bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calibration of two validated SARS-CoV-2 pseudovirus neutralization assays for COVID-19 vaccine evaluation
Authors: Huang Yunda , Borisov Oleg , Kee Jia Jin , Carpp Lindsay N. , Wrin Terri , Cai Suqin , Sarzotti-Kelsoe Marcella , McDanal Charlene , Eaton Amanda , Pajon Rolando , Hural John , Posavad Christine M. , Gill Katherine , Karuna Shelly , Corey Lawrence , McElrath M. Juliana , Gilbert Peter B. , Petropoulos Christos J. , Montefiori David C. 
Published: December 2021

AbstractVaccine-induced neutralizing antibodies (nAbs) are key biomarkers considered to be associated with vaccine efficacy. In United States government-sponsored phase 3 efficacy trials of COVID-19 vaccines, nAbs are measured by two different validated pseudovirus-based SARS-CoV-2 neutralization assays, with each trial using one of the two assays. Here we describe and compare the nAb titers obtained in the two assays. We observe that one assay consistently yielded higher nAb titers than the other when both assays were performed on the World Health Organization’s anti-SARS-CoV-2 immunoglobulin International Standard, COVID-19 convalescent sera, and mRNA-1273 vaccinee sera. To overcome the challenge this difference in readout poses in comparing/combining data from the two assays, we evaluate three calibration approaches and show that readouts from the two assays can be calibrated to a common scale. These results may aid decision-making based on data from these assays for the evaluation and licensure of new or adapted COVID-19 vaccines.
The effect of Propofol versus Dexmedetomidine as anesthetic agents for oocyte pick-up on in vitro fertilization (IVF) outcomes
Authors: Budak Özcan , Bostancı Mehmet Sühha , Tuna AyçaTaş , Toprak Veysel , Çakiroğlu Hüseyin , Gök Koray 
Published: December 2021

AbstractThis study aimed to evaluate the effects of propofol and dexmedetomidine over different timescales on the IVF outcomes for transvaginal oocyte retrieval (TVOR). Twenty-four rats included in the study were divided into two main groups and three subgroups were subjected to the ovulation induction process. Group 1 was administered propofol (100 mg/kg i.v.) and group 2 were administered dexmedetomidine (25 µg/kg i.p.) The oviduct collection procedure was completed within 15 min for subgroup Pro15min, Dex15min (n = 4), within 16 to 30 min for subgroup Pro30min, Dex30min (n = 4) and within 31 to 60 min for subgroup Pro60min, Dex60min (n = 4) after euthanasia. The total number of oocytes was counted. After in vitro fertilization, the number and quality of embryos were evaluated. The number of pups born were evaluated after embryo transfer. The embryo number, quality and pup count decreased as the administration time for propofol increased (p < 0.05). No statistically significant difference was found between the dexmedetomidine subgroups for embryo number, quality and pup count(p > 0.05). As the exposure time to propofol increased, the number and quality of embryos obtained, and the pup count, decreased. The use of dexmedetomidine had no negative impacts on the number of embryos, their quality or the number of pups.
Circulating microRNA-197-3p as a potential biomarker for asbestos exposure
Authors: Frontini Francesca , Bononi Ilaria , Torreggiani Elena , Di Mauro Giulia , Mazzoni Elisa , Stendardo Mariarita , Boschetto Piera , Libener Roberta , Guaschino Roberto , Grosso Federica , Guerra Giovanni , Martini Fernanda , Tognon Mauro 
Published: December 2021

