bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll
Authors: von Hoyningen-Huene Avril Jean Elisabeth , Schneider Dominik , Fussmann Dario , Reimer Andreas , Arp Gernot , Daniel Rolf 
Published: March 2022

AbstractThe remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO42−/Cl− and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.
Genome-wide pharmacogenetics of anti-drug antibody response to bococizumab highlights key residues in HLA DRB1 and DQB1
Authors: Chasman Daniel I. , Hyde Craig L. , Giulianini Franco , Danning Rebecca D. , Wang Ellen Q. , Hickling Timothy , Ridker Paul M , Loomis A. Katrina 
Published: March 2022

AbstractIn this largest to-date genetic analysis of anti-drug antibody (ADA) response to a therapeutic monoclonal antibody (MAb), genome-wide association was performed for five measures of ADA status among 8844 individuals randomized to bococizumab, which targets PCSK9 for LDL-C lowering and cardiovascular protection. Index associations prioritized specific amino acid substitutions at theDRB1andDQB1MHC class II genes rather than canonical haplotypes. Two clusters of missense variants atDRB1were associated with general ADA measures (residues 9, 11, 13; and 96, 112, 120, 180) and a third cluster of missense variants inDQB1was associated with ADA measures including neutralizing antibody (NAb) titers (residues 66, 67, 71, 74, 75). The structural disposition of the missense substitutions implicates peptide antigen binding and CD4 effector function, mechanisms that are potentially generalizable to other therapeutic mAbs.Clinicaltrials.gov: NCT01968954, NCT01968967, NCT01968980, NCT01975376, NCT01975389, NCT02100514.
Quantitative interocular comparison of total corneal surface area and corneal diameter in patients with highly asymmetric keratoconus
Authors: Crahay François-Xavier , Debellemanière Guillaume , Tobalem Stephan , Ghazal Wassim , Moran Sarah , Gatinel Damien 
Published: March 2022

AbstractKeratoconus is a progressive corneal disorder which is frequently asymmetric. The aetiology of keratoconus remains unclear, and the concept of keratoconus as an ectatic disorder has been challenged recently. We carried out a retrospective study in 160 eyes of 80 patients, to evaluate and compare interocular differences in corneal diameter and surface area in patients with unilateral or highly asymmetric keratoconus (UHAKC). Calculations were performed using raw topographic elevation data derived from topographic measurements using Orbscan II, and we extrapolated surface areas up to measured corneal diameter. We also evaluated inter-eye correlation, and correlation between corneal surface area, corneal diameter and keratoconus severity. Our results showed a statistically significant but not clinically important greater corneal diameter (12.14 mm and 12.17 mm; p = 0.04), and corneal surface area (paired t-test, p < 0.0001; p = 0.0009 respectively) in more affected eyes. Inter-eye comparison revealed corneal diameter, anterior chamber depth, and corneal surface area were strongly correlated between eyes. Corneal surface area remained strongly correlated, and Bland–Altman analysis also showed strong inter-ocular agreement. Our results show that in patients with UHAKC the interocular difference in corneal diameter and corneal surface area is clinically insignificant, and are consistent with a redistribution, rather than increase, of corneal surface area with keratoconus progression.
Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing
Authors: Mosharaf Md. Parvez , Reza Md. Selim , Kibria Md. Kaderi , Ahmed Fee Faysal , Kabir Md. Hadiul , Hasan Sohel , Mollah Md. Nurul Haque 
Published: March 2022

