bluuebunny/crossref_metadata_2025_split huggingface dataset:
A candidate reference method and multiple commutable control materials for serum 25‐hydroxyvitamin D measurement
Authors: Zhang Li , Long Qichen , Zhang Jiangtao , Zeng Qingzhang , Zhao Haijian , Chen Wenxiang , Zhang Tianjiao , Zhang Chuanbao 
Published: November 2022

AbstractObjectivesThe aim of the current study was to establish a reliable candidate reference method for serum 25‐hydroxyvitamin D [25(OH)D] measurement and to assess the commutability of multiple control materials among liquid chromatography–tandem mass spectrometry (LC–MS/MS) methods.MethodsSerum 25‐hydroxyvitamin D2 [25(OH)D2] and 25‐hydroxyvitamin D3 [25(OH)D3] together with spiked internal standards were extracted with a one‐step approach and then analyzed by LC–MS/MS. The commutability assessment for 25(OH)D was conducted according to the Clinical and Laboratory Standards Institute (CLSI) EP14‐A3 protocol. 25(OH)D concentrations in 5 levels of unprocessed serum pools, 7 levels of serum pools spiked with 25(OH)D3 or 25(OH)D2, 3 levels of commercial control materials, 2 levels of spiked bovine serum, and 4 levels of external quality assessment (EQA) materials were measured along with 30 single‐donor samples using the candidate reference method and two routine LC–MS/MS methods.ResultsThe candidate reference method could separate 25(OH)D2 and 25(OH)D3 from 14 potential interfering compounds completely within a 9‐min analysis time. Good method precision was obtained, and measurement results on certified reference material NIST SRM 972a were within the uncertainty of the certified values. All candidate materials were assessed commutable for LC–MS/MS methods.ConclusionsThe candidate reference method for serum 25(OH)D measurement is precise, accurate, and robust against interferences and can provide an accuracy base for routine methods. The multiple alternative control materials with commutability among LC–MS/MS methods will facilitate the further standardization for serum 25(OH)D measurement.
LINC00511 aggravates the malignancy of lung adenocarcinoma through sponging microRNA miR‐4739 to regulate pyrroline‐5‐carboxylate reductase 1 expression
Authors: Ye Lu , Wang Linxiu , Zeng Yu 
Published: November 2022

AbstractBackgroundLong non‐coding RNA LINC00511 is known to exacerbate lung adenocarcinoma (LUAD) progression. However, the specific mechanism by which LINC00511 affects LUAD progression has not been investigated as yet, and we aimed to elucidate the same in the present study.MethodsThe expression levels of LINC00511, microRNA miR‐4739, and pyrroline‐5‐carboxylate reductase 1 (PYCR1) were determined by quantitative reverse transcription PCR and Western blotting. The Cell Counting Kit‐8 and bromodeoxyuridine assays were used to evaluate cell proliferation. Apoptosis was evaluated by flow cytometry, and Bax and Bcl‐2 protein levels were determined by western blotting. Cell migration was assessed using transwell assay. The interaction between LINC00511, miR‐4739, and PYCR1 was analyzed using luciferase, RNA immunoprecipitation, and RNA pull‐down assays.ResultsThe expression levels of LINC00511 and PYCR1 in LUAD were downregulated, whereas that of miR‐4739 was upregulated. Functional studies showed that knockdown of LINC00511 or PYCR1 suppressed the proliferation and migration of LUAD cells, and promoted apoptosis. On the contrary, knockdown of miR‐4739 had tumor‐promoting effects. Mechanistically, LINC00511 prevented the miR‐4739 led inhibition of PYCR1, resulting in PYCR1 overexpression.ConclusionThis study demonstrates for the first time that LINC00511 aggravates the malignancy of LUAD by sponging miR‐4739 to upregulate PYCR1 expression.
Accompanying a semi‐nested PCR assay to support histopathology findings of fungal keratitis in formalin‐fixed paraffin‐embedded corneal samples
Authors: Ashraf Mohammad Javad , Shamsizadeh Foroogh , Morovati Hamid , Hejazinia Safoora , Kord Mohammad , Ansari Saham , Pakshir Keyvan , Shekarkhar Golsa , Zomorodian Kamiar 
Published: November 2022

