bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of metabolomics and transcriptomics data in head and neck squamous cell carcinoma
Authors: Li Wen , Li Yang , Chen Zhuo , Lam Alfred King‐yin , Li Zeping , Liu Xiaoling , Zhu Baoyu , Qiao Bin 
Published: January 2022

AbstractObjectiveStudies have shown that cancer progression of head and neck squamous cell carcinoma (HNSCC) is related with metabolic alterations. The aim of this study is to identify the clinical roles of metabolic alterations in HNSCC.Materials and methodsMetabolism‐related genes associated with HNSCC were searched in public databases. A predictive and efficacious LASSO model was fabricated to optimize the diagnosis that was based on these genes. Meantime, ultra‐performance liquid chromatography‐quadrupole/orbitrap high resolution mass spectrometry (UHPLC‐Q‐Orbitrap HRMS) was used to compare patients with HNSCC (n = 73) with healthy controls (n = 51) for serum metabolites. Potential biomarkers and alterations in serum metabolites were analysed and evaluated using t test analysis, principal component analysis and orthogonal partial least square‐discrimination analysis.ResultsOverall, 21 differential metabolites were probed in serum, of which eight metabolites had potential for clinical uses. Transcriptome analysis showed that four genes in the constructed LASSO model were found to be associated with seven differential metabolites. Metabolic pathway analysis by MetaboAnalyst showed that the biomarkers that were related with HNSCC were closely related to four metabolism pathways (p < 0.05).ConclusionTo conclude, future research on HNSCC should be directed towards multi‐omics to provide treatment, intervention or diagnosis of the disease.
Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates
Authors: Nunn Adam , Rodríguez‐Arévalo Isaac , Tandukar Zenith , Frels Katherine , Contreras‐Garrido Adrián , Carbonell‐Bejerano Pablo , Zhang Panpan , Ramos Cruz Daniela , Jandrasits Katharina , Lanz Christa , Brusa Anthony , Mirouze Marie , Dorn Kevin , Galbraith David W , Jarvis Brice A. , Sedbrook John C. , Wyse Donald L. , Otto Christian , Langenberger David , Stadler Peter F. , Weigel Detlef , Marks M. David , Anderson James A. , Becker Claude , Chopra Ratan 
Published: January 2022

SummaryThlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field‐based model species for genetics and epigenetics. The availability of a high‐quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome‐level genome assembly of var. MN106‐Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32‐10) that are highly amenable to genetic transformation. We describe non‐coding RNAs, pseudogenes and transposable elements, and highlight tissue‐specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome‐wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
Exposure to different light intensities affects emission of volatiles and accumulations of both pigments and phenolics in Azolla filiculoides
Authors: Brilli Federico , Dani K. G. Srikanta , Pasqualini Stefania , Costarelli Alma , Cannavò Sara , Paolocci Francesco , Zittelli Graziella Chini , Mugnai Gianmarco , Baraldi Rita , Loreto Francesco 
Published: January 2022

AbstractMany agronomic trials demonstrated the nitrogen‐fixing ability of the ferns Azolla spp. and its obligate cyanobiont Trichormus azollae. In this study, we have screened the emission of volatile organic compounds (VOCs) and analyzed pigments (chlorophylls, carotenoids) as well as phenolic compounds in Azolla filiculoides–T. azollae symbionts exposed to different light intensities. Our results revealed VOC emission mainly comprising isoprene and methanol (~82% and ~13% of the overall blend, respectively). In particular, by dissecting VOC emission from A. filiculoides and T. azollae, we found that the cyanobacterium does not emit isoprene, whereas it relevantly contributes to the methanol flux. Enhanced isoprene emission capacity (15.95 ± 2.95 nmol m−2 s−1), along with increased content of both phenolic compounds and carotenoids, was measured in A. filiculoides grown for long‐term under high (700 μmol m−2 s−1) rather than medium (400 μmol m−2 s−1) and low (100 μmol m−2 s−1) light intensity. Moreover, light‐responses of chlorophyll fluorescence demonstrated that A. filiculoides was able to acclimate to high growth light. However, exposure of A. filiculoides from low (100 μmol m−2 s−1) to very high light (1000 μmol m−2 s−1) did not affect, in the short term, photosynthesis, but slightly decreased isoprene emission and leaf pigment content whereas, at the same time, dramatically raised the accumulation of phenolic compounds (i.e. deoxyanthocyanidins and phlobaphenes). Our results highlight a coordinated photoprotection mechanism consisting of isoprene emission and phenolic compounds accumulation employed by A. filiculoides to cope with increasing light intensities.
Socioeconomic Status and Public Sector Worker Stereotypes: Results from a Representative Survey
Authors: Bertram Isa , Bouwman Robin , Tummers Lars 
Published: January 2022

