bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biallelic loss of BCMA as a resistance mechanism to CAR T cell therapy in a patient with multiple myeloma
Authors: Samur Mehmet Kemal , Fulciniti Mariateresa , Aktas Samur Anil , Bazarbachi Abdul Hamid , Tai Yu-Tzu , Prabhala Rao , Alonso Alejandro , Sperling Adam S. , Campbell Timothy , Petrocca Fabio , Hege Kristen , Kaiser Shari , Loiseau Hervé Avet , Anderson Kenneth C. , Munshi Nikhil C. 
Published: February 2021

AbstractBCMA targeting chimeric antigen receptor (CAR) T cell therapy has shown deep and durable responses in multiple myeloma. However, relapse following therapy is frequently observed, and mechanisms of resistance remain ill-defined. Here, we perform single cell genomic characterization of longitudinal samples from a patient who relapsed after initial CAR T cell treatment with lack of response to retreatment. We report selection, following initial CAR T cell infusion, of a clone with biallelic loss of BCMA acquired by deletion of one allele and a mutation that creates an early stop codon on the second allele. This loss leads to lack of CAR T cell proliferation following the second infusion and is reflected by lack of soluble BCMA in patient serum. Our analysis suggests the need for careful detection of BCMA gene alterations in multiple myeloma cells from relapse following CAR T cell therapy.
Engineering fast high-fidelity quantum operations with constrained interactions
Authors: Figueiredo Roque T. , Clerk Aashish A. , Ribeiro Hugo 
Published: February 2021

AbstractUnderstanding how to tailor quantum dynamics to achieve the desired evolution is a crucial problem in almost all quantum technologies. Oftentimes an otherwise ideal quantum dynamics is corrupted by unavoidable interactions, and finding ways to mitigate the unwanted effects of such interactions on the dynamics is a very active field of research. Here, we present a very general method for designing high-efficiency control sequences that are fully compatible with experimental constraints on available interactions and their tunability. Our approach relies on the Magnus expansion to find order by order the necessary corrections that result in a high-fidelity operation. In the end finding, the control fields are reduced to solve a set of linear equations. We illustrate our method by applying it to a number of physically relevant problems: the strong-driving limit of a two-level system, fast squeezing in a parametrically driven cavity, the leakage problem in transmon qubit gates, and the acceleration of SNAP gates in a qubit-cavity system.
Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials
Authors: Saarimäki Laura Aliisa , Federico Antonio , Lynch Iseult , Papadiamantis Anastasios G. , Tsoumanis Andreas , Melagraki Georgia , Afantitis Antreas , Serra Angela , Greco Dario 
Published: February 2021

AbstractToxicogenomics (TGx) approaches are increasingly applied to gain insight into the possible toxicity mechanisms of engineered nanomaterials (ENMs). Omics data can be valuable to elucidate the mechanism of action of chemicals and to develop predictive models in toxicology. While vast amounts of transcriptomics data from ENM exposures have already been accumulated, a unified, easily accessible and reusable collection of transcriptomics data for ENMs is currently lacking. In an attempt to improve the FAIRness of already existing transcriptomics data for ENMs, we curated a collection of homogenized transcriptomics data from human, mouse and rat ENM exposures in vitro and in vivo including the physicochemical characteristics of the ENMs used in each study.
Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing
Authors: Valliyodan Babu , Brown Anne V. , Wang Juexin , Patil Gunvant , Liu Yang , Otyama Paul I. , Nelson Rex T. , Vuong Tri , Song Qijian , Musket Theresa A. , Wagner Ruth , Marri Pradeep , Reddy Sam , Sessions Allen , Wu Xiaolei , Grant David , Bayer Philipp E. , Roorkiwal Manish , Varshney Rajeev K. , Liu Xin , Edwards David , Xu Dong , Joshi Trupti , Cannon Steven B. , Nguyen Henry T. 
Published: February 2021

AbstractWe report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.
Dynamical visualization of anisotropic electromagnetic re-emissions from a single metal micro-helix at THz frequencies
Authors: Notake T. , Iyoda T. , Arikawa T. , Tanaka K. , Otani C. , Minamide H. 
Published: February 2021