AbstractBackgroundFungal species are responsible for 40%–50% of all microbial keratitis cases. Due to the low amount of extracted DNA in ocular Formalin‐fixed Paraffin‐embedded (FFPE) samples, selecting a reliable molecular method is a substantial issue in this field.MethodsSixty‐six samples were collected via the penetrating keratoplasty (PK) technique. Histopathology assays were performed using hematoxylin–eosin (H&E) and periodic acid Schiff (PAS) staining methods. The ITS1/ITS4 and ITS1/ITS2 primer pairs were used in a semi‐nested polymerase chain reaction (PCR) to target the universal internal transcribed spacer (ITS) region. Some PCR results were validated through sequencing.ResultsFungal DNA was detected in 44 of 66 samples (66.7%), and histopathology was positive for 41 of 66 samples (62.1%). Of 41 histopathologically proven fungal‐positive cases, 39 were PCR‐positive (95%). Moreover, of 44 PCR‐positive samples, 39 (88.6%) were histopathology‐positive, and 5 (11.3%) were histopathology‐negative. Totally in 39 cases (59%), both histopathology and PCR yielded positive results. The Kappa agreement rate between the two diagnostic methods, including histopathology and PCR, was 0.77. Sensitivity, specificity, positive predictive value, and false predictive value were reported as 88.64%, 90.9%, 95.12%, and 80%, respectively.ConclusionAs we reached the acceptable Kappa agreement rate, we concluded that applying the semi‐nested PCR assay is a promising method for supporting the evidence by histopathology. Finally, we suggest targeting more specific gene regions using primer pairs that amplify smaller amplicon sizes and surveying novel molecular methods such as NGS to achieve higher sensitivity and Kappa agreement rates.
Diisobutylaluminium hydride mediated efficient synthesis of Morita–Baylis–Hilman adducts through α‐functionalization of alkyl propiolates
Authors: Gogula Sailam Sri , Konakalla Ramakrishna , Kamireddy Kamalaker Reddy , Puchakayala Muralidar Reddy , Lincoln Ch. Abraham , Basireddy Venkata Subba Reddy 
Published: November 2022

AbstractGenerally, oxindole derivatives are biologically important molecules and valuable building blocks in organic synthesis. Herein, we report a diisobutylaluminium hydride mediated efficient one‐pot synthesis of oxindole derivatives using N‐substituted isatins with methyl or ethyl propiolates at lower temperature (−78°C) through Morita‐Baylis‐Hillman (MBH) reaction. Within a short reaction time, a wide range of N‐alkyl or N‐aryl 3‐hydroxy oxindole derivatives (MBH adducts) were easily accessed in excellent yields under mild reaction conditions.
Cellular and computational models reveal environmental and metabolic interactions in MMUT‐type methylmalonic aciduria
Authors: Ramon Charlotte , Traversi Florian , Bürer Céline , Froese D. Sean , Stelling Jörg 
Published: November 2022

AbstractMethylmalonyl‐coenzyme A (CoA) mutase (MMUT)‐type methylmalonic aciduria is a rare inherited metabolic disease caused by the loss of function of the MMUT enzyme. Patients develop symptoms resembling those of primary mitochondrial disorders, but the underlying causes of mitochondrial dysfunction remain unclear. Here, we examined environmental and genetic interactions in MMUT deficiency using a combination of computational modeling and cellular models to decipher pathways interacting with MMUT. Immortalized fibroblast (hTERT BJ5ta) MMUT‐KO (MUTKO) clones displayed a mild mitochondrial impairment in standard glucose‐based medium, but they did not to show increased reliance on respiratory metabolism nor reduced growth or viability. Consistently, our modeling predicted MUTKO specific growth phenotypes only for lower extracellular glutamine concentrations. Indeed, two of three MMUT‐deficient BJ5ta cell lines showed a reduced viability in glutamine‐free medium. Further, growth on 183 different carbon and nitrogen substrates identified increased NADH (nicotinamide adenine dinucleotide) metabolism of BJ5ta and HEK293 MUTKO cells compared with controls on purine‐ and glutamine‐based substrates. With this knowledge, our modeling predicted 13 reactions interacting with MMUT that potentiate an effect on growth, primarily those of secondary oxidation of propionyl‐CoA, oxidative phosphorylation and oxygen diffusion. Of these, we validated 3‐hydroxyisobutytyl‐CoA hydrolase (HIBCH) in the secondary propionyl‐CoA oxidation pathway. Altogether, these results suggest compensation for the loss of MMUT function by increasing anaplerosis through glutamine or by diverting flux away from MMUT through the secondary propionyl‐CoA oxidation pathway, which may have therapeutic relevance.
GLIM‐defined malnutrition and overall survival in cancer patients: A meta‐analysis
Authors: Yin Liangyu , Chong Feifei , Huo Zhenyu , Li Na , Liu Jie , Xu Hongxia 
Published: November 2022