AbstractThe pandemic threat of COVID-19 has severely destroyed human life as well as the economy around the world. Although, the vaccination has reduced the outspread, but people are still suffering due to the unstable RNA sequence patterns of SARS-CoV-2 which demands supplementary drugs. To explore novel drug target proteins, in this study, a transcriptomics RNA-Seq data generated from SARS-CoV-2 infection and control samples were analyzed. We identified 109 differentially expressed genes (DEGs) that were utilized to identify 10 hub-genes/proteins (TLR2, USP53, GUCY1A2, SNRPD2, NEDD9, IGF2, CXCL2, KLF6, PAG1 and ZFP36) by the protein–protein interaction (PPI) network analysis. The GO functional and KEGG pathway enrichment analyses of hub-DEGs revealed some important functions and signaling pathways that are significantly associated with SARS-CoV-2 infections. The interaction network analysis identified 5 TFs proteins and 6 miRNAs as the key regulators of hub-DEGs. Considering 10 hub-proteins and 5 key TFs-proteins as drug target receptors, we performed their docking analysis with the SARS-CoV-2 3CL protease-guided top listed 90 FDA approved drugs. We found Torin-2, Rapamycin, Radotinib, Ivermectin, Thiostrepton, Tacrolimus and Daclatasvir as the top ranked seven candidate drugs. We investigated their resistance performance against the already published COVID-19 causing top-ranked 11 independent and 8 protonated receptor proteins by molecular docking analysis and found their strong binding affinities, which indicates that the proposed drugs are effective against the state-of-the-arts alternatives independent receptor proteins also. Finally, we investigated the stability of top three drugs (Torin-2, Rapamycin and Radotinib) by using 100 ns MD-based MM-PBSA simulations with the two top-ranked proposed receptors (TLR2, USP53) and independent receptors (IRF7, STAT1), and observed their stable performance. Therefore, the proposed drugs might play a vital role for the treatment against different variants of SARS-CoV-2 infections.
Isotopic signatures and source apportionment of Pb in ambient PM2.5
Authors: Jung Chien-Cheng , Chou Charles C.-K. , Huang Yi-Tang , Chang Shih-Yu , Lee Chung-Te , Lin Chuan-Yao , Cheung Hing-Cho , Kuo Wei-Chen , Chang Chih-Wei , Chang Shuenn-Chin 
Published: March 2022

AbstractParticulate lead (Pb) is a primary air pollutant that affects society because of its health impacts. This study investigates the source sectors of Pb associated with ambient fine particulate matter (PM2.5) over central-western Taiwan (CWT) with new constraints on the Pb-isotopic composition. We demonstrate that the contribution of coal-fired facilities is overwhelming, which is estimated to reach 35 ± 16% in the summertime and is enhanced to 57 ± 24% during the winter monsoon seasons. Moreover, fossil-fuel vehicles remain a major source of atmospheric Pb, which accounts for 12 ± 5%, despite the current absence of a leaded gasoline supply. Significant seasonal and geographical variations in the Pb-isotopic composition are revealed, which suggest that the impact of East Asian (EA) pollution outflows is important in north CWT and drastically declines toward the south. We estimate the average contribution of EA outflows as accounting for 35 ± 15% (3.6 ± 1.5 ng/m3) of the atmospheric Pb loading in CWT during the winter monsoon seasons.
Mathematical modeling of metal recovery from E-waste using a dark-fermentation-leaching process
Authors: Russo Fabiana , Luongo Vincenzo , Mattei Maria Rosaria , Frunzo Luigi 
Published: March 2022

AbstractIn this work, an original mathematical model for metals leaching from electronic waste in a dark fermentation process is proposed. The kinetic model consists of a system of non-linear ordinary differential equations, accounting for the main biological, chemical, and physical processes occurring in the fermentation of soluble biodegradable substrates and in the dissolution process of metals. Ad-hoc experimental activities were carried out for model calibration purposes, and all experimental data were derived from specific lab-scale tests. The calibration was achieved by varying kinetic and stoichiometric parameters to match the simulation results to experimental data. Cumulative hydrogen production, glucose, organic acids, and leached metal concentrations were obtained from analytical procedures and used for the calibration. The results confirmed the high accuracy of the model in describing biohydrogen production, organic acids accumulation, and metals leaching during the biological degradation process. Thus, the mathematical model represents a useful and reliable tool for the design of strategies for valuable metals recovery from waste or mineral materials. Moreover, further numerical simulations were carried out to analyze the interactions between the fermentation and the leaching processes and to maximize the efficiency of metals recovery due to the fermentation by-products.
Micro-Fourier-transform infrared reflectance spectroscopy as tool for probing IgG glycosylation in COVID-19 patients
Authors: Bandeira Carla Carolina Silva , Madureira Karen Cristina Rolim , Rossi Meire Bocoli , Gallo Juliana Failde , da Silva Ana Paula Marques Aguirra , Torres Vilanilse Lopes , de Lima Vinicius Alves , Júnior Norival Kesper , Almeida Janete Dias , Zerbinati Rodrigo Melim , Braz-Silva Paulo Henrique , Lindoso José Angelo Lauletta , da Silva Martinho Herculano 
Published: March 2022

