bluuebunny/crossref_metadata_2025_split huggingface dataset:
High oncostatin M predicts lack of clinical remission for patients with inflammatory bowel disease on tumor necrosis factor α antagonists
Authors: Guo Angela , Ross Cameron , Chande Nilesh , Gregor Jamie , Ponich Terry , Khanna Reena , Sey Michael , Beaton Melanie , Yan Brian , Kim Richard B. , Wilson Aze 
Published: January 2022

AbstractThe interleukin-6 family cytokine, oncostatin-M (OSM) has been associated with response to tumor necrosis factor-α antagonists (anti-TNFs) in small cohorts of patients with inflammatory bowel disease (IBD). We aimed to evaluate the association between plasma OSM concentrations and response to anti-TNFs (infliximab and adalimumab) in both ulcerative colitis (UC) and Crohn’s disease (CD). A retrospective cohort study was conducted in patients with IBD with a history of anti-TNF exposure. Blood samples, collected prior to anti-TNF exposure, were analyzed by enzyme-linked immunosorbent assay for the presence and quantity of OSM. Clinical remission was assessed at 1-year post anti-TNF exposure in addition to the occurrence of surgery, hospitalization, corticosteroid use, and adverse drug events. Lastly the threshold OSM plasma concentration associated with anti-TNF non-response was assessed by receiver operator characteristic (ROC) curve analysis.
Patients with IBD (CD, n = 82; UC, n = 40) were assessed. In both UC and CD, mean pre-treatment OSM concentrations were significantly lower in those who achieved clinical remission at 1-year (p < 0.0001). A threshold plasma OSM concentration of 168.7 pg/ml and 233.6 pg/ml respectively separated those who achieved clinical remission at 1-year on an anti-TNF from those who did not in CD and UC respectively (CD: area under the receiver operator characteristic curve, AUROC = 0.880, 95% CI 0.79–0.96; UC: AUROC = 0.938, 95% CI 0.87–1.00). High OSM concentrations were associated with anti-TNF discontinuation and use of rescue steroids in CD and UC. High pre-treatment OSM concentrations identify IBD patients at-risk of anti-TNF non-response at 1-year as well as other deleterious clinical outcomes.
The multicausal twilight of South American native mammalian predators (Metatheria, Sparassodonta)
Authors: Tarquini Sergio Daniel , Ladevèze Sandrine , Prevosti Francisco Juan 
Published: January 2022

AbstractSparassodonts were the apex mammalian predators of South America throughout most of the Cenozoic, diversifying into a wide array of niches including fox-like and even saber-toothed forms. Their extinction is still controversial, with different authors suggesting competition with other predators (placental carnivorans, terror birds, and carnivorous opossums), extinction of prey, and climate change as causal explanations. Here, we analyse these hypotheses using a novel approach implicating Bayesian analyses. We find that speciation and extinction rates of sparassodonts can be correlated with (i) intrinsic biotic factors such as changes in body mass and diversity of sparassodonts, (ii) extrinsic biotic factors such as potential prey diversity, and iii) extrinsic abiotic factors like the atmospheric CO2, sea level, temperature, and uplift of the Andes. Thus, sparassodonts are a good example of a multilevel mixed model of evolution, where various factors drove the evolutionary history of this clade in a pluralistic way. There is no evidence for competition between Sparassodonta and others predators, and the effect of competition in the face of extinctions of fossil species should be tested and not assumed. Furthermore, we propose a novel approach for evaluating the fossil record when performing macroevolutionary analyses.
Proteome alterations in the aqueous humor reflect structural and functional phenotypes in patients with advanced normal-tension glaucoma
Authors: Lee Si Hyung , Jung Jae Hun , Park Tae Kwann , Moon Chae-Eun , Han Kyusun , Lee Jinhyoung , Lee Hyung Keun , Ji Yong Woo , Kim Chan Yun 
Published: January 2022