AbstractThe capability for actual measurements—not just simulations—of the dynamical behavior of THz electromagnetic waves, including interactions with prevalent 3D objects, has become increasingly important not only for developments of various THz devices, but also for reliable evaluation of electromagnetic compatibility. We have obtained real-time visualizations of the spatial evolution of THz electromagnetic waves interacting with a single metal micro-helix. After the micro-helix is stimulated by a broadband pico-second pulse of THz electromagnetic waves, two types of anisotropic re-emissions can occur following overall inductive current oscillations in the micro-helix. They propagate in orthogonally crossed directions with different THz frequency spectra. This unique radiative feature can be very useful for the development of a smart antenna with broadband multiplexing/demultiplexing ability and directional adaptivity. In this way, we have demonstrated that our advanced measurement techniques can lead to the development of novel functional THz devices.
China’s city-level carbon emissions during 1992–2017 based on the inter-calibration of nighttime light data
Authors: Chen Jiandong , Gao Ming , Cheng Shulei , Liu Xin , Hou Wenxuan , Song Malin , Li Ding , Fan Wei 
Published: February 2021

AbstractAccurate, long-term, full-coverage carbon dioxide (CO2) data in units of prefecture-level cities are necessary for evaluations of CO2 emission reductions in China, which has become one of the world’s largest carbon-emitting countries. This study develops a novel method to match satellite-based Defense Meteorological Satellite Program’s Operational Landscan System (DMSP/OLS) and Suomi National Polar-orbiting Partnership’s Visible Infrared Imaging Radiometer Suite (NPP/VIIRS) nighttime light data, and estimates the CO2 emissions of 334 prefecture-level cities in China from 1992 to 2017. Results indicated that the eastern and coastal regions had higher carbon emissions, but their carbon intensity decreased more rapidly than other regions. Compared to previous studies, we provide the most extensive and long-term CO2 dataset to date, and these data will be of great value for further socioeconomic research. Specifically, this dataset provides a foundational data source for China’s future CO2 research and emission reduction strategies. Additionally, the methodology can be applied to other regions around the world.
Replication of HLA class II locus association with susceptibility to podoconiosis in three Ethiopian ethnic groups
Authors: Gebresilase Tewodros , Finan Chris , Suveges Daniel , Tessema Tesfaye Sisay , Aseffa Abraham , Davey Gail , Hatzikotoulas Konstantinos , Zeggini Eleftheria , Newport Melanie J. , Tekola-Ayele Fasil 
Published: February 2021

AbstractPodoconiosis, a debilitating lymphoedema of the leg, results from barefoot exposure to volcanic clay soil in genetically susceptible individuals. A previous genome-wide association study (GWAS) conducted in the Wolaita ethnic group from Ethiopia showed association between single nucleotide polymorphisms (SNPs) in the HLA class II region and podoconiosis. We aimed to conduct a second GWAS in a new sample (N = 1892) collected from the Wolaita and two other Ethiopian populations, the Amhara and the Oromo, also affected by podoconiosis. Fourteen SNPs in the HLA class II region showed significant genome-wide association (P < 5.0 × 10−8) with podoconiosis. The lead SNP was rs9270911 (P = 5.51 × 10−10; OR 1.53; 95% CI 1.34–1.74), located near HLA-DRB1. Inclusion of data from the first GWAS (combined N = 2289) identified 47 SNPs in the class II HLA region that were significantly associated with podoconiosis (lead SNP also rs9270911 (P = 2.25 × 10−12). No new loci outside of the HLA class II region were identified in this more highly-powered second GWAS. Our findings confirm the HLA class II association with podoconiosis suggesting HLA-mediated abnormal induction and regulation of immune responses may have a direct role in its pathogenesis.
High β-lactam resistance in Gram-negative bacteria associated with kennel cough and cat flu in Egypt
Authors: Khalifa Hazim O. , Oreiby Atef F. , Okanda Takashi , Kato Yasuyuki , Matsumoto Tetsuya 
Published: February 2021