AbstractAsbestos is considered the main cause of diseases in workers exposed to this mineral in the workplace as well as an environmental pollutant. The association between asbestos and the onset of different diseases has been reported, but asbestos exposure specific biomarkers are not known. MicroRNAs (miRNAs) are small, single-strand, non-coding RNAs, with potential value as diagnostic, prognostic, and predictive markers in liquid biopsies. Sera collected from workers ex-exposed to asbestos (WEA) fibers were compared with sera from healthy subjects (HS) of similar age, as liquid biopsies. The expression of the circulating miRNA 197-3p was investigated employing two different highly analytical PCR methods, i.e. RT-qPCR and ddPCR. MiR-197-3p levels were tested in sera from WEA compared to HS. MiR-197-3p tested dysregulated in sera from WEA (n = 75) compared to HS (n = 62). Indeed, miR-197-3p was found to be 2.6 times down-regulated in WEA vs. HS (p = 0.0001***). In addition, an inverse correlation was detected between miR-197-3p expression level and cumulative asbestos exposure, being this miRNA down-regulated 2.1 times in WEA, with high cumulative asbestos exposure, compared to WEA with low exposure (p = 0.0303*). Circulating miR-197-3p, found to be down regulated in sera from WEA, is proposed as a new potential biomarker of asbestos exposure.
Common osteoporosis drug associated with increased rates of depression and anxiety
Authors: Keshishi Dro , Makunts Tigran , Abagyan Ruben 
Published: December 2021

AbstractOsteoporosis affects over 10 million Americans over 50. Bisphosphonate therapy, mainly alendronate, is amongst the most prescribed treatments for the disease. The use of alendronate and other bisphosphonates has been associated with depressive symptoms in recent case reports. In this study we quantified this association by analyzing over 100,000 adverse events reports from the Food and Drug Administration Adverse Events Reporting System (FAERS) and the World Health Organization’s (WHO) global database for adverse drug reactions, ADRs, VigiAccess. We found that alendronate therapy is significantly associated with depression and anxiety when compared to other first-line osteoporosis treatments. The reported risk of depressive ADRs was found to be over 14-fold greater in patients taking alendronate under the age of 65 and over fourfold greater for patients over 65 compared to the control. Several hypotheses concerning the molecular mechanism of the observed association of alendronate and depressive symptoms were discussed.
Estimating the SARS-CoV-2 infected population fraction and the infection-to-fatality ratio: a data-driven case study based on Swedish time series data
Authors: Wacker Andreas , Jöud Anna , Bernhardsson Bo , Gerlee Philip , Gustafsson Fredrik , Soltesz Kristian 
Published: December 2021

AbstractWe demonstrate that finite impulse response (FIR) models can be applied to analyze the time evolution of an epidemic with its impact on deaths and healthcare strain. Using time series data for COVID-19-related cases, ICU admissions and deaths from Sweden, the FIR model gives a consistent epidemiological trajectory for a simple delta filter function. This results in a consistent scaling between the time series if appropriate time delays are applied and allows the reconstruction of cases for times before July 2020, when RT-PCR testing was not widely available. Combined with randomized RT-PCR study results, we utilize this approach to estimate the total number of infections in Sweden, and the corresponding infection-to-fatality ratio (IFR), infection-to-case ratio (ICR), and infection-to-ICU admission ratio (IIAR). Our values for IFR, ICR and IIAR are essentially constant over large parts of 2020 in contrast with claims of healthcare adaptation or mutated virus variants importantly affecting these ratios. We observe a diminished IFR in late summer 2020 as well as a strong decline during 2021, following the launch of a nation-wide vaccination program. The total number of infections during 2020 is estimated to 1.3 million, indicating that Sweden was far from herd immunity.
Conventional agriculture and not drought alters relationships between soil biota and functions
Authors: Birkhofer Klaus , Fliessbach Andreas , Gavín-Centol María Pilar , Hedlund Katarina , Ingimarsdóttir María , Jørgensen Helene Bracht , Kozjek Katja , Meyer Svenja , Montserrat Marta , Moreno Sara Sánchez , Laraño Jordi Moya , Scheu Stefan , Serrano-Carnero Diego , Truu Jaak , Kundel Dominika 
Published: December 2021