AbstractPrevious reports have shown possible association between altered protein levels in aqueous humor (AH) and normal-tension glaucoma (NTG), but the underlying pathogenetic mechanism as well as specific molecular biomarkers for NTG remains still elusive. Here, we aimed to identify novel biomarkers for advanced NTG by analyzing the proteome of patient-derived AH and their correlation with various functional and structural parameters from the visual field test (VF), optical coherence tomography (OCT), and OCT angiography (OCTA). We determined differentially expressed proteins (DEPs) of the AH of patients with advanced NTG (n = 20) using label-free quantitative (LFQ) proteomics with pooled samples and data-independent acquisition (DIA) analysis with individual samples, and the roles of AH DEPs in biological pathways were evaluated using bioinformatics. We identified 603 proteins in the AH of patients with advanced NTG, and 61 of them were selected as DEPs via global proteome LFQ profiling. Individual DIA analyses identified a total of 12 DEPs as biomarker candidates, seven of which were upregulated, and five were downregulated. Gene ontology enrichment analysis revealed that those DEPs were mainly involved in the immune response. Moreover, IGFBP2, ENO1, C7, B2M, AMBP, DSP, and DCD showed a significant correlation with the mean deviation of VF and with peripapillary and macular parameters from OCT and OCTA. The present study provides possible molecular biomarkers for the diagnosis of advanced NTG.
A 14-day ecological momentary assessment study on whether resilience and early family risk moderate daily stress and affect on cortisol diurnal slope
Authors: Tung Natasha Yan Chi , Yap Yang , Bei Bei , Luecken Linda J. , Wiley Joshua F. 
Published: January 2022

AbstractThis study examined whether resilience capacity moderates the association of daily perceived stress and affect with cortisol diurnal slope among relocated emerging adults. Relocated undergraduates (N = 98; aged 18–25 years) were recruited from three groups: Resilient, Vulnerable, and Control. The Resilient group required Risky Family Questionnaire (RFQ) scores ≥ 29 and Brief Resilience Scale (BRS) scores ≥ 3.6. The Vulnerable group required RFQ scores ≥ 29 and BRS scores ≤ 3. The comparison Control group required RFQ scores ≤ 21 and T-scores < 60 on PROMIS anxiety and depression symptoms. Mixed-effects models were used to test the unique associations of perceived stress, negative affect, and positive affect x group interactions (predictors) on diurnal cortisol slope (outcome) across 14 consecutive days. The Resilient group did not moderate the associations between daily stress or affect on cortisol diurnal slope. Instead, both the Resilient and Vulnerable groups with early family risk, showed a steeper diurnal slope unique to higher stress and a flatter slope unique to higher negative affect. Results suggest that riskier early family life was significantly associated with altered cortisol diurnal slope outcomes to stress (i.e., demand) and negative affect (i.e., distress). These associations were not attenuated by current resilience capacity.
External validation of deep learning-based bone-age software: a preliminary study with real world data
Authors: Lea Winnah Wu-in , Hong Suk-Joo , Nam Hyo-Kyoung , Kang Woo-Young , Yang Ze-Pa , Noh Eun-Jin 
Published: January 2022

AbstractArtificial intelligence (AI) is increasingly being used in bone-age (BA) assessment due to its complicated and lengthy nature. We aimed to evaluate the clinical performance of a commercially available deep learning (DL)–based software for BA assessment using a real-world data. From Nov. 2018 to Feb. 2019, 474 children (35 boys, 439 girls, age 4–17 years) were enrolled. We compared the BA estimated by DL software (DL-BA) with that independently estimated by 3 reviewers (R1: Musculoskeletal radiologist, R2: Radiology resident, R3: Pediatric endocrinologist) using the traditional Greulich–Pyle atlas, then to his/her chronological age (CA). A paired t-test, Pearson’s correlation coefficient, Bland–Altman plot, mean absolute error (MAE) and root mean square error (RMSE) were used for the statistical analysis. The intraclass correlation coefficient (ICC) was used for inter-rater variation. There were significant differences between DL-BA and each reviewer’s BA (P < 0.025), but the correlation was good with one another (r = 0.983, P < 0.025). RMSE (MAE) values were 10.09 (7.21), 10.76 (7.88) and 13.06 (10.06) months between DL-BA and R1, R2, R3 BA. Compared with the CA, RMSE (MAE) values were 13.54 (11.06), 15.18 (12.11), 16.19 (12.78) and 19.53 (17.71) months for DL-BA, R1, R2, R3 BA, respectively. Bland–Altman plots revealed the software and reviewers’ tendency to overestimate the BA in general. ICC values between 3 reviewers were 0.97, 0.85 and 0.86, and the overall ICC value was 0.93. The BA estimated by DL-based software showed statistically similar, or even better performance than that of reviewers’ compared to the chronological age in the real world clinic.
Successful pseudopregnancy of rats by short period artificial stimulation using sonic vibration
Authors: Endo Marina , Tsunoda Shigemi , Tawara Hirosuke , Abe Hisayuki , Kaneko Takehito 
Published: January 2022