AbstractAntimicrobial resistance within pets has gained worldwide attention due to pets close contact with humans. This report examined at the molecular level, the antimicrobial resistance mechanisms associated with kennel cough and cat flu. 1378 pets in total were assessed for signs of respiratory infection, and nasal and conjunctival swabs were collected across 76 diseased animals. Phenotypically, 27% of the isolates were characterized by multidrug resistance and possessed high levels of resistance rates to β-lactams. Phenotypic ESBLs/AmpCs production were identified within 40.5% and 24.3% of the isolates, respectively. Genotypically, ESBL- and AmpC-encoding genes were detected in 33.8% and 10.8% of the isolates, respectively, with blaSHV comprising the most identified ESBL, and blaCMY and blaACT present as the AmpC with the highest levels. qnr genes were identified in 64.9% of the isolates, with qnrS being the most prevalent (44.6%). Several antimicrobial resistance determinants were detected for the first time within pets from Africa, including blaCTX-M-37, blaCTX-M-156, blaSHV-11, blaACT-23, blaACT25/31, blaDHA-1, and blaCMY-169. Our results revealed that pets displaying symptoms of respiratory illness are potential sources for pathogenic microbes possessing unique resistance mechanisms which could be disseminated to humans, thus leading to the development of severe untreatable infections in these hosts.
Bioconvection flow in accelerated couple stress nanoparticles with activation energy: bio-fuel applications
Authors: Khan Sami Ullah , Al-Khaled Kamel , Aldabesh A. , Awais Muhammad , Tlili Iskander 
Published: February 2021

AbstractOn the account of significance of bioconvection in biotechnology and several biological systems, valuable contributions have been performed by scientists in current decade. In current framework, a theoretical bioconvection model is constituted to examine the analyzed the thermally developed magnetized couple stress nanoparticles flow by involving narrative flow characteristics namely activation energy, chemical reaction and radiation features. The accelerated flow is organized on the periodically porous stretched configuration. The heat performances are evaluated via famous Buongiorno’s model which successfully reflects the important features of thermophoretic and Brownian motion. The composed fluid model is based on the governing equations of momentum, energy, nanoparticles concentration and motile microorganisms. The dimensionless problem has been solved analytically via homotopic procedure where the convergence of results is carefully examined. The interesting graphical description for the distribution of velocity, heat transfer of nanoparticles, concentration pattern and gyrotactic microorganism significance are presented with relevant physical significance. The variation in wall shear stress is also graphically underlined which shows an interesting periodic oscillation near the flow domain. The numerical interpretation for examining the heat mass and motile density transfer rate is presented in tubular form.
BAX and SMAC regulate bistable properties of the apoptotic caspase system
Authors: McKenna Stephanie , García-Gutiérrez Lucía , Matallanas David , Fey Dirk 
Published: February 2021

AbstractThe initiation of apoptosis is a core mechanism in cellular biology by which organisms control the removal of damaged or unnecessary cells. The irreversible activation of caspases is essential for apoptosis, and mathematical models have demonstrated that the process is tightly regulated by positive feedback and a bistable switch. BAX and SMAC are often dysregulated in diseases such as cancer or neurodegeneration and are two key regulators that interact with the caspase system generating the apoptotic switch. Here we present a mathematical model of how BAX and SMAC control the apoptotic switch. Formulated as a system of ordinary differential equations, the model summarises experimental and computational evidence from the literature and incorporates the biochemical mechanisms of how BAX and SMAC interact with the components of the caspase system. Using simulations and bifurcation analysis, we find that both BAX and SMAC regulate the time-delay and activation threshold of the apoptotic switch. Interestingly, the model predicted that BAX (not SMAC) controls the amplitude of the apoptotic switch. Cell culture experiments using siRNA mediated BAX and SMAC knockdowns validated this model prediction. We further validated the model using data of the NCI-60 cell line panel using BAX protein expression as a cell-line specific parameter and show that model simulations correlated with the cellular response to DNA damaging drugs and established a defined threshold for caspase activation that could distinguish between sensitive and resistant melanoma cells. In summary, we present an experimentally validated dynamic model that summarises our current knowledge of how BAX and SMAC regulate the bistable properties of irreversible caspase activation during apoptosis.
Neuropeptide Y (NPY) intranasal delivery alleviates Machado–Joseph disease
Authors: Duarte-Neves Joana , Cavadas Cláudia , Pereira de Almeida Luís 
Published: February 2021

