bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple carbon cycle mechanisms associated with the glaciation of Marine Isotope Stage 4
Authors: Menking James A. , Shackleton Sarah A. , Bauska Thomas K. , Buffen Aron M. , Brook Edward J. , Barker Stephen , Severinghaus Jeffrey P. , Dyonisius Michael N. , Petrenko Vasilii V. 
Published: September 2022

AbstractHere we use high-precision carbon isotope data (δ13C-CO2) to show atmospheric CO2 during Marine Isotope Stage 4 (MIS 4, ~70.5-59 ka) was controlled by a succession of millennial-scale processes. Enriched δ13C-CO2 during peak glaciation suggests increased ocean carbon storage. Variations in δ13C-CO2 in early MIS 4 suggest multiple processes were active during CO2 drawdown, potentially including decreased land carbon and decreased Southern Ocean air-sea gas exchange superposed on increased ocean carbon storage. CO2 remained low during MIS 4 while δ13C-CO2 fluctuations suggest changes in Southern Ocean and North Atlantic air-sea gas exchange. A 7 ppm increase in CO2 at the onset of Dansgaard-Oeschger event 19 (72.1 ka) and 27 ppm increase in CO2 during late MIS 4 (Heinrich Stadial 6, ~63.5-60 ka) involved additions of isotopically light carbon to the atmosphere. The terrestrial biosphere and Southern Ocean air-sea gas exchange are possible sources, with the latter event also involving decreased ocean carbon storage.
Molecular architecture of the augmin complex
Authors: Gabel Clinton A. , Li Zhuang , DeMarco Andrew G. , Zhang Ziguo , Yang Jing , Hall Mark C. , Barford David , Chang Leifu 
Published: September 2022

AbstractAccurate segregation of chromosomes during mitosis depends on the correct assembly of the mitotic spindle, a bipolar structure composed mainly of microtubules. The augmin complex, or homologous to augmin subunits (HAUS) complex, is an eight-subunit protein complex required for building robust mitotic spindles in metazoa. Augmin increases microtubule density within the spindle by recruiting the γ-tubulin ring complex (γ-TuRC) to pre-existing microtubules and nucleating branching microtubules. Here, we elucidate the molecular architecture of augmin by single particle cryo-electron microscopy (cryo-EM), computational methods, and crosslinking mass spectrometry (CLMS). Augmin’s highly flexible structure contains a V-shaped head and a filamentous tail, with the head existing in either extended or contracted conformational states. Our work highlights how cryo-EM, complemented by computational advances and CLMS, can elucidate the structure of a challenging protein complex and provides insights into the function of augmin in mediating microtubule branching nucleation.
Electrical switching of spin-polarized current in multiferroic tunneling junctions
Authors: Zhang Ligong , Wang Yuchen , Liu Xiaoyan , Liu Fei 
Published: September 2022

AbstractThe generation and manipulation of spin-polarized current are critical for spintronic devices. In this work, we propose a mechanism to generate and switch spin-polarized current by an electric field in multiferroic tunnel junctions (MFTJs), with symmetric interface terminations in an antiparallel magnetic state. In such devices, different spin tunneling barriers are realized by the magnetoelectric coupling effect, resulting in a spin-polarized current. By reversing the electric polarization of the ferroelectric layer, the spin polarization of current is efficiently switched for the exchange of spin tunneling barriers. By first-principles quantum transport calculations, we show that a highly spin-polarized current is obtained and manipulated by the electric field in hafnia-based MFTJs based on the proposed mechanism. We also demonstrate that four resistance states are realized in Co/HfO2/Co junctions with asymmetric interface terminations. This work provides a promising approach for realizing the electrical control of spin current for spintronic applications.
The synovial microenvironment suppresses chondrocyte hypertrophy and promotes articular chondrocyte differentiation
Authors: Chau Michael , Dou Zelong , Baroncelli Marta , Landman Ellie B. , Bendre Ameya , Kanekiyo Masaru , Gkourogianni Alexandra , Barnes Kevin , Ottosson Lars , Nilsson Ola 
Published: September 2022