AbstractWhat views do people have of public sector workers? Public sector workers are often portrayed negatively. It is unclear, however, to what extent such negative perceptions are shared among different groups in society. Using a large representative survey in the Netherlands, we study whether people's socioeconomic status is related to having more negative stereotypes about public sector workers. Contrary to expectations, education and income are unrelated to stereotypes. We do find a relation with subjective income: People with low subjective income have more negative stereotypes. Moreover, the sector people work in is highly relevant. People working in core governmental sectors such as central and local government have positive stereotypes. Other groups—such as private sector and non‐profit workers—have a far more negative image of public sector workers. These findings help us to understand people's perceptions of public sector workers and the problems various groups have with the state.
Consensus‐based sampling
Authors: Carrillo J. A. , Hoffmann F. , Stuart A. M. , Vaes U. 
Published: January 2022

AbstractWe propose a novel method for sampling and optimization tasks based on a stochastic interacting particle system. We explain how this method can be used for the following two goals: (i) generating approximate samples from a given target distribution and (ii) optimizing a given objective function. The approach is derivative‐free and affine invariant, and is therefore well‐suited for solving inverse problems defined by complex forward models: (i) allows generation of samples from the Bayesian posterior and (ii) allows determination of the maximum a posteriori estimator. We investigate the properties of the proposed family of methods in terms of various parameter choices, both analytically and by means of numerical simulations. The analysis and numerical simulation establish that the method has potential for general purpose optimization tasks over Euclidean space; contraction properties of the algorithm are established under suitable conditions, and computational experiments demonstrate wide basins of attraction for various specific problems. The analysis and experiments also demonstrate the potential for the sampling methodology in regimes in which the target distribution is unimodal and close to Gaussian; indeed we prove that the method recovers a Laplace approximation to the measure in certain parametric regimes and provide numerical evidence that this Laplace approximation attracts a large set of initial conditions in a number of examples.
A comparison of obfuscation methods used for privacy protection: Exploring the challenges of polygon data in agricultural research
Authors: Nowbakht Parvaneh , O'Sullivan Lilian , Cawkwell Fiona , Wall David P. , Holloway Paul 
Published: January 2022

AbstractA major challenge of sharing spatially explicit agricultural and agri‐environmental data is to identify the trade‐off between field parcel confidentiality and spatial pattern preservation. In this work, 27 point‐based obfuscation and evaluation methods were applied on agricultural data, collected by the Irish Nutrient Management Planning Online (NMP Online) platform, which is a high‐density polygon dataset developed to inform precision agriculture through nutrient management based on soil fertility and agronomic targets. Broad categorizations of methods—including N*Rand, Donut, Density, Pinwheel, AHilb, and k‐anonymity—were developed, combined, and modified to achieve the best trade‐off between security and accuracy. To improve geoprivacy and spatial pattern preservation of existing Donut and Density methods, qualitative approaches, including Donut‐k and Density‐k methods, were introduced which identify the optimal values of radii based on a combination of the Donut method and k‐anonymity satisfaction, and subsequently optimal k‐anonymity determination. Modified AHilb and Donut‐AHilb methods were also developed to generate smaller and arbitrary obfuscation areas to improve location security. The Donut‐AHilb method was found to be the best at spatial pattern preservation and satisfying larger k‐anonymity, but the risk of false identification and non‐unique obfuscation was high when considering the polygon nature of agricultural data such as field parcels. Further, we introduce the term “non‐unique obfuscated points,” which is important when obfuscating static objects as two or more points might have the same obfuscated location, which has relevance to the wider GIScience community.
Effect of lactic acid addition to equine whole blood on platelet aggregation measured by impedance aggregometry
Authors: Lanier Christopher J. , Taintor Jennifer S. , Christopherson Peter W. , Spangler Elizabeth A. 
Published: January 2022