AbstractMachado–Joseph disease (MJD) is the most common dominantly-inherited ataxia worldwide with no effective treatment to prevent, stop or alleviate its progression. Neuropeptide Y (NPY) is a neuroprotective agent widely expressed in the mammalian brain. Our previous work showed that NPY overexpression mediated by stereotaxically-injected viral vectors mitigates motor deficits and neuropathology in MJD mouse models. To pursue a less invasive translational approach, we investigated whether intranasal administration of NPY would alleviate cerebellar neuropathology and motor and balance impairments in a severe MJD transgenic mouse model. For that, a NPY solution was administered into mice nostrils 5 days a week. Upon 8 weeks of treatment, we observed a mitigation of motor and balance impairments through the analysis of mice behavioral tests (rotarod, beam walking, pole and swimming tests). This was in line with a reduction of cerebellar pathology, evidenced by a preservation of cerebellar granular layer and of Purkinje cells and reduction of mutant ataxin-3 aggregate numbers. Furthermore, intranasal administration of NPY did not alter body weight gain, food intake, amount of body fat nor cholesterol or triglycerides levels. Our findings support the translational potential of intranasal infusion of NPY as a pharmacological intervention in MJD.
High probability of yield gain through conservation agriculture in dry regions for major staple crops
Authors: Su Yang , Gabrielle Benoit , Beillouin Damien , Makowski David 
Published: February 2021

AbstractConservation agriculture (CA) has been promoted to mitigate climate change, reduce soil erosion, and provide a variety of ecosystem services. Yet, its impacts on crop yields remains controversial. To gain further insight, we mapped the probability of yield gain when switching from conventional tillage systems (CT) to CA worldwide. Relative yield changes were estimated with machine learning algorithms trained by 4403 paired yield observations on 8 crop species extracted from 413 publications. CA has better productive performance than no-till system (NT), and it stands a more than 50% chance to outperform CT in dryer regions of the world, especially with proper agricultural management practices. Residue retention has the largest positive impact on CA productivity comparing to other management practices. The variations in the productivity of CA and NT across geographical and climatical regions were illustrated on global maps. CA appears as a sustainable agricultural practice if targeted at specific climatic regions and crop species.
Pentapartite fractionation of particles in oral fluids by differential centrifugation
Authors: Hiraga Chiho , Yamamoto Satoshi , Hashimoto Sadamitsu , Kasahara Masataka , Minamisawa Tamiko , Matsumura Sachiko , Katakura Akira , Yajima Yasutomo , Nomura Takeshi , Shiba Kiyotaka 
Published: February 2021

AbstractOral fluids (OFs) contain small extracellular vesicles (sEVs or exosomes) that carry disease-associated diagnostic molecules. However, cells generate extracellular vesicles (EVs) other than sEVs, so the EV population is quite heterogeneous. Furthermore, molecules not packaged in EVs can also serve as diagnostic markers. For these reasons, developing a complete picture of particulate matter in the oral cavity is important before focusing on specific subtypes of EVs. Here, we used differential centrifugation to fractionate human OFs from healthy volunteers and patients with oral squamous cell carcinoma into 5 fractions, and we characterized the particles, nucleic acids, and proteins in each fraction. Canonical exosome markers, including CD63, CD9, CD133, and HSP70, were found in all fractions, whereas CD81 and AQP5 were enriched in the 160K fraction, with non-negligible amounts in the 2K fraction. The 2K fraction also contained its characteristic markers that included short derivatives of EGFR and E-cadherin, as well as an autophagosome marker, LC3, and large multi-layered vesicles were observed by electronic microscopy. Most of the DNA and RNA was recovered from the 0.3K and 2K fractions, with some in the 160K fraction. These results can provide guideline information for development of purpose-designed OF-based diagnostic systems.
The design of X-band EPR cavity with narrow detection aperture for in vivo fingernail dosimetry after accidental exposure to ionizing radiation
Authors: Guo Junwang , Luan Xiaoxiao , Tian Ye , Ma Lei , Bi Xiaoguang , Zou Jierui , Dong Guofu , Liu Ye , Li Yonggang , Ning Jing , Wu Ke 
Published: February 2021