AbstractDuring the development of the appendicular skeleton, the cartilaginous templates undergo hypertrophic differentiation and remodels into bone, except for the cartilage most adjacent to joint cavities where hypertrophic differentiation and endochondral bone formation are prevented, and chondrocytes instead form articular cartilage. The mechanisms that prevent hypertrophic differentiation and endochondral bone formation of the articular cartilage have not been elucidated. To explore the role of the synovial microenvironment in chondrocyte differentiation, osteochondral allografts consisting of articular cartilage, epiphyseal bone, and growth plate cartilage from distal femoral epiphyses of inbred Lewis rats expressing enhanced green fluorescent protein from a ubiquitous promoter were transplanted either in inverted or original (control) orientation to matching sites in wildtype littermates, thereby allowing for tracing of transplanted cells and their progenies. We found that no hypertrophic differentiation occurred in the growth plate cartilage ectopically placed at the joint surface. Instead, the transplanted growth plate cartilage, with time, remodeled into articular cartilage. This finding suggests that the microenvironment at the articular surface inhibits hypertrophic differentiation and supports articular cartilage formation. To explore this hypothesis, rat chondrocyte pellets were cultured with and without synoviocyte-conditioned media. Consistent with the hypothesis, hypertrophic differentiation was inhibited and expression of the articular surface marker lubricin (Prg4) was dramatically induced when chondrocyte pellets were exposed to synovium- or synoviocyte-conditioned media, but not to chondrocyte- or osteoblast-conditioned media. Taken together, we present evidence for a novel mechanism by which synoviocytes, through the secretion of a factor or factors, act directly on chondrocytes to inhibit hypertrophic differentiation and endochondral bone formation and promote articular cartilage formation. This mechanism may have important implications for articular cartilage development, maintenance, and regeneration.
Discovery, isolation, heterologous expression and mode-of-action studies of the antibiotic polyketide tatiomicin from Amycolatopsis sp. DEM30355
Authors: Kepplinger Bernhard , Mardiana Lina , Cowell Joseph , Morton-Laing Stephanie , Dashti Yousef , Wills Corinne , Marrs Emma C. L. , Perry John D. , Gray Joe , Goodfellow Michael , Errington Jeff , Probert Michael R. , Clegg William , Bogaerts Jonathan , Herrebout Wouter , Allenby Nick E. E. , Hall Michael J. 
Published: September 2022

AbstractA genomic and bioactivity informed analysis of the metabolome of the extremophile Amycolatopsis sp. DEM30355 has allowed for the discovery and isolation of the polyketide antibiotic tatiomicin. Identification of the biosynthetic gene cluster was confirmed by heterologous expression in Streptomyces coelicolor M1152. Structural elucidation, including absolute stereochemical assignment, was performed using complementary crystallographic, spectroscopic and computational methods. Tatiomicin shows antibiotic activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Cytological profiling experiments suggest a putative antibiotic mode-of-action, involving membrane depolarisation and chromosomal decondensation of the target bacteria.
Synthesis of a nitrogen doped reduced graphene oxide based ceramic polymer composite nanofiber film for wearable device applications
Authors: Ji Jae-Hoon , Lee Gwangseop , Koh Jung-Hyuk 
Published: September 2022

AbstractIn this study, piezoelectric composite nanofiber films were fabricated by introducing nitrogen-doped-reduced-graphene-oxide as a conductive material to a P(VDF-TrFE) polymer and a BiScO3–PbTiO3 ceramic composite employing an electrospinning process. Nitrogen was doped/substituted into rGO to remove or compensate defects formed during the reduction process. Electro-spinning process was employed to extract piezoelectric composite nanofiber films under self-poling condition. Interdigital electrodes was employed to make planner type energy harvesters to collect electro-mechanical energy applied to the flexible energy harvester. From the piezoelectric composite with interdigital electrode, the effective dielectric permittivity extracted from the conformal mapping method. By introducing BS–PT ceramics and N-rGO conductors to the P(VDF-TrFE) piezoelectric composite nanofiber films, the effective dielectric permittivity was improved from 8.2 to 15.5. This improved effective dielectric constant probably come from the increased electric flux density due to the increased conductivity. Fabricated interdigital electrode using this thin composite nanofiber film was designed and tested for wearable device applications. An external mechanical force of 350 N was applied to the composite nanofiber-based energy harvester with interdigital electrodes at a rate of 0.6 Hz, the peak voltage and current were 13 V and 1.25 μA, respectively. By optimizing the device fabrication, the open-circuit voltage, stored voltage, and generated output power obtained were 12.4 V, 3.78 V, and 6.3 μW, respectively.
A novel factor graph-based optimization technique for stereo correspondence estimation
Authors: Shabanian Hanieh , Balasubramanian Madhusudhanan 
Published: September 2022