AbstractBackgroundMalnutrition defined by the Global Leadership Initiative on Malnutrition (GLIM) has been associated with cancer mortality, but the effect is limited and inconsistent. We performed this meta‐analysis aiming to assess this relationship in patients with cancer.MethodsWe systematically searched Embase, PubMed, Web of Science, Cochrane, CINAHL, CNKI, Wanfang, and VIP databases from January 1, 2019, to July 1, 2022. Studies evaluating the prognostic effect of GLIM‐defined malnutrition on cancer survival were included. A fixed‐effect model was fitted to estimate the combined hazard ratio (HR) with a 95% CI. Heterogeneity of studies was analyzed using the I2 statistic. Quality assessment were performed using the Newcastle‐Ottawa Scale (NOS) and the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) tool.ResultsThe search strategy identified 4378 articles in all databases combined. Nine studies (8829 patients) meeting the inclusion criteria were included for quantitative analysis. Meta‐analysis revealed significant associations between GLIM‐defined pooled malnutrition (HR = 1.75; 95% CI, 1.43–2.15), moderate malnutrition (HR = 1.44; 95% CI, 1.29–1.62), and severe malnutrition (HR = 1.79; 95% CI, 1.58–2.02) with all‐cause mortality. Sensitivity analysis supported the robustness of these associations. The between‐study heterogeneity was low (all I2 < 50%), and study quality assessed with NOS was high (all scores > 6). The evidence quality according to the GRADE tool was very low.ConclusionsOur meta‐analysis suggests a significant negative association of malnutrition, as defined by the GLIM, with overall survival in patients with cancer. However, definitive conclusions cannot be made, owing to the low quality of the source data.
Bacterial biomarkers are linked more closely to wheat yield formation than overall bacteria in fertilized soil
Authors: Ma Li , Niu Wenquan , Li Guochun , Zhang Erxin , Sun Jun , Zhang Qian , Siddique Kadambot H. M. 
Published: November 2022

AbstractSoil bacteria play pivotal roles in agroecosystem functioning. However, the immense diversity of soil bacterial communities masks the effects of some species, such as bacterial biomarkers, on soil nutrient cycling and crop growth. We analyzed biological and chemical soil parameters of five fertilization treatments (CK, LN, CN, HN, LNM: 0, 150, 200, 250 kg N hm−2, 150 kg N hm−2 + 15,000 kg hm−2 sheep manure). The random forest models were used to select bacterial biomarkers and assess the contributions of bacterial biomarkers and overall bacteria to wheat yield. Moreover, we used a partial least squares path modelling to explore the relationship between fertilization, bacterial biomarkers, carbon (C) and nitrogen (N) cycling functions, soil nutrients, and wheat yield. The results showed that bacterial biomarkers are better predictors of wheat yield than overall bacteria, explaining 52.54% and 16.00% of the variation in yield, respectively. Bacterial biomarkers affected wheat production by increasing soil organic carbon, and available nitrogen content. The LNM treatment significantly improved the relative abundance of beneficial biomarkers, such as Sphingomonadales, Xanthomonadaceae, Lysobacter, and Streptomyces, compared to the LN treatment. In addition, the LNM treatment promoted chitinlysis, cellulolysis, xylanolysis, aromatic hydrocarbon degradation, and aerobic ammonia oxidation, relative to the other inorganic N treatments (LN, CN, and HN). Our results emphasize the role of bacterial biomarkers in wheat yield formation, providing new insights into maintaining agricultural productivity by taking advantage of soil bacterial biomarkers.
Targeting intra‐tumoral heterogeneity of human brain tumors with in vivo imaging: A roadmap for imaging genomics from multiparametric MR signals
Authors: Parker Jason G. , Servati Mahsa , Diller Emily E. , Cao Sha , Ho Chang , Lober Robert , Cohen‐Gadol Aaron 
Published: November 2022

AbstractResistance of high grade tumors to treatment involves cancer stem cell features, deregulated cell division, acceleration of genomic errors, and emergence of cellular variants that rely upon diverse signaling pathways. This heterogeneous tumor landscape limits the utility of the focal sampling provided by invasive biopsy when designing strategies for targeted therapies. In this roadmap review paper, we propose and develop methods for enabling mapping of cellular and molecular features in vivo to inform and optimize cancer treatment strategies in the brain. This approach leverages (1) the spatial and temporal advantages of in vivo imaging compared with surgical biopsy, (2) the rapid expansion of meaningful anatomical and functional magnetic resonance signals, (3) widespread access to cellular and molecular information enabled by next‐generation sequencing, and (4) the enhanced accuracy and computational efficiency of deep learning techniques. As multiple cellular variants may be present within volumes below the resolution of imaging, we describe a mapping process to decode micro‐ and even nano‐scale properties from the macro‐scale data by simultaneously utilizing complimentary multiparametric image signals acquired in routine clinical practice. We outline design protocols for future research efforts that marry revolutionary bioinformation technologies, growing access to increased computational capability, and powerful statistical classification techniques to guide rational treatment selection.
Implicit dynamic buckling analysis of thin‐shell isogeometric structures considering geometric imperfections
Authors: Guo Yujie , Pan Maodong , Wei Xiaohui , Luo Fei , Sun Fangbin , Ruess Martin 
Published: November 2022