AbstractIt has been reported that patients diagnosed with COVID-19 become critically ill primarily around the time of activation of the adaptive immune response. However the role of antibodies in the worsening of disease is not obvious. Higher titers of anti-spike immunoglobulin IgG1 associated with low fucosylation of the antibody Fc tail have been associated to excessive inflammatory response. In contrast it has been also reported that NP-, S-, RBD- specific IgA, IgG, and IgM are not associated with SARS-CoV-2 viral load, indicating that there is no obvious correlation between antibody response and viral antigen detection. In the present work the micro-Fourier-transform infrared reflectance spectroscopy (micro-FTIR) was employed to investigate blood serum samples of healthy and COVID-19-ill (mild or oligosymptomatic) individuals (82 healthcare workers volunteers in “Instituto de Infectologia Emilio Ribas”, São Paulo, Brazil). The molecular-level-sensitive, multiplexing quantitative and qualitative FTIR data probed on 1 µL of dried biofluid was compared to signal-to-cutoff index of chemiluminescent immunoassays CLIA and ELISA (IgG antibodies against SARS-CoV-2). Our main result indicated that 1702–1785 $$\hbox {cm}^{-1}$$

cm

-
1

spectral window (carbonyl C=O vibration) is a spectral marker of the degree of IgG glycosylation, allowing to probe distinctive sub-populations of COVID-19 patients, depending on their degree of severity. The specificity was 87.5 % while the detection rate of true positive was 100%. The computed area under the receiver operating curve was equivalent to CLIA, ELISA and other ATR-FTIR methods ($$>0.85$$

>
0.85

). In summary, overall discrimination of healthy and COVID-19 individuals and severity prediction as well could be potentially implemented using micro-FTIR reflectance spectroscopy on blood serum samples. Considering the minimal and reagent-free sample preparation procedures combined to fast (few minutes) outcome of FTIR we can state that this technology is suitable for fast screening of immune response of individuals with COVID-19. It would be an important tool in prospective studies, helping investigate the physiology of the asymptomatic, oligosymptomatic, or severe individuals and measure the extension of infection dissemination in patients.
Numerical analysis of Casson nanofluid three-dimensional flow over a rotating frame exposed to a prescribed heat flux with viscous heating
Authors: Al-Kouz Wael , Owhaib Wahib 
Published: March 2022

AbstractThis study investigates heat transfer characteristics and three-dimensional flow of non-Newtonian Casson nanofluid over a linearly stretching flat surface in the rotating frame of a reference. The current model includes the Buongiorno nanofluid model comprises nanoparticles’ haphazard motion and thermo-migration. It also considered mechanisms for viscous heating and constant heat flux at the boundary. The nonlinear partial differential system modeling includes the non-Newtonian Casson fluid model and the boundary layer approximation. The system governing equations were nondimensionalized and numerically solved. A parametric study was conducted to analyze the significance of dimensionless parameters on velocities, the concentration, temperatures, Nusselt number, friction factors, and Sherwood number. The study reveals that the Casson nanoliquid temperature enhanced significantly due to the mechanisms of haphazard motion and thermo-migration. The momentum layer thickness of nano Casson fluid reduced due to the rotation phenomenon while the thermal layer structure amended notably. In the absence of rotation, there is no transverse velocity. The thermal layer structure is enhanced owing to the viscous heating process. The intense haphazard motion and thermo-migration mechanisms lead to maximum heat transfer rate at the plate. In addition, results show that the Coriolis force strength elevation shows similar axial and transverse velocities behavior. In addition, the nanoparticle concentration is observed higher due to the rotation aspect and Casson fluid parameter. Furthermore, the Casson fluid factor decreases with velocities, but the trend is the opposite for the high Casson fluid factor. The thermal and solute layer thickness growth is due to the nanoparticles’ thermo-diffusion. In conclusion, the larger rotation factor increases the friction factors. The maximum plate heat transfer rate is when higher Nb and Nt are higher.
Immune-related lincRNA pairs predict prognosis and therapeutic response in hepatocellular carcinoma
Authors: Zhang Yingna , Yang Xiaofeng , Zhou Lisha , Gao Xiangting , Wu Xiangwei , Chen Xueling , Hou Jun , Wang Lianghai 
Published: March 2022