AbstractDense disparities among multiple views are essential for estimating the 3D architecture of a scene based on the geometrical relationship between the scene and the views or cameras. Scenes with larger extents of homogeneous textures, differing scene illumination among the multiple views and with occluding objects affect the accuracy of the estimated disparities. Markov random fields based methods for disparity estimation address these limitations using spatial dependencies among the observations and among the disparity estimates. These methods, however, are limited by spatially fixed and smaller neighborhood systems or cliques. Recent learning-based methods generate rich set of stereo features for generating cost volume and estimating disparity. In this work, we present a new factor graph-based probabilistic graphical model for disparity estimation that allows a larger and a spatially variable neighborhood structure determined based on the local scene characteristics. Our algorithm improves the accuracy of disparity estimates in stereo image pairs with varying texture and illumination characteristics by enforcing spatial dependencies among scene characteristics as well as among disparity estimates. We evaluated our method using theMiddlebury benchmark stereo datasetsand theMiddlebury evaluation dataset version 3.0and compared its performance with recent state-of-the-art disparity estimation algorithms. Our factor graph-based algorithm provided disparity estimates with higher accuracy when compared to the recent non-learning- and learning-based disparity estimation algorithms. The factor graph formulation can be used for obtainingmaximum a posterioriestimates from models or optimization problems with complex dependency structure among hidden variables. The strategies of using a priori distributions with shorter support and spatial dependencies were useful for reducing the computational cost and improving message convergence in the model. The factor-graph algorithm is also useful for other dense estimation problems such as optical flow estimation.
Impact of EFEMP1 on the survival outcome of biliary atresia in Thai infants
Authors: Laochareonsuk Wison , Kayasut Kanita , Surachat Komwit , Chiengkriwate Piyawan , Sangkhathat Surasak 
Published: September 2022

AbstractGenome-wide association studies (GWASs) have identified a genetic associated between EFEMP1 and biliary atresia (BA). To examine the susceptibility of single nucleotide polymorphisms (SNPs) in EFEMP1 in Thai BA patients, we performed an analysis of the genetic associations and biological interactions with previously reported key SNPs in ADD3, a key gene associated with BA. The study also used high-throughput sequencing to detect novel variants in both genes. In addition, the clinical impact of EFEMP1 SNPs in terms of survival association was also evaluated. The genotypes of 60 BA patients and 179 controls were evaluated using a TaqMan genotyping assay for rs2501577 and rs17095355 in ADD3 and rs6761893 and rs727878 in EFEMP1. The genotype frequencies were analyzed together with the SNP-SNP interactions. Fine mapping by whole-exome sequencing was performed to identify deleterious variants within both genes, and the survival analysis results were analyzed with the EFEMP1 SNPs. The recessive genotypes of rs2501577, rs17095355 and rs6761893 showed significantly higher frequencies in the BA patients than the controls, and a logistic regression showed that minor alleles of those SNPs increased the BA risk by ORs of 1.86, 1.67, and 1.84, respectively. Moreover, the SNP-SNP interference suggested that a combination of recessive alleles from the 2 genes resulted in an additive risk to BA. In addition, rare missense variants in the gene coding sequences were identified in 7 cases. Immunohistochemical studies revealed a pattern of ADD3 downregulation and EFEMP1 overexpression in the bile ducts of BA patients. Patients with the AA genotype of rs6761893 had significantly lower 5-year native liver survival (34.0%) than those with AT/TT (75.0%), with a log-rank p value of 0.041. Variants in EFEMP1 are associated with the occurrence of BA in Thai patients. In addition, these variants have an additive influence on BA risk when combined with ADD3 variants. Moreover, rs6761893 in EFEMP1 was indicative of survival in Thai BA patients.
Population-based screening to detect benzodiazepine drug-drug-drug interaction signals associated with unintentional traumatic injury
Authors: Chen Cheng , Hennessy Sean , Brensinger Colleen M. , Acton Emily K. , Bilker Warren B. , Chung Sophie P. , Dawwas Ghadeer K. , Horn John R. , Miano Todd A. , Pham Nguyen Thanh Phuong , Leonard Charles E. 
Published: September 2022