AbstractBackgroundAcidemia in sick or injured horses is often due to lactic acid accumulation. Alterations in platelet function and hemostasis are among numerous deleterious effects caused by decreased physiologic pH.ObjectivesWe aimed to evaluate the effect of hyperlactatemia and resultant acidemia on platelet aggregation in equine whole blood using impedance aggregometry.MethodsPlatelet aggregation was measured using the Multiplate analyzer in whole blood from 34 healthy horses at baseline and after in vitro addition of lactic acid to adjust the pH. Platelet aggregation of each sample was quantified by the area under the curve measurement reported by the Multiplate system. The association between platelet aggregation and pH was analyzed using a linear mixed‐effects model. The association of baseline platelet aggregation with hematocrits (Hcts), white blood cell (WBC) counts, and platelet counts was evaluated using Pearson's correlations.ResultsThere was a significant association between acidemia and decreased platelet aggregation. No significant correlations were detected between platelet aggregation and Hct, WBC count, or platelet count. Platelet aggregation measured in healthy horses using the Multiplate analyzer showed substantial variation between animals.ConclusionsAcidemia caused by the addition of lactic acid to equine whole blood was associated with a mild though statistically significant decrease in platelet aggregation. In conjunction with other factors, this change may contribute to morbidity‐related disorders of hemostasis, although its precise clinical relevance is uncertain.
Outcomes of dogs undergoing surgery for gastric dilatation volvulus after rapid versus prolonged medical stabilization
Authors: Lhuillery Eloïse , Velay Ludivine , Libermann Stéphane , Le Boedec Kevin , Gautherot Audrey , Bonneau Lucie , Mongellas Emilie , Harris Karen , Etchepareborde Sébastien 
Published: January 2022

AbstractObjectiveTo compare the outcomes of dogs surgically treated for gastric dilatation volvulus (GDV) after rapid versus prolonged medical stabilization.Study DesignProspective cohort study, monoinstitutional.Sample PopulationOne hundred and sixty‐two dogs with GDV.MethodsDogs presenting with a GDV were allocated to 1 of 2 groups,immediateordelayed. In theimmediategroup, dogs were stabilized for 90 min prior to undergoing surgery. In thedelayedgroup, dogs underwent surgery after at least 5 h of stabilization. Medical stabilization included gastric decompression and placement of an indwelling nasogastric tube to prevent further gastric dilatation in all dogs. Short‐term outcomes were compared between surgical timings by univariate and multivariate analyses.ResultsDogs (n = 89) in theimmediategroup underwent surgery a median time of 2.1 h after presentation (range 1.9‐2.5 h), whereas those in thedelayedsurgery group (n = 73) were operated a median time of 9.8 h (range 5.4‐13.7 h) after presentation. Survival rates did not differ between dogs undergoing immediate or delayed surgery at discharge (70/89 and 60/73, respectively) or at 1 month postoperatively (68/89 and 55/73, respectively). The degree of gastric torsion was differently distributed between the 2 groups (P = .05). In theimmediategroup, 19, 52, and 9 dogs had a 0°, 180° and 270° gastric torsion respectively, whereas in thedelayedgroup, 27, 32, and 5 dogs had a 0°, 180° and 270° gastric torsion respectively. Hyperlactatemia 24 h after initiation of fluid therapy was associated with an increased in‐hospital mortality risk and at 1 month postoperatively.ConclusionNo survival benefit was detected as a result of proceeding to surgery after either a rapid or a prolonged medical stabilization.Clinical SignificanceThe aggressive stabilization and monitoring protocol described here can be considered as an alternative to stabilize dogs with GDV prior to surgery within 13.7 h of presentation. Further research is required to investigate the potential risks and benefits of prolonged over rapid stabilization and to identify candidates for each approach.
Topology Optimization of Lightweight Structures With Application to Bone Scaffolds and 3D Printed Shoes for Diabetics
Authors: Wang Zhujiang , Srinivasa Arun , Reddy J. N. , Dubrowski Adam 
Published: January 2022