AbstractGrowing evidence has demonstrated the functional relevance of long intergenic noncoding RNAs (lincRNAs) to tumorigenesis and immune response. However, immune-related lincRNAs and their value in predicting the clinical outcomes of patients with liver cancer remain largely unexplored. Herein, we utilized the strategy of iterative gene pairing to construct a tumor-specific immune-related lincRNA pairs signature (IRLPS), which did not require specific expression levels, as an indicator of patient outcomes. The 18-IRLPS we developed was associated with overall survival, tumor progression, and recurrence in liver cancer patients. Multivariate analysis revealed that the risk model was an independent predictive factor. A high IRLPS risk was correlated suppressive immune microenvironment, and IRLPS-high patients might benefit more from CD276 blockade or TMIGD2 agonist. Patients in the high-risk group were associated with elevated tumor mutation, increased sensitivity to dopamine receptor antagonists, cisplatin, doxorubicin, and mitomycin but more resistance to vinblastine. Mechanistically, IRLPS high scores might lead to poor prognosis by promoting cell proliferation and metabolic reprogramming. The prognostic significance of the 18-IRLPS was confirmed in independent cancer datasets. These findings highlighted the robust predictive performances of the 18-IRLPS for prognosis and personalized treatment.
Long descending commissural V0v neurons ensure coordinated swimming movements along the body axis in larval zebrafish
Authors: Kawano Kohei , Kato Kagayaki , Sugioka Takumi , Kimura Yukiko , Tanimoto Masashi , Higashijima Shin-ichi 
Published: March 2022

AbstractDevelopmental maturation occurs in slow swimming behavior in larval zebrafish; older larvae acquire the ability to perform slow swimming while keeping their head stable in the yaw dimension. A class of long-distance descending commissural excitatory V0v neurons, called MCoD neurons, are known to develop in a later phase of neurogenesis, and participate in slow swimming in older larvae. We hypothesized that these MCoD neurons play a role in coordinating the activities of trunk muscles in the diagonal dimension (e.g., the rostral left and the caudal right) to produce the S-shaped swimming form that contributes to the stability of the head. Here, we show that MCoD neurons do indeed play this role. In larvae in which MCoD neurons were laser-ablated, the swimming body form often adopted a one-sided (C-shaped) bend with reduced appearance of the normal S-shaped bend. With this change in swimming form, the MCoD-ablated larvae exhibited a greater degree of head yaw displacement during slow swimming. In mice, the long-distance descending commissural V0v neurons have been implicated in diagonal interlimb coordination during walking. Together with this, our study suggests that the long-distance descending commissural V0v neurons form an evolutionarily conserved pathway in the spinal locomotor circuits that coordinates the movements of the diagonal body/limb muscles.
Microengineered filters for efficient delivery of nanomaterials into mammalian cells
Authors: Morshedi Rad Dorsa , Rezaei Meysam , Radfar Payar , Ebrahimi Warkiani Majid 
Published: March 2022