AbstractSoil biodiversity constitutes the biological pillars of ecosystem services provided by soils worldwide. Soil life is threatened by intense agricultural management and shifts in climatic conditions as two important global change drivers which are not often jointly studied under field conditions. We addressed the effects of experimental short-term drought over the wheat growing season on soil organisms and ecosystem functions under organic and conventional farming in a Swiss long term trial. Our results suggest that activity and community metrics are suitable indicators for drought stress while microbial communities primarily responded to agricultural practices. Importantly, we found a significant loss of multiple pairwise positive and negative relationships between soil biota and process-related variables in response to conventional farming, but not in response to experimental drought. These results suggest a considerable weakening of the contribution of soil biota to ecosystem functions under long-term conventional agriculture. Independent of the farming system, experimental and seasonal (ambient) drought conditions directly affected soil biota and activity. A higher soil water content during early and intermediate stages of the growing season and a high number of significant relationships between soil biota to ecosystem functions suggest that organic farming provides a buffer against drought effects.
Differentiation of cancer stem cells into erythroblasts in the presence of CoCl2
Authors: Kumon Kazuki , Afify Said M. , Hassan Ghmkin , Ueno Shunsuke , Monzur Sadia , Nawara Hend M. , Quora Hagar A. Abu , Sheta Mona , Xu Yanning , Fu Xiaoying , Zahra Maram H. , Seno Akimasa , Seno Masaharu 
Published: December 2021

AbstractCancer stem cells (CSCs) are subpopulations in the malignant tumors that show self-renewal and multilineage differentiation into tumor microenvironment components that drive tumor growth and heterogeneity. In previous studies, our group succeeded in producing a CSC model by treating mouse induced pluripotent stem cells. In the current study, we investigated the potential of CSC differentiation into blood cells under chemical hypoxic conditions using CoCl2. CSCs and miPS-LLCcm cells were cultured for 1 to 7 days in the presence of CoCl2, and the expression of VEGFR1/2, Runx1, c-kit, CD31, CD34, and TER-119 was assessed by RT-qPCR, Western blotting and flow cytometry together with Wright-Giemsa staining and immunocytochemistry. CoCl2 induced significant accumulation of HIF-1α changing the morphology of miPS-LLCcm cells while the morphological change was apparently not related to differentiation. The expression of VEGFR2 and CD31 was suppressed while Runx1 expression was upregulated. The population with hematopoietic markers CD34+ and c-kit+ was immunologically detected in the presence of CoCl2. Additionally, high expression of CD34 and, a marker for erythroblasts, TER-119, was observed. Therefore, CSCs were suggested to differentiate into erythroblasts and erythrocytes under hypoxia. This differentiation potential of CSCs could provide new insight into the tumor microenvironment elucidating tumor heterogenicity.
The effect of the use of commercial tempeh starter on the diversity of Rhizopus tempeh in Indonesia
Authors: Sjamsuridzal Wellyzar , Khasanah Mangunatun , Febriani Rela , Vebliza Yura , Oetari Ariyanti , Santoso Iman , Gandjar Indrawati 
Published: December 2021

AbstractAt present, only a singleRhizopusspecies,R. microsporus, can be found in fresh tempeh produced in Java, Indonesia. The loss of diversity ofRhizopusin tempeh has been associated with the widespread use of commercial tempeh starter in Indonesia since the 2000s. However, the identities of the previousRhizopusstrains associated with tempeh, which have been preserved in a culture collection in Indonesia, have not been verified. The present study aimed to verify the identities of 22Rhizopusstrains isolated from tempeh produced using the traditional tempeh starters from the 1960s to the 2000s. Phylogenetic analysis based on the ITS regions in the rRNA gene sequence data, revealed that theRhizopusstrains belonged to the speciesR. arrhizus(five strains);R. delemar(14 strains); andR. microsporus(three strains).Verification of the identities of theseRhizopusstrains in the present study confirmed the loss of diversity ofRhizopusspecies in tempeh produced in Indonesia, particularly in Java. Our findings confirmed that the morphological changes inRhizopusspecies isolated from tempeh as a result of centuries of domestication.
Returning to work after a sickness absence due to cancer: a cohort study of salaried workers in Catalonia (Spain)
Authors: Ayala-Garcia Amaya , Serra Laura , Hernando-Rodriguez Julio C. , Benavides Fernando G. 
Published: December 2021