AbstractPsuedopregnancy for embryo transfer (ET) is usually induced in rats by mating with vasectomized males. Previously, we successfully induced pseudopregnancy using sonic vibration instead (Easy-ET method). The transferred embryos developed normally. Conventionally, stimulation is performed 7 × 30 s with 5 min intervals at the day before ET. However, this protocol is time-consuming because it imitates natural mating behavior. Here, we investigated pseudopregnancy induction with shorter stimulation times. Stimulation was performed 2 × 30 s, with 30 s intervals at the proestrus stage at the day before ET. Of the transferred pronuclear or two-cell embryos, 43% or 62% developed normally, respectively. Furthermore, 67% or 68% of transferred pronuclear or two-cell embryos in rats at estrus stage stimulated on the day of ET developed normally, respectively. Pseudopregnancy was successfully induced with shorter stimulation. Furthermore, this protocol may be used to perform a single-day stimulation and ET operation at the estrus stage.
Joint rushing alters internal timekeeping in non-musicians and musicians
Authors: Wolf Thomas , Knoblich Günther 
Published: January 2022

AbstractRecent studies have shown that people engaging in joint rhythmic activity unintentionally increase their tempo. The same tempo increase does not occur when the same rhythmic activity is performed alone. This phenomenon is known as joint rushing. In two experiments, we investigated whether joint rushing is caused by correction mechanisms that facilitate sensorimotor synchronization. Because such correction mechanisms require perceptual input, joint rushing should discontinue when auditory feedback in a joint rhythmic activity is interrupted. This prediction was clearly supported in two experiments, one with musicians and one with non-musicians. Surprisingly, there was no indication that the amount of joint rushing differed between musicians and non-musicians. Furthermore, neither musicians nor non-musicians were able to return to the initially instructed tempo after feedback had been interrupted. This result indicates that joint rushing has a lasting effect on an internal timekeeper. An important question for future research is whether joint rushing is only a dysfunctional side effect of the way sensorimotor synchronization works or whether it has a function in enabling precise temporal coordination between different individuals.
Behavioral coping phenotypes and associated psychosocial outcomes of pregnant and postpartum women during the COVID-19 pandemic
Authors: Werchan Denise M. , Hendrix Cassandra L. , Ablow Jennifer C. , Amstadter Ananda B. , Austin Autumn C. , Babineau Vanessa , Anne Bogat G. , Cioffredi Leigh-Anne , Conradt Elisabeth , Crowell Sheila E. , Dumitriu Dani , Fifer William , Firestein Morgan R. , Gao Wei , Gotlib Ian H. , Graham Alice M. , Gregory Kimberly D. , Gustafsson Hanna C. , Havens Kathryn L. , Howell Brittany R. , Humphreys Kathryn L. , King Lucy S. , Kinser Patricia A. , Krans Elizabeth E. , Lenniger Carly , Levendosky Alytia A. , Lonstein Joseph S. , Marcus Rachel , Monk Catherine , Moyer Sara , Muzik Maria , Nuttall Amy K. , Potter Alexandra S. , Salisbury Amy , Shuffrey Lauren C. , Smith Beth A. , Smith Lynne , Sullivan Elinor L. , Zhou Judy , Thomason Moriah E. , Brito Natalie H. 
Published: January 2022