AbstractDrug interactions involving benzodiazepines and related drugs (BZDs) are increasingly recognized as a contributor to increased risk of unintentional traumatic injury. Yet, it remains unknown to what extent drug interaction triads (3DIs) may amplify BZDs’ inherent injury risk. We identified BZD 3DI signals associated with increased injury rates by conducting high-throughput pharmacoepidemiologic screening of 2000–2019 Optum’s health insurance data. Using self-controlled case series design, we included patients aged ≥ 16 years with an injury while using a BZD + co-dispensed medication (i.e., base pair). During base pair-exposed observation time, we identified other co-dispensed medications as candidate interacting precipitants. Within each patient, we compared injury rates during time exposed to the drug triad versus to the base pair only using conditional Poisson regression, adjusting for time-varying covariates. We calculated rate ratios (RRs) with 95% confidence intervals (CIs) and accounted for multiple estimation via semi-Bayes shrinkage. Among the 65,123 BZD triads examined, 79 (0.1%) were associated with increased injury rates and considered 3DI signals. Adjusted RRs for signals ranged from 3.01 (95% CI = 1.53–5.94) for clonazepam + atorvastatin with cefuroxime to 1.42 (95% CI = 1.00–2.02, p = 0.049) for alprazolam + hydrocodone with tizanidine. These signals may help researchers prioritize future etiologic studies to investigate higher-order BZD interactions.
The marine natural product mimic MPM-1 is cytolytic and induces DAMP release from human cancer cell lines
Authors: von Hofsten Susannah , Paulsen Marianne Hagensen , Magnussen Synnøve Norvoll , Ausbacher Dominik , Kranz Mathias , Bayer Annette , Strøm Morten B. , Berge Gerd 
Published: September 2022

AbstractBioprospecting contributes to the discovery of new molecules with anticancer properties. Compounds with cytolytic activity and the ability to induce immunogenic cell death can be administered as intratumoral injections with the aim to activate anti-tumor immune responses by causing the release of tumor antigens as well as damage-associated molecular patterns (DAMPs) from dying cancer cells. In the present study, we report the cytolytic and DAMP-releasing effects of a new natural product mimic termed MPM-1 that was inspired by the marine Eusynstyelamides. We found that MPM-1 rapidly killed cancer cells in vitro by inducing a necrosis-like death, which was accompanied by lysosomal swelling and perturbation of autophagy in HSC-3 (human oral squamous cell carcinoma) cells. MPM-1 also induced release of the DAMPs adenosine triphosphate (ATP) and high mobility group box 1 (HMGB1) from Ramos (B-cell lymphoma) and HSC-3 cells, as well as cell surface expression of calreticulin in HSC-3 cells. This indicates that MPM-1 has the ability to induce immunogenic cell death, further suggesting that it may have potential as a novel anticancer compound.
Modeling of the combined dynamics of leptospirosis transmission and seroconversion in herds
Authors: Chadsuthi Sudarat , Chalvet-Monfray Karine , Kodjo Angeli , Wiratsudakul Anuwat , Bicout Dominique J. 
Published: September 2022

AbstractLeptospirosis is a zoonotic disease-causing illness in both humans and animals resulting in related economic impacts due to production loss as well as prevention and control efforts. Several mathematical models have been proposed to study the dynamics of infection but none of them has so far taken into account the dynamics of seroconversion. In this study, we have developed a general framework, based on the kinetic model for animal leptospirosis, that combines both the antibody (exposure marker) and infection dynamics to simultaneously follows both seroconversion and infection status of leptospirosis in a herd population. It is a stochastic compartmental model (for transition rates) with time delay (for seroconversion) which describes the progression of infection by a SEIRS (susceptible, exposed, infected, removed and susceptible) approach and seroconversion by four-state antibody kinetics (antibody negative and three antibody positive states of different antibody levels). The model shows that it is possible to assess and follow both seroconversion and infection status through the prism of diagnostic testing. Such an approach of combined kinetics could prove very useful to assist the competent authorities in their analyzes of epidemic situations and in the implementation of strategies for controlling and managing the associated risks.
Bos taurus (A-2) urine assisted bioactive cobalt oxide anchored ZnO: a novel nanoscale approach
Authors: Karvekar Omkar S. , Vadanagekar Apurva S. , Sarvalkar Prashant D. , Suryawanshi Suresh S. , Jadhav Sarita M. , Singhan Richa D. , Jadhav Jyoti P. , Sharma Kiran Kumar K. , Prasad Neeraj R. 
Published: September 2022