AbstractIn continuation of our previous work on nonlinear stability analysis of trimmed isogeometric thin shells, this contribution is an extension to dynamic buckling analyses for predicting reliably complex snap‐through and mode‐jumping behavior. Specifically, a modified generalized‐ time integration scheme is used and combined with a nonlinear isogeometric Kirchhoff–Love shell element to provide second‐order accuracy while introducing controllable high‐frequency dissipation. In addition, a weak enforcement of essential boundary conditions based on a penalty approach is considered with a particular focus on the inhomogeneous case of imposed prescribed displacements. Moreover, we propose a least‐squares B‐spline surface fitting approach and corresponding error measures to model both eigenmode based and measured geometric imperfections. The imperfect geometries thus obtained can be naturally integrated into the framework of isogeometric nonlinear dynamic shell analysis. Based on this idea, the different modeling methods and the influence of the appropriately considered geometric imperfections on the dynamic buckling behavior can be investigated systematically. Both perfect and geometrically imperfect shell models are considered to assess the performance of the proposed method. We compare our method with established developments in this field and demonstrate superior achievements with regard to solution quality and robustness.
Resolving vibro‐acoustics in poroelastic media via a multiscale virtual element method
Authors: Sreekumar Abhilash , Triantafyllou Savvas P. , Chevillotte Fabien , Bécot François‐Xavier 
Published: November 2022

AbstractWe introduce a novel heterogeneous multi‐scale method for the frequency response analysis of waves propagating in porous domains with a complex micro‐structure. In this, the domain is decomposed onto polygonal coarse elements each clustering its local micro‐structure. The micro‐structure is resolved using the virtual element method hence providing ample flexibility into capturing fine scale heterogeneities of arbitrary polygonal shapes. The upscaling is performed through a set of numerically evaluated multi‐scale basis functions. Rather than evaluating the basis for a broad band set of frequencies, a reduced order modeling approach is opted for. In this, the basis is evaluated for a select subset of frequencies, that is used as a basis for the evaluation of the remaining set through a proper orthogonal decomposition procedure. The solution of the coupled governing equations is then performed at the coarse‐scale at a reduced computational cost. The performance of the method in terms of accuracy and computational efficiency is evaluated through a set of numerical examples for poro‐elastic materials with heterogeneities of various shapes.
Technology‐based Comprehensive Cardiac Rehabilitation Therapy (TaCT) for women with cardiovascular disease in a middle‐income setting: A randomized controlled trial protocol
Authors: Menezes Henita Joshna , D' Souza Sonia R. B. , Padmakumar Ramachandran , Babu Abraham Samuel , Rao Rohini R. , Kamath Veena G. , Kamath Asha , Grace Sherry L. 
Published: November 2022

AbstractWomen are underrepresented in cardiac rehabilitation (CR) despite the benefits, and this is exacerbated in lower‐resource settings where CR is insufficiently available. In this randomized controlled trial, the effectiveness of the Technology‐based Comprehensive Cardiac Rehabilitation Therapy (TaCT) electronic cardiac rehabilitation (eCR) intervention on functional capacity, risk factors, quality of life, heart‐health behaviors, symptoms, and morbidity will be tested among women with CVD in a middle‐income country. Following a pilot study, a single‐center, single‐blinded, 2 parallel‐arm (1:1 SNOSE) superiority trial comparing an eCR intervention (TaCT) to usual care, with assessments pre‐intervention and at 3 and 6 months will be undertaken. One hundred adult women will be recruited. Permuted block (size 10) randomization will be applied. The 6‐month intervention comprises an app, website, SMS texts with generic heart‐health management advice, and bi‐weekly 1:1 telephone calls with a nurse trainee. Individualized exercise prescriptions will be developed based on an Incremental Shuttle Walk Test (primary outcome) and dietary plans based on 24 h dietary recall. A yoga/relaxation video will be provided via WhatsApp, along with tobacco cessation support and a moderated group chat. At 3 months, intervention engagement and acceptability will be assessed. Analyses will be conducted based on intent‐to‐treat. If results of this novel trial of women‐focused eCR in a middle‐income country demonstrate clinically‐significant increases in functional capacity, this could represent an important development for the field considering this would be an important outcome for women and would translate to lower mortality.
Integrated molecular characterization of esophageal basaloid squamous cell carcinoma: a subtype with distinct RNA expression pattern and immune characteristics, but no specific genetic mutations
Authors: Li Yan , Liu Linxiu , Pan Yi , Fang Fang , Xie Tongji , Cheng Na , Guo Changyuan , Xue Xuemin , Zeng Hua , Xue Liyan 
Published: November 2022