AbstractIntracellular delivery of nanomaterials into the cells of interest has enabled cell manipulation for numerous applications ranging from cell-based therapies to biomedical research. To date, different carriers or membrane poration-based techniques have been developed to load nanomaterials to the cell interior. These biotools have shown promise to surpass the membrane barrier and provide access to the intracellular space followed by passive diffusion of exogenous cargoes. However, most of them suffer from inconsistent delivery, cytotoxicity, and expensive protocols, somewhat limiting their utility in a variety of delivery applications. Here, by leveraging the benefits of microengineered porous membranes with a suitable porosity, we demonstrated an efficient intracellular loading of diverse nanomaterials to different cell types based on inducing mechanical disruption to the cell membrane. In this work, for the first time, we used ultra-thin silicon nitride (SiN) filter membranes with uniform micropores smaller than the cell diameter to load impermeable nanomaterials into adherent and non-adherent cell types. The delivery performance using SiN microsieves has been validated through the loading of functional nanomaterials from a few nanometers to hundreds of nanometers into mammalian cells with minimal undesired impacts. Besides the high delivery efficiency and improved cell viability, this simple and low-cost approach offers less clogging and higher throughput (107 cell min−1). Therefore, it yields to the efficient introduction of exogenous nanomaterials into the large population of cells, illustrating the potential of these microengineered filters to be widely used in the microfiltroporation (MFP) setup.
Mid-infrared photon sensing using InGaN/GaN nanodisks via intersubband absorption
Authors: Xing Zhang , Akter Afroja , Kum Hyun S. , Baek Yongmin , Ra Yong-Ho , Yoo Geonwook , Lee Kyusang , Mi Zetian , Heo Junseok 
Published: March 2022

AbstractIntersubband (intraband) transitions allow absorption of photons in the infrared spectral regime, which is essential for IR-photodetector and optical communication applications. Among various technologies, nanodisks embedded in nanowires offer a unique opportunity to be utilized in intraband devices due to the ease of tuning the fundamental parameters such as strain distribution, band energy, and confinement of the active region. Here, we show the transverse electric polarized intraband absorption using InGaN/GaN nanodisks cladded by AlGaN. Fourier transform infrared reflection (FTIR) measurement confirms absorption of normal incident in-plane transverse electric polarized photons in the mid-IR regime (wavelength of ~ 15 μm) at room temperature. The momentum matrix of the nanodisk energy states indicates electron transition from the ground state s into the px or py orbital-like excited states. Furthermore, the absorption characteristics depending on the indium composition and nanowire diameter exhibits tunability of the intraband absorption spectra within the nanodisks. We believe nanodisks embedded nanowires is a promising technology for achieving tunable detection of photons in the IR spectrum.
CTSB is a negative prognostic biomarker and therapeutic target associated with immune cells infiltration and immunosuppression in gliomas
Authors: Ma Kaiming , Chen Xin , Liu Weihai , Chen Suhua , Yang Chenlong , Yang Jun 
Published: March 2022

AbstractPrevious researches have demonstrated the meaning of CTSB for the progress of several tumors, whereas few clues about its immunological characteristic in gliomas. Here we systematically explored its biologic features and clinical significance for gliomas. 699 glioma cases of TCGA and 325 glioma cases of CGGA were respectively included as training and validating cohorts. R software was used for data analysis and mapping. We found that CTSB was remarkably highly-expressed for HGG, IDH wild type, 1p19q non-codeletion type, MGMT promoter unmethylation type and mesenchymal gliomas. CTSB could specifically and sensitively indicate mesenchymal glioma. Upregulated CTSB was an independent hazard correlated with poor survival. CTSB-related biological processes in gliomas chiefly concentrated on immunoreaction and inflammation response. Then we proved that CTSB positively related to most inflammatory metagenes except IgG, including HCK, LCK, MHC II, STAT1 and IFN. More importantly, the levels of glioma-infiltrating immune cells were positively associated with the expression of CTSB, especially for TAMs, MDSCs and Tregs. In conclusion, CTSB is closely related to the malignant pathological subtypes, worse prognosis, immune cells infiltration and immunosuppression of gliomas, which make it a promising biomarker and potential target in the diagnosis, treatment and prognostic assessment of gliomas.