eating behaviour items of the HBSC questionnaire have a sufficient test–retest reliability to be used in national self-report surveys for Vietnamese adolescents while health complaints items showed borderline reliability.
Opioid prescribing practices prior to elective foot and ankle surgery: a population-based evaluation using health administrative data from a tertiary hospital in Canada
Authors: Goplen C. Michael , Pedersen M. Elizabeth , Ramadi Ailar , Beaupre Lauren A. 
Published: May 2022

AbstractBackgroundComplex elective foot and ankle surgery is known to be painful so most patients are prescribed opioids at the time of surgery; however, the number of patients prescribed opioids while waiting for surgery in Canada is unknown. Our primary objective was to describe the pre and postoperative prescribing practices for patients in Alberta, Canada undergoing complex elective foot and ankle surgery. Secondarily, we evaluated postoperative opioid usage and hospital outcomes.MethodsIn this population-based retrospective analysis, we identified all adult patients who underwent unilateral elective orthopedic foot and ankle surgery at a single tertiary hospital between May 1, 2015 and May 31, 2017. Patient and surgical data were extracted from a retrospective chart review and merged with prospectively collected, individual level drug dispensing administrative data to analyze opioid dispensing patterns, including dose, duration, and prescriber for six months before and after foot and ankle surgery.ResultsOf the 100 patients, 45 had at least one opioid prescription dispensed within six months before surgery, and of these, 19 were long-term opioid users (> 90 days of continuous use). Most opioid users obtained opioid prescriptions from family physicians both before (78%) and after (65%) surgery. No preoperative non-users transitioned to long-term opioid use postoperatively, but 68.4% of the preoperative long-term opioid users remained long-term opioid users postoperatively. During the index hospitalization, preoperative long-term opioid users consumed higher doses of opioids (99.7 ± 120.5 mg/day) compared to opioid naive patients (28.5 ± 36.1 mg/day) (p < 0.001). Long-term opioid users stayed one day longer in hospital than opioid-naive patients (3.9 ± 2.8 days vs 2.7 ± 1.1 days;p = 0.01).ConclusionsA significant number of patients were dispensed opioids before and after foot and ankle surgery with the majority of prescriptions coming from primary care practitioners. Patients who were prescribed long-term opioids preoperatively were more likely to continue to use opioids at follow-up and required larger in-hospital opioid dosages and stayed longer in hospital. Further research and education for both patients and providers are needed to reduce the community-based prescribing of opioid medication pre-operatively and provide alternative pain management strategies prior to surgery to improve postoperative outcomes and reduce long-term postoperative opioid use.
Diagnostic yield of inpatient capsule endoscopy
Authors: Levine Irving , Hong Soonwook , Bhakta Dimpal , McNeill Matthew B. , Gross Seth A. , Latorre Melissa 
Published: May 2022

Abstract
Background
Capsule endoscopy (CE) provides a novel approach to evaluate obscure gastrointestinal bleeding. Yet CE is not routinely utilized in the inpatient setting for a variety of reasons. We sought to identify factors that predict complete CE and diagnostically meaningful CE, as well as assess the impact of inpatient CE on further hospital management.1 na d2

Methods
We conducted a retrospective review of patients undergoing inpatient CE at a tertiary referral, academic center over a 3 year period. We analyzed data on patient demographics, medical history, endoscopic procedures, hospital course, and results of CE. The primary outcome was complete CE and the secondary outcome was positive findings of pathology on CE.

Results
131 patients were included (56.5% were men 43.5% women, median age of 71.0 years). Overall, CE was complete in 77.1% of patients. Complete CE was not related to motility risk factors, gender, or administration modality. Patients with incomplete CE tended to be older, have lower BMI, and Caucasian, however results did not reach statistical significance (p = 0.06; p = 0.06; p = 0.08 respectively). Positive CE was noted in 73.3% of patients, with 35.1% of all patients having active bleeding. Positive CE was not associated with AVM risk factors or medication use. 28.0% of patients underwent subsequent hospital procedures, among which 67.6% identified the same pathology seen on CE.

Conclusions
Contrary to previous studies, we found the majority of inpatient CEs were complete and positive for pathology. We found high rates of correlation between CE and subsequent procedures. The use of CE in the inpatient setting helps to guide the diagnosis and treatment of hospitalized patients with obscure gastrointestinal bleeding.
Quality of life and associated factors among people receiving second-line anti-retroviral therapy in Johannesburg, South Africa
Authors: Mokgethi Nomcebo Oratile , Christofides Nicola , Machisa Mercilene , Akpomiemie Godspower , Lalla-Edward Samantha 
Published: May 2022

Abstract
Background
Studies which examine quality of life (QOL) provide important insights that are needed to understand the impacts of HIV/AIDS anti-retroviral treatment (ART), comorbid conditions and other factors on the daily activities of people living with HIV/AIDS (PLH). This study aimed to determine the inter-relationships between clinical factors, behavioural, socio-demographic variables and QOL among PLH.