AbstractEsophageal basaloid squamous cell carcinoma (bSCC) is a subtype of squamous cell carcinoma (SCC) with a different behavior and poor prognosis. Exploring bSCC's molecular characteristics and treatment strategies are of great clinical significance. We performed multi‐omics analysis of paired bSCC and common SCC (cSCC) using whole exome sequencing and a NanoString nCounter gene expression panel. Immunohistochemistry was used for verification of candidate biomarkers. Different treatment response was analyzed on both patients receiving neoadjuvant treatment and late‐stage patients. The common genetically‐clonal origin of bSCC and cSCC was confirmed. No significant differences between their genetic alterations or mutation spectra were observed. Mutation signature 15 (associated with defective DNA damage repair) was less prominent, and tumor mutational burden (TMB) was lower in bSCC. bSCC with an RNA expression pattern resembling cSCC had a better survival than other bSCCs. Moreover, bSCC showed significant upregulation of expression of genes associated with angiogenesis response, basement membranes, and epithelial–mesenchymal transition, and downregulation of KRT14 (squamous differentiation) and CCL21 (associated with immune response). Immunohistochemistry for SFRP1 was shown to be highly sensitive and specific for bSCC diagnosis (p < 0.001). In addition, bSCC receiving neoadjuvant immuno‐chemotherapy had a worse pathological response than bSCC receiving neoadjuvant chemotherapy (but without statistical significance), even in bSCC positive for PD‐L1. Our results demonstrated the molecular characteristics of esophageal bSCC as a subtype with a distinct RNA expression pattern and immune characteristics, but no specific genetic mutations. We provided a useful biomarker, SFRP1, for diagnosis. After outcome analysis for six bSCCs with neoadjuvant immunotherapy treatment and four late‐stage bSCCs with immunotherapy, we found that immunotherapy may not be an effective treatment option for most bSCCs. This may also provide a clue for the same subtypes of lung and head and neck cancer. Our study highlighted the heterogeneity among bSCC patients, and might explain the conflicting results of bSCC outcomes in existing studies. © 2022 The Pathological Society of Great Britain and Ireland.
Do reproductive history and information given through genetic counselling influence patients' decisions on mosaic embryo transfer?
Authors: Coll Lluc , Parriego Mònica , Palacios Gabriela , Garcia Sandra , Boada Montserrat , Coroleu Buenaventura , Polyzos Nikolaos P. , Vidal Francesca , Veiga Anna 
Published: November 2022

AbstractObjectiveTo assess patients' and embryonic characteristics that may have an influence on the decision to transfer a mosaic embryo.MethodSingle centre retrospective cohort study including 1247 PGT‐A cycles. Demographic and clinical factors associated with a decision to transfer a mosaic embryo were studied. Female age, number of previous cycles, previous availability of euploid embryos, history of miscarriages and parity as well as percentage of mosaicism, type of anomaly and chromosome risk were studied in relation to decision‐making. Outcomes after mosaic embryo transfer were assessed.ResultsTo date, in 7.9% of cycles (99/1247), patients have had to make a decision on the fate of their mosaic embryos. In 23.2% of cycles (23/99), patients decided to transfer. In most cases (79.8%; 79/99), patients underwent genetic counselling before the decision. None of the variables analysed were associated with the patients' decision, although parity and the high‐degree mosaicism (>50%) seemed to be negatively associated with the decision to transfer (18.2% vs. 29.8%, p = 0.294; 10% vs. 32.2%, p = 0.052).ConclusionsNeither reproductive history nor information on mosaic embryo characteristics through counselling seems to be determinative for patients when deciding to transfer a mosaic embryo. Promising and increasing data on clinical outcomes after mosaic embryo transfer will be of utmost importance to soften risk perception regarding mosaic embryos and give a better, simplified and more evidence‐based counselling.