AbstractFor the purpose of assessing the radiation dose of the victims involved in the nuclear emergency or radiation accident, a new type of X-band EPR resonant cavity for in vivo fingernail EPR dosimetry was designed and a homemade EPR spectrometer for in vivo fingernail detection was constructed. The microwave resonant mode of the cavity was rectangular TE101, and there was a narrow aperture for fingernail detection opened on the cavity’s wall at the position of high detection sensitivity. The DPPH dot sample and the fingernail samples were measured based on the in vivo fingernail EPR spectrometer. The measurements of the DPPH dot sample verified the preliminary functional applicable of the EPR spectrometer and illustrated the microwave power and modulation response features. The fingernails after irradiation by gamma-ray were measured and the radiation-induced signal was acquired. The results indicated that the cavity and the in vivo EPR dosimeter instrument was able to detect the radiation-induced signal in irradiated fingernail, and preliminarily verified the basic function of the instrument and its potential for emergency dose estimate after a radiation accident.
Correlation of cardiac function and cerebral perfusion in a murine model of subarachnoid hemorrhage
Authors: Neulen Axel , Molitor Michael , Kosterhon Michael , Pantel Tobias , Holzbach Elisa , Rudi Wolf-Stephan , Karbach Susanne H. , Wenzel Philip , Ringel Florian , Thal Serge C. 
Published: February 2021

AbstractCerebral hypoperfusion is a key factor for determining the outcome after subarachnoid hemorrhage (SAH). A subset of SAH patients develop neurogenic stress cardiomyopathy (NSC), but it is unclear to what extent cerebral hypoperfusion is influenced by cardiac dysfunction after SAH. The aims of this study were to examine the association between cardiac function and cerebral perfusion in a murine model of SAH and to identify electrocardiographic and echocardiographic signs indicative of NSC. We quantified cortical perfusion by laser SPECKLE contrast imaging, and myocardial function by serial high-frequency ultrasound imaging, for up to 7 days after experimental SAH induction in mice by endovascular filament perforation. Cortical perfusion decreased significantly whereas cardiac output and left ventricular ejection fraction increased significantly shortly post-SAH. Transient pathological ECG and echocardiographic abnormalities, indicating NSC (right bundle branch block, reduced left ventricular contractility), were observed up to 3 h post-SAH in a subset of model animals. Cerebral perfusion improved over time after SAH and correlated significantly with left ventricular end-diastolic volume at 3, 24, and 72 h. The murine SAH model is appropriate to experimentally investigate NSC. We conclude that in addition to cerebrovascular dysfunction, cardiac dysfunction may significantly influence cerebral perfusion, with LVEDV presenting a potential parameter for risk stratification.
3D phonon microscopy with sub-micron axial-resolution
Authors: Smith Richard J. , Pérez-Cota Fernando , Marques Leonel , Clark Matt 
Published: February 2021

AbstractBrillouin light scattering (BLS) is an emerging method for cell imaging and characterisation. It allows elasticity-related contrast, optical resolution and label-free operation. Phonon microscopy detects BLS from laser generated coherent phonon fields to offer an attractive route for imaging since, at GHz frequencies, the phonon wavelength is sub-optical. Using phonon fields to image single cells is challenging as the signal to noise ratio and acquisition time are often poor. However, recent advances in the instrumentation have enabled imaging of fixed and living cells. This work presents the first experimental characterisation of phonon-based axial resolution provided by the response to a sharp edge. The obtained axial resolution is up to 10 times higher than that of the optical system used to take the measurements. Validation of the results are obtained with various polymer objects, which are in good agreement with those obtained using atomic force microscopy. Edge localisation, and hence profilometry, of a phantom boundary is measured with accuracy and precision of approximately 60 nm and 100 nm respectively. Finally, 3D imaging of fixed cells in culture medium is demonstrated.