Methods
The secondary analysis used data collected from 293 people living with HIV/AIDS (PLH) receiving second-line ART in Johannesburg in a clinical trial which evaluated the non-inferiority of ritonavir-boosted darunavir (DRV/r 400/100 mg) compared to ritonavir-boosted lopinavir (LPV/r) over a 48 week-period. Physical functioning, cognitive and mental QOL were measured using the Aids Clinical Trial Group questionnaire. Exploratory factor analyses were used to examine the structure, the relationships between and the construct validity of QOL items. Structural equation models which tested the a priori-hypothesised inter-relationships between QOL and other variables were estimated and goodness of fit of the models to the data was assessed.

Results
Patients on darunavir presented with lower pill burden. Older patients and women were more likely to report lower QOL scores. Pill burden mediated the effects of age, sex and treatment regimen on physical functioning QOL and adverse effects; the effects of age, sex, treatment regimen and adverse effects on cognitive QOL; and the effects of sex on mental QOL.

Conclusion
QOL among PLH is associated with socio-demographic and clinical factors. Therefore, QOL could be enhanced by considering PLH characteristics, clinical factors such as regimen side-effects profile, management of comorbid conditions and mitigating risks such as potential adverse drug-to-drug interactions among patients on ART.
Different evolutionary dynamics of hepatitis B virus genotypes A and D, and hepatitis D virus genotypes 1 and 2 in an endemic area of Yakutia, Russia
Authors: Karlsen Anastasia A. , Kyuregyan Karen K. , Isaeva Olga V. , Kichatova Vera S. , Asadi Mobarkhan Fedor A. , Bezuglova Lyudmila V. , Netesova Irina G. , Manuylov Victor A. , Pochtovyi Andrey A. , Gushchin Vladimir A. , Sleptsova Snezhana S. , Ignateva Margarita E. , Mikhailov Mikhail I. 
Published: May 2022

Abstract
Background
The geographic distribution of the hepatitis B virus (HBV) and the hepatitis D virus (HDV) genotypes is uneven. We reconstructed the temporal evolution of HBV and HDV in Yakutia, one of the regions of Russia most affected by HBV and HDV, in an attempt to understand the possible mechanisms that led to unusual for Russia pattern of viral genotypes and to identify current distribution trends.

Methods
HBV and HDV genotypes were determined in sera collected in 2018–2019 in Yakutia from randomly selected 140 patients with HBV monoinfection and 59 patients with HBV/HDV. Total 86 HBV and 88 HDV genomic sequences isolated in Yakutia between 1997 and 2019 were subjected to phylodynamic and philogeographic Bayesian analysis using BEAST v1.10.4 software package. Bayesian SkyGrid reconstruction and Birth–Death Skyline analysis were applied to estimate HBV and HDV population dynamics.

Results
Currently, HBV-A and HDV-D genotypes are prevalent in Yakutia, in both monoinfected and HDV-coinfected patients. Bayesian analysis has shown that the high prevalence of HBV-A in Yakutia, which is not typical for Russia, initially emerged after the genotype was introduced from Eastern Europe in the fifteenth century (around 600 (95% HPD: 50–715) years ago). The acute hepatitis B epidemics in the 1990s in Yakutia were largely associated with this particular genotype, as indicated by temporal changes in HBV-A population dynamics. HBV-D had a longer history in Yakutia and demonstrated stable population dynamics, indicating ongoing viral circulation despite vaccination. No correlation between HBV and HDV genotypes was observed for coinfected patients in Yakutia (r = − 0.016069332). HDV-2b circulates in Russia in Yakutia only and resulted from a single wave of introduction from Central Asia 135 years ago (95% HPD: 60–350 years), while HDV-1 strains resulted from multiple introductions from Europe, the Middle East, Central Asia, and different parts of Russia starting 180 years ago (95% HPD: 150–210 years) and continuing to the present day. The population dynamics of HDV-1 and HDV-2 show no signs of decline despite 20 years of HBV vaccination. The Birth–Death Skyline analysis showed an increase in the viral population in recent years for both HDV genotypes, indicating ongoing HDV epidemics.