Abstract
An automatic complex topology lightweight structure generation method (ACTLSGM) is presented to automatically generate 3D models of lightweight truss structures with a boundary surface of any shape. The core idea of the ACTLSGM is to use the PIMesh, a mesh generation algorithm developed by the authors, to generate node distributions inside the object representing the boundary surface of the target complex topology structures; raw lightweight truss structures are then generated based on the node distributions; the resulting lightweight truss structure is then created by adjusting the radius of the raw truss structures using an optimization algorithm based on finite element truss analysis. The finite element analysis-based optimization algorithm can ensure that the resulting structures satisfy the design requirements on stress distributions or stiffness. Three demos, including a lightweight structure for a cantilever beam, a femur bone scaffold, and a 3D shoe sole model with adaptive stiffness, can be used to adjust foot pressure distributions for patients with diabetic foot problems and are generated to demonstrate the performance of the ACTLSGM. The ACTLSGM is not limited to generating 3D models of medical devices, but can be applied in many other fields, including 3D printing infills and other fields where customized lightweight structures are required.
Impact of statin treatment on non-invasive tests based predictions of fibrosis in a referral pathway for NAFLD
Authors: Al-Karaghouli Mustafa , Fuentes Sonia , Davyduke Tracy , Ma Mang , Abraldes Juan G 
Published: January 2022

ObjectiveIn non-alcoholic fatty liver disease (NAFLD), fibrosis determines the risk of liver complications. Non-invasive tests (NITs) such as FIB-4, NAFLD Fibrosis Score (NFS) and Hepamet, have been proposed as a tool to triage NAFLD patients in primary care (PC). These NITs include AST±ALT in their calculations. Many patients with NAFLD take statins, which can affect AST/ALT, but it is unknown if statin affects NITs fibrosis prediction.MethodsWe included 856 patients referred through a standardised pathway from PC with a final diagnosis of NAFLD. 832 had reliable vibration controlled transient elastography (VCTE) measurements. We assessed the effects of statins on the association between NITs and VCTE at different fibrosis thresholds.Results129 out of 832 patients were taking a statin and 138 additional patients had indication for a statin. For any given FIB-4 value, patients on a statin had higher probabilities of high VCTE than patients not on a statin. Adjusting for body mass index, diabetes and age almost completely abrogated these differences, suggesting that these were related to patient’s profile rather to a specific effect of statins. Negative predictive values (NPVs) of FIB-4 <1.3 for VCTE >8, 10, 12 and 16 were, respectively, 89, 94, 96% and 100% in patients on a statin and 92, 95, 98% and 99% in patients not on a statin. Statins had similar impact on Hepamet predictions but did not modify NFS predictions.ConclusionIn patients with NAFLD referred from PC, those on statins had higher chances of a high VCTE for a given FIB-4 value, but this had a negligible impact on the NPV of the commonly used FIB-4 threshold (<1.3).
Does adherence to a quality indicator regarding early weaning from invasive ventilation improve economic outcome? A single-centre retrospective study
Authors: Zuber Alexander , Kumpf Oliver , Spies Claudia , Höft Moritz , Deffland Marc , Ahlborn Robert , Kruppa Jochen , Jochem Roland , Balzer Felix 
Published: January 2022