AbstractIn this study, a novel synthetic method for cobalt oxide (Co3O4) nanoparticles using Bos taurus (A-2) urine as a reducing agent was developed. In addition to this ZnO nanorods were produced hydrothermally and a nanocomposite is formed through a solid-state reaction. The synthesized materials were characterized through modern characterization techniques such as XRD, FE-SEM with EDS, DLS, zeta potential, FT-IR, Raman spectroscopic analysis, and TGA with DSC. The free radical destructive activity was determined using two different methods viz. ABTS and DPPH. The potential for BSA denaturation in vitro, which is measured in comparison to heat-induced denaturation of egg albumin and results in anti-inflammatory effects of nanomaterial was studied. All synthesized nanomaterials have excellent antibacterial properties, particularly against Salmonella typhi and Staphylococcus aureus. The composite exhibits excellent antioxidant and anti-inflammatory activities in comparison to pure nanomaterials. This reveals that these nanomaterials are advantageous in medicine and drug administration.
Validity of age estimation methods and reproducibility of bone/dental maturity indices for chronological age estimation: a systematic review and meta-analysis of validation studies
Authors: Marconi V. , Iommi M. , Monachesi C. , Faragalli A. , Skrami E. , Gesuita R. , Ferrante L. , Carle F. 
Published: September 2022

AbstractSeveral approaches have been developed to estimate age, an important aspect of forensics and orthodontics, using different measures and radiological examinations. Here, through meta-analysis, we determined the validity of age estimation methods and reproducibility of bone/dental maturity indices used for age estimation. The PubMed and Google Scholar databases were searched to December 31, 2021 for human cross-sectional studies meeting pre-defined PICOS criteria that simultaneously assessed the reproducibility and validity. Meta-estimates of validity (mean error: estimated age-chronological age) and intra- and inter-observer reproducibility (Cohen’s kappa, intraclass correlation coefficient) and their predictive intervals (PI) were calculated using mixed-effect models when heterogeneity was high (I2 > 50%). The literature search identified 433 studies, and 23 met the inclusion criteria. The mean error meta-estimate (mixed effects model) was 0.08 years (95% CI − 0.12; 0.29) in males and 0.09 (95% CI − 0.12; 0.30) in females. The PI of each method spanned zero; of nine reported estimation methods, Cameriere’s had the smallest (− 0.82; 0.47) and Haavikko’s the largest (− 7.24; 4.57) PI. The reproducibility meta-estimate (fixed effects model) was 0.98 (95% CI 0.97; 1.00) for intra- and 0.99 (95% CI 0.98; 1.00) for inter-observer agreement. All methods were valid but with different levels of precision. The intra- and inter-observer reproducibility was high and homogeneous across studies.
Prediction of drug-drug interaction events using graph neural networks based feature extraction
Authors: Al-Rabeah Mohammad Hussain , Lakizadeh Amir 
Published: September 2022

AbstractThe prevalence of multi_drug therapies has been increasing in recent years, particularly among the elderly who are suffering from several diseases. However, unexpected Drug_Drug interaction (DDI) can cause adverse reactions or critical toxicity, which puts patients in danger. As the need for multi_drug treatment increases, it's becoming increasingly necessary to discover DDIs. Nevertheless, DDIs detection in an extensive number of drug pairs, both in-vitro and in-vivo, is costly and laborious. Therefore, DDI identification is one of the most concerns in drug-related researches. In this paper, we propose GNN-DDI, a deep learning-based method for predicting DDI-associated events in two stages. In the first stage, we collect the drugs information from different sources and then integrate them through the formation of an attributed heterogeneous network and generate a drug embedding vector based on different drug interaction types and drug attributes. In the second stage, we aggregate the representation vectors then predictions of the DDIs and their events are performed through a deep multi-model framework. Various evaluation results show that the proposed method can outperform state-of-the methods in the prediction of drug-drug interaction-associated events. The experimental results indicate that producing the drug's representations based on different drug interaction types and attributes is efficient and effective and can better show the intrinsic characteristics of a drug.