AbstractThe impact of COVID-19-related stress on perinatal women is of heightened public health concern given the established intergenerational impact of maternal stress-exposure on infants and fetuses. There is urgent need to characterize the coping styles associated with adverse psychosocial outcomes in perinatal women during the COVID-19 pandemic to help mitigate the potential for lasting sequelae on both mothers and infants. This study uses a data-driven approach to identify the patterns of behavioral coping strategies that associate with maternal psychosocial distress during the COVID-19 pandemic in a large multicenter sample of pregnant women (N = 2876) and postpartum women (N = 1536). Data was collected from 9 states across the United States from March to October 2020. Women reported behaviors they were engaging in to manage pandemic-related stress, symptoms of depression, anxiety and global psychological distress, as well as changes in energy levels, sleep quality and stress levels. Using latent profile analysis, we identified four behavioral phenotypes of coping strategies. Critically, phenotypes with high levels of passive coping strategies (increased screen time, social media, and intake of comfort foods) were associated with elevated symptoms of depression, anxiety, and global psychological distress, as well as worsening stress and energy levels, relative to other coping phenotypes. In contrast, phenotypes with high levels of active coping strategies (social support, and self-care) were associated with greater resiliency relative to other phenotypes. The identification of these widespread coping phenotypes reveals novel behavioral patterns associated with risk and resiliency to pandemic-related stress in perinatal women. These findings may contribute to early identification of women at risk for poor long-term outcomes and indicate malleable targets for interventions aimed at mitigating lasting sequelae on women and children during the COVID-19 pandemic.
Multicentre study on the reproducibility of MALDI-TOF MS for nontuberculous mycobacteria identification
Authors: Rodriguez-Temporal David , Alcaide Fernando , Mareković Ivana , O’Connor James Anthony , Gorton Rebecca , van Ingen Jakko , Van den Bossche An , Héry-Arnaud Genevieve , Beauruelle Clémence , Orth-Höller Dorothea , Palacios-Gutiérrez Juan-José , Tudó Griselda , Bou Germán , Ceyssens Pieter-Jan , Garrigó Montserrat , González-Martin Julià , Greub Gilbert , Hrabak Jaroslav , Ingebretsen André , Mediavilla-Gradolph Maria Concepción , Oviaño Marina , Palop Begoña , Pranada Arthur B. , Quiroga Lidia , Ruiz-Serrano Maria Jesús , Rodríguez-Sánchez Belén 
Published: January 2022

AbstractThe ability of MALDI-TOF for the identification of nontuberculous mycobacteria (NTM) has improved recently thanks to updated databases and optimized protein extraction procedures. Few multicentre studies on the reproducibility of MALDI-TOF have been performed so far, none on mycobacteria. The aim of this study was to evaluate the reproducibility of MALDI-TOF for the identification of NTM in 15 laboratories in 9 European countries. A total of 98 NTM clinical isolates were grown on Löwenstein-Jensen. Biomass was collected in tubes with water and ethanol, anonymized and sent out to the 15 participating laboratories. Isolates were identified using MALDI Biotyper (Bruker Daltonics). Up to 1330 MALDI-TOF identifications were collected in the study. A score ≥ 1.6 was obtained for 100% of isolates in 5 laboratories (68.2–98.6% in the other). Species-level identification provided by MALDI-TOF was 100% correct in 8 centres and 100% correct to complex-level in 12 laboratories. In most cases, the misidentifications obtained were associated with closely related species. The variability observed for a few isolates could be due to variations in the protein extraction procedure or to MALDI-TOF system status in each centre. In conclusion, MALDI-TOF showed to be a highly reproducible method and suitable for its implementation for NTM identification.
The structure of a novel antibody against the spike protein inhibits Middle East respiratory syndrome coronavirus infections
Authors: Jang Tae-Ho , Park Woo-Jung , Lee Hansaem , Woo Hye-Min , Lee So-young , Kim Kyung-Chang , Kim Sung Soon , Hong Eunmi , Song Jaeyoung , Lee Joo-Yeon 
Published: January 2022

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus, responsible for outbreaks of a severe respiratory illness in humans with a fatality rate of 30%. Currently, there are no vaccines or United States food and drug administration (FDA)-approved therapeutics for humans. The spike protein displayed on the surface of MERS-CoV functions in the attachment and fusion of virions to host cellular membranes and is the target of the host antibody response. Here, we provide a molecular method for neutralizing MERS-CoV through potent antibody-mediated targeting of the receptor-binding subdomain (RBD) of the spike protein. The structural characterization of the neutralizing antibody (KNIH90-F1) complexed with RBD using X-ray crystallography revealed three critical epitopes (D509, R511, and E513) in the RBD region of the spike protein. Further investigation of MERS-CoV mutants that escaped neutralization by the antibody supported the identification of these epitopes in the RBD region. The neutralizing activity of this antibody is solely provided by these specific molecular structures. This work should contribute to the development of vaccines or therapeutic antibodies for MERS-CoV.
Construction and validation of a novel gene signature for predicting the prognosis of osteosarcoma
Authors: Yang Jinpo , Zhang Anran , Luo Huan , Ma Chao 
Published: January 2022