AbstractCancer incidence and survival rates have increased in the last decades and as a result, the number of working age people diagnosed with cancer who return to work. In this study the probability of accumulating days of employment and employment participation trajectories (EPTs) in a sample of salaried workers in Catalonia (Spain) who had a sickness absence (SA) due to cancer were compared to salaried workers with SA due to other diagnoses or without SA. Each individual with SA due to cancer between 2012 and 2015 was matched by age, sex, and onset of time at risk to a worker with SA due to other diagnoses and another worker without SA. Accumulated days of employment were measured, and negative binomial models were applied to assess differences between comparison groups. Latent class models were applied to identify EPTs and multinomial regression models to analyse the probability of belonging to one EPT of each group. Men and women without SA or with SA due to other diagnoses had at least a 9% higher probability of continuing in employment compared to workers who had a SA due to cancer, especially among men without SA (adjusted IRR 1.27, 95% CI 1.06‒1.53). Men without SA had the highest probability of having high stable EPT compared to workers who had a SA due to cancer (adjusted RRR 3.21, 95% CI 1.87‒5.50). Even though workers with SA due to cancer continue working afterwards, they do it less often than matched controls and with a less stable employment trajectory. Health and social protection systems should guaranty cancer survivors the opportunity to continue voluntary participation in the labour market.
Transcriptomic adaptation during skeletal muscle habituation to eccentric or concentric exercise training
Authors: Willis Craig R. G. , Deane Colleen S. , Ames Ryan M. , Bass Joseph J. , Wilkinson Daniel J. , Smith Kenneth , Phillips Bethan E. , Szewczyk Nathaniel J. , Atherton Philip J. , Etheridge Timothy 
Published: December 2021

AbstractEccentric (ECC) and concentric (CON) contractions induce distinct muscle remodelling patterns that manifest early during exercise training, the causes of which remain unclear. We examined molecular signatures of early contraction mode-specific muscle adaptation via transcriptome-wide network and secretome analyses during 2 weeks of ECC- versus CON-specific (downhill versus uphill running) exercise training (exercise ‘habituation’). Despite habituation attenuating total numbers of exercise-induced genes, functional gene-level profiles of untrained ECC or CON were largely unaltered post-habituation. Network analysis revealed 11 ECC-specific modules, including upregulated extracellular matrix and immune profiles plus downregulated mitochondrial pathways following untrained ECC. Of 3 CON-unique modules, 2 were ribosome-related and downregulated post-habituation. Across training, 376 ECC-specific and 110 CON-specific hub genes were identified, plus 45 predicted transcription factors. Secreted factors were enriched in 3 ECC- and/or CON-responsive modules, with all 3 also being under the predicted transcriptional control of SP1 and KLF4. Of 34 candidate myokine hubs, 1 was also predicted to have elevated expression in skeletal muscle versus other tissues: THBS4, of a secretome-enriched module upregulated after untrained ECC. In conclusion, distinct untrained ECC and CON transcriptional responses are dampened after habituation without substantially shifting molecular functional profiles, providing new mechanistic candidates into contraction-mode specific muscle regulation.
An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae)
Authors: Jacobs Sarah J. , Grundler Michael C. , Henriquez Claudia L. , Zapata Felipe 
Published: December 2021

AbstractWhat we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question inEscallonia(Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist inEscalloniaas an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species ($$< 20\%$$<20%) and that phenomic and genomic data seldom delimit congruent entities ($$< 20\%$$<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.
Association of loss of spleen visualization on whole-body diffusion-weighted imaging with prognosis and tumor burden in patients with multiple myeloma
Authors: Terao Toshiki , Machida Youichi , Tateishi Ukihide , Tsushima Takafumi , Narita Kentaro , Ikeda Daisuke , Fukumoto Ami , Kuzume Ayumi , Tabata Rikako , Miura Daisuke , Takeuchi Masami , Matsue Kosei 
Published: December 2021