ObjectivesTo measure and assess the economic impact of adherence to a single quality indicator (QI) regarding weaning from invasive ventilation.DesignRetrospective observational single-centre study, based on electronic medical and administrative records.SettingIntensive care unit (ICU) of a German university hospital, reference centre for acute respiratory distress syndrome.ParticipantsRecords of 3063 consecutive mechanically ventilated patients admitted to the ICU between 2012 and 2017 were extracted, of whom 583 were eligible adults for further analysis. Patients’ weaning protocols were evaluated for daily adherence to quality standards until ICU discharge. Patients with <65% compliance were assigned to the low adherence group (LAG), patients with ≥65% to the high adherence group (HAG).Primary and secondary outcome measuresEconomic healthcare costs, clinical outcomes and patients’ characteristics.ResultsThe LAG consisted of 378 patients with a median negative economic results of −€3969, HAG of 205 (−€1030), respectively (p<0.001). Median duration of ventilation was 476 (248; 769) hours in the LAG and 389 (247; 608) hours in the HAG (p<0.001). Length of stay (LOS) in the LAG on ICU was 21 (12; 35) days and 16 (11; 25) days in the HAG (p<0.001). LOS in the hospital was 36 (22; 61) days in the LAG, and within the HAG, respectively, 26 (18; 48) days (p=0.001).ConclusionsHigh adherence to this single QI is associated with better clinical outcome and improved economic returns. Therefore, the results support the adherence to QI. However, the examined QI does not influence economic outcome as the decisive factor.
Preoperative sonographic prediction of intra-abdominal adhesions using sliding sign at repeat caesarean section at the University of Maiduguri Teaching Hospital, Nigeria: a prospective observational study
Authors: Bukar Mohammed , Mana Asta Umar , Ikunaiye Nasiru 
Published: January 2022

ObjectiveTo determine if the presence or absence of sonographic sliding sign preoperatively is a good predictor of the presence and type of intra-abdominal adhesions; and to determine the time taken to demonstrate this sign.DesignA prospective, observational, triple-blind study using tests of diagnostic accuracy.SettingSingle-centre tertiary health institution in north-east Nigeria.Participants67 women in the third trimester scheduled for repeat elective caesarean sections (CS) had transabdominal sonography to determine the absence or presence and degree of sliding sign. The time taken to make these decisions were noted. Surgeons blinded to the ultrasound findings graded adhesions intraoperatively and comparison between sonographic and intraoperative findings made. Women who were scheduled for emergency CS were excluded.Main outcome measuresAccuracy of preoperative ultrasound to determine no/mild, moderate and severe adhesions. Secondary outcomes were interobserver correlations and time taken to determine sliding.ResultsWhen classified as adhesion and no adhesion, the sliding sign demonstrated a sensitivity of 100.00% (CI95 85.18% to 100.00%), specificity of 100.00% (CI95 92.13% to 100.00%). In predicting presence of moderate intra-abdominal adhesions, a sensitivity of 65.0% (CI95 40.78% to 84.61%) and specificity of 82.98% (CI95 69.19% to 92.35%) was found. For predicting severe intra-abdominal adhesions, it had a sensitivity of 25.00% (CI95 0.63% to 80.59%) and specificity of 98.41 (CI95 91.47 to 99.96). Disease prevalence for mild, moderate and severe adhesions was 33.82% (CI95 22.79% to 46.32%), 29.85% (CI95 19.28% to 42.27%) and 5.97% (CI95 1.65% to 14.59%), respectively. Interobserver Cohen’s kappa coefficient and PPA were 0.58 (CI95 0.39 to 0.76) and 58.82 (CI95 52.82 to 64.82), respectively. The mean duration to determine sliding sign was 7.56±2.86 s.ConclusionThis study supports the role of transabdominal sliding sign in preoperative prediction of intra-abdominal adhesions in women with previous CS without significant increase in sonography duration. This information can encourage planning for CS by ensuring that surgeons of appropriate seniority are deployed to undertake anticipated complex operations.