bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct SARS-CoV-2 antibody reactivity patterns elicited by natural infection and mRNA vaccination
Authors: Assis Rafael , Jain Aarti , Nakajima Rie , Jasinskas Algis , Khan Saahir , Palma Anton , Parker Daniel M. , Chau Anthony ,   Specimen Collection Group, Hosseinian Sina , Vasudev Milind , Au Connie , Powers Kathleen , Birring Paramveer S. , Chin Brandon , Andary Rana , Obiero Joshua M. , Tifrea Delia , Leung Amanda , Grabar Christina , Muqolli Fjolla , Khalil Ghali , Escobar Jessica Colin , Ventura Jenny , Davies D. Huw , Albala Bruce , Boden-Albala Bernadette , Schubl Sebastian , Felgner Philip L. 
Published: November 2021

AbstractWe analyzed data from two ongoing COVID-19 longitudinal serological surveys in Orange County, CA., between April 2020 and March 2021. A total of 8476 finger stick blood specimens were collected before and after a vaccination campaign. IgG levels were determined using a multiplex antigen microarray containing antigens from SARS-CoV-2, SARS, MERS, Common CoV, and Influenza. Twenty-six percent of specimens from unvaccinated Orange County residents in December 2020 were SARS-CoV-2 seropositive; out of 852 seropositive individuals 77 had symptoms and 9 sought medical care. The antibody response was predominantly against nucleocapsid (NP), full length, and S2 domain of spike. Anti-receptor binding domain (RBD) reactivity was low and not cross-reactive against SARS S1 or SARS RBD. A vaccination campaign at the University of California Irvine Medical Center (UCIMC) started on December, 2020 and 6724 healthcare workers were vaccinated within 3 weeks. Seroprevalence increased from 13% pre-vaccination to 79% post-vaccination in January, 93% in February, and 99% in March. mRNA vaccination induced higher antibody levels than natural exposure, especially against the RBD domain and cross-reactivity against SARS RBD and S1 was observed. Nucleocapsid protein antibodies can be used to distinguish vaccinees to classify pre-exposure to SARS-CoV-2 Previously infected individuals developed higher antibody titers to the vaccine than non pre-exposed individuals. Hospitalized patients in intensive care with severe disease reach significantly higher antibody levels than mild cases, but lower antibody levels compared to the vaccine. These results indicate that mRNA vaccination rapidly induces a much stronger and broader antibody response than SARS-CoV-2 infection.
Zn(II) binding causes interdomain changes in the structure and flexibility of the human prion protein
Authors: Gielnik Maciej , Taube Michał , Zhukova Lilia , Zhukov Igor , Wärmländer Sebastian K. T. S. , Svedružić Željko , Kwiatek Wojciech M. , Gräslund Astrid , Kozak Maciej 
Published: November 2021

AbstractThe cellular prion protein (PrPC) is a mainly α-helical 208-residue protein located in the pre- and postsynaptic membranes. For unknown reasons, PrPC can undergo a structural transition into a toxic, β-sheet rich scrapie isoform (PrPSc) that is responsible for transmissible spongiform encephalopathies (TSEs). Metal ions seem to play an important role in the structural conversion. PrPC binds Zn(II) ions and may be involved in metal ion transport and zinc homeostasis. Here, we use multiple biophysical techniques including optical and NMR spectroscopy, molecular dynamics simulations, and small angle X-ray scattering to characterize interactions between human PrPC and Zn(II) ions. Binding of a single Zn(II) ion to the PrPC N-terminal domain via four His residues from the octarepeat region induces a structural transition in the C-terminal α-helices 2 and 3, promotes interaction between the N-terminal and C-terminal domains, reduces the folded protein size, and modifies the internal structural dynamics. As our results suggest that PrPC can bind Zn(II) under physiological conditions, these effects could be important