AbstractThis study investigated the clinical significance of loss of spleen visualization (LSV) on whole-body diffusion-weighted imaging (WB-DWI) in patients with multiple myeloma (MM). The WB-DWI of 96 patients with newly diagnosed MM (NDMM) and 15 patients with smoldering MM (sMM) were retrospectively reviewed. LSV was observed in 56 patients with NDMM (58.3%) and 1 patient with sMM (6.7%). Patients with NDMM with LSV had a higher median infiltration of bone marrow plasma cells (80.0% vs. 50.0%, p < 0.001) and median total diffusion volume (median; 540.2 vs. 137.0 mL, p = 0.003) than patients without LSV. Patients with LSV had a lower spleen-to-spinal cord ratio (0.36 vs. 0.96, p < 0.001) and worse 2-year overall survival (OS) (84.6% vs. 100%, p = 0.032). Patients who did not recover spleen visualization during treatment had a worse prognosis, even when they obtained very good partial response (median progression-free survival: 13.2 months). Spleen histopathological findings revealed higher cellularity and diffuse myeloma cell infiltration in a patient with LSV and splenic amyloidosis without extramedullary hematopoiesis in a patient without LSV. Therefore, LSV indicates worse prognosis for patients with MM, even when the patient responds to treatment. Further studies are warranted to clarify the immunological role of spleen in MM.
The minor T allele of the MUC5B promoter rs35705950 associated with susceptibility to idiopathic pulmonary fibrosis: a meta-analysis
Authors: Wu Xiaozheng , Li Wen , Luo Zhenliang , Chen Yunzhi 
Published: December 2021

AbstractMUC5B promoter rs35705950 T/G gene polymorphism has been associated with the risk of IPF, but the influence of this relationship varies among different populations. In the past 2 years, there were new clinical studies with different results, but none of them reached unified conclusions. Therefore, this study further included the latest case–control studies, integrated their results and carried out meta-analysis on them to draw reliable conclusions. PubMed, EMBASE, CNKI, Wanfang database and VIP Chinese science were searched by a computer to collect the related literatures of MUC5B gene polymorphism and IPF susceptibility published before June 15, 2021. The first author, year of publication, diagnostic criteria and gene frequency were extracted after screened them. Forest plot was drawn and the trial sequential analysis (TSA) was carried out to confirm the stability of the meta-analysis results. Registration number: CRD42021272940. A total of 24 case–control studies (13 studies on the Caucasian, 7 studies on the Asian and 4 studies on the mixed population), and a total of 6749 IPF patients and 13,898 healthy controls were included in this study. The T vs.G, TT vs. GG, GT vs. GG, GT + TT vs. GG and TT vs. GG + GT genetic models of MUC5B promoter rs35705950 T/G polymorphism were associated with IPF risk in all populations, and the effect values were ([OR] 4.12, 95% CI [3.64, 4.67]), ([OR] 10.12, 95% CI [7.06, 14.49]), ([OR] 4.84, 95% CI [3.85, 6.08]), ([OR] 4.84, 95% CI [3.79, 6.19]) and ([OR] 5.11, 95% CI [4.02, 6.49]), respectively. The results of TSA confirmed the stability of the results. Subgroup analysis showed that T vs.G, TT vs. GG, GT vs. GG, GT + TT vs. GG and TT vs. GG + GT genetic models of MUC5B polymorphism were associated with IPF risk in Caucasian population. The effect values were ([OR] 4.50, 95% CI [3.93, 5.16]), ([OR] 10.98, 95% CI [7.59, 15.89]), ([OR] 6.27, 95% CI [5.37, 7.32]), ([OR] 6.30, 95% CI [5.19, 7.64]) and ([OR] 5.15, 95% CI [4.01, 6.61]), respectively. Similar results were also found in Asian and mixed populations. The association strength of the minor T allele in the Caucasian was more significant than that of the Asian population ([OR] 4.50 vs. [OR] 2.39), and the association strength of all genetic models carrying "T" was more significant than that of the Asian population ([OR] 10.98 vs. [OR] 4.29). In Caucasian, Asian and mixed populations, T minor allele carriers were more likely to be susceptible to pulmonary fibrosis, and TT genotype carriers were more likely to be susceptible to IPF than GT genotype carriers. The association between IPF and Caucasian population with minor T allele and all "T" genetic model was more significant than that of Asian population.