Conclusions
Taken together, these data call for strict control of HBV vaccination quality and coverage, and implementation of HBV and HDV screening programs in Yakutia.
Neoadjuvant irradiation of extremity soft tissue sarcoma with ions (Extrem-ion): study protocol for a randomized phase II pilot trial
Authors: Brügemann D. , Lehner B. , Kieser M. , Krisam J. , Hommertgen A. , Jaekel C. , Harrabi S. B. , Herfarth K. , Mechtesheimer G. , Sedlaczek O. , Egerer G. , Geisbüsch A. , Uhl M. , Debus J. , Seidensaal K. 
Published: May 2022

Abstract
Background
The standard of care treatment for soft tissue sarcoma of the extremities is a wide resection in combination with pre- or postoperative radiotherapy with high local control rates, sparing patients the necessity of amputation without compromising on overall survival rates.
The currently preferred timing of radiotherapy is under debate. Albeit having higher rates of acute wound complications, late side effects like fibrosis, joint stiffness or edema are less frequent in preoperative compared to postoperative radiotherapy. This can be explained in smaller treatment volumes and a lower dose in the preoperative setting. Particles allow better sparing of surrounding tissues at risk, and carbon ions additionally offer biologic advantages and are preferred in less radiosensitive tumors. Hypofractionation allows for a significantly shorter treatment duration.

Methods
Extrem-ion is a prospective, randomized, monocentric phase II trial. Patients with resectable or marginally resectable, histologically confirmed soft tissue sarcoma of the extremities will be randomized between neoadjuvant proton or neoadjuvant carbon ion radiotherapy in active scanning beam application technique (39 Gy [relative biological effectiveness, RBE] in 13 fractions [5–6 fractions per week] in each arm). The primary objective is the proportion of therapies without wound healing disorder the first 120 days after surgery or discontinuation of treatment for any reason related to the treatment. The secondary endpoints of the study consist of local control, local progression-free survival, disease-free survival, overall survival, and quality of life.

Discussion
The aim of this study is to confirm that hypofractionated, preoperative radiotherapy is safe and feasible. The potential for reduced toxicity by the utilization of particle therapy is the rational of this trial. A subsequent randomized phase III trial will compare the hypofractionated proton and carbon ion irradiation in regards to local control.

Trial registration
ClinicalTrials.gov Identifier: NCT04946357; Retrospectively registered June 30, 2021.
Impact of geriatric nutritional risk index on outcomes after gastrectomy in elderly patients with gastric cancer: a retrospective multicenter study in Japan
Authors: Matsunaga Tomoyuki , Saito Hiroaki , Osaki Tomohiro , Takahashi Sadamu , Iwamoto Akemi , Fukuda Kenji , Taniguchi Kenjiro , Kuroda Hirohiko , Takeuchi Tsutomu , Sugamura Kenji , Sumi Kenichi , Katano Kuniyuki , Shishido Yuji , Miyatani Kozo , Fujiwara Yoshiyuki 
Published: May 2022

Abstract
Background
Several studies investigated the utility of inflammation and nutritional markers in predicting the prognosis in patients with gastric cancer; however, the markers with the best predictive ability remain unclear. This retrospective study aimed to determine inflammation and nutritional markers that predicted prognosis in elderly patients over 75 years of age undergoing curative gastrectomy for gastric cancer.

Methods
Between January 2005 and December 2015, 497 consecutive elderly gastric cancer patients aged over 75 years underwent curative gastrectomy in 12 institutions. The geriatric nutritional risk index (GNRI), prognostic nutritional index, neutrophil/lymphocyte ratio, platelet/lymphocyte ratio, and C-reactive protein/albumin ratio were examined as prognostic markers for overall survival (OS) and disease-specific survival (DSS) using area under the curve (AUC) using receiver operating characteristic (ROC) curve analysis.

Results
The GNRI had the highest AUC and predictive value for both OS (0.637, p < 0.001) and DSS (AUC 0.645, p < 0.001). The study cohort was categorized into the high and low GNRI groups based on the optimal GNRI cut-off values for OS (97.0) and DSS (95.8) determined with the ROC analysis. For both OS and DSS, there was a significant correlation between the GNRI and several clinicopathological factors including age, body mass index, albumin, American Society of Anesthesiologists physical status score, depth of tumor invasion, lymph node metastasis, lymphatic invasion, pathological stage, operation duration, bleeding, procedure, approach, death due to primary disease, and death due to other disease. The GNRI remained a crucial independent prognostic factor for both OS (Hazard ratio [HR] = 1.905, p < 0.001) and DSS in multivariate analysis (HR = 1.780, p = 0.043).

Conclusions
Among a panel of inflammation and nutritional markers, the GNRI exhibited the best performance as a prognostic factor after curative gastrectomy in elderly patients with gastric cancer, indicating its utility as a simple and promising index for predicting OS and DSS in these patients.