AbstractOsteosarcoma (OS) is the most common type of primary malignant bone tumor. The high-throughput sequencing technology has shown potential abilities to illuminate the pathogenic genes in OS. This study was designed to find a powerful gene signature that can predict clinical outcomes. We selected OS cases with gene expression and survival data in the TARGET-OS dataset and GSE21257 datasets as training cohort and validation cohort, respectively. The univariate Cox regression and Kaplan–Meier analysis were conducted to determine potential prognostic genes from the training cohort. These potential prognostic genes underwent a LASSO regression, which then generated a gene signature. The harvested signature’s predictive ability was further examined by the Kaplan–Meier analysis, Cox analysis, and receiver operating characteristic (ROC curve). More importantly, we listed similar studies in the most recent year and compared theirs with ours. Finally, we performed functional annotation, immune relevant signature correlation identification, and immune infiltrating analysis to better study he functional mechanism of the signature and the immune cells’ roles in the gene signature’s prognosis ability. A seventeen-gene signature (UBE2L3, PLD3, SLC45A4, CLTC, CTNNBIP1, FBXL5, MKL2, SELPLG, C3orf14, WDR53, ZFP90, UHRF2, ARX, CORT, DDX26B, MYC, and SLC16A3) was generated from the LASSO regression. The signature was then confirmed having strong and stable prognostic capacity in all studied cohorts by several statistical methods. We revealed the superiority of our signature after comparing it to our predecessors, and the GO and KEGG annotations uncovered the specifically mechanism of action related to the gene signature. Six immune signatures, includingPRF1, CD8A, HAVCR2, LAG3, CD274,andGZMAwere identified associating with our signature. The immune-infiltrating analysis recognized the vital roles of T cells CD8 and Mast cells activated, which potentially support the seventeen-gene signature’s prognosis ability. We identified a robust seventeen-gene signature that can accurately predict OS prognosis. We identified potential immunotherapy targets to the gene signature. The T cells CD8 and Mast cells activated were identified linked with the seventeen-gene signature predictive power.
Time-efficient fabrication method for 3D-printed microfluidic devices
Authors: Jin Yan , Xiong Peng , Xu Tongyu , Wang Jingyi 
Published: January 2022

AbstractRecent developments in 3D-printing technology have provided a time-efficient and inexpensive alternative to the fabrication of microfluidic devices. At present, 3D-printed microfluidic systems face the challenges of post-processing, non-transparency, and being time consuming, limiting their practical application. In this study, a time-efficient and inexpensive fabrication method was developed for 3D-printed microfluidic devices. The material for 3D-printed microfluidic chips is Dowsil 732, which is used as a sealant or encapsulant in various industries. The curing time and surface hydrophobicity of the materials were evaluated. The results indicated that the surface of Dowsil 732 is hydrophilic. An optimization model of the direct ink writing method is proposed to establish a time-efficient and accurate fabrication method for microfluidic devices. The results indicate that the optimization model can effectively describe the change trend between printing speed, printing pressure, and channel wall accuracy, and the model accuracy rate exceeds 95%. Three examples—a micromixer, concentration gradient generator, and droplet generator—were printed to demonstrate the functionality and feasibility of the fabrication method.
M-CSF supports medullary erythropoiesis and erythroid iron demand following burn injury through its activity on homeostatic iron recycling
Authors: Noel John G. , Ramser Seth W. , Pitstick Lori , Bonamer John P. , Mackenzie Bryan , Seu Katie G. , Kalfa Theodosia A. , Cancelas Jose A. , Gardner Jason C. 
Published: January 2022

AbstractM-CSF receptor signaling supports the development and survival of mononuclear phagocytes and is thought to play a role in post burn anemia by promoting myeloid lineage bias. We found M-CSF secretion was increased in burn patients and a murine model of post burn ACI, so we neutralized M-CSF in ACI mice to determine if erythropoiesis was improved. Instead, M-CSF blockade further impaired erythropoiesis and erythroid cells access to iron. M-CSF blockade enhanced inflammatory cytokine secretion, further increased systemic neutrophil counts, and led to tissue iron sequestration that was dependent, in part, on augmented IL-6 secretion which induced hepcidin. Deleterious effects of post burn M-CSF blockade were associated with arrest of an iron recycling gene expression signature in the liver and spleen that included Spi-C transcription factor and heme oxygenase-1, which promote heme metabolism and confer a non-inflammatory tone in macrophages. Hepatic induction of these factors in ACI mice was consistent with a recovery of ferroportin gene expression and reflected an M-CSF dependent expansion and differentiation of Spi-C+ monocytes into Kupffer cells. Together, this data indicates M-CSF secretion supports a homeostatic iron recycling program that plays a key role in the maintenance of erythroid cells access to iron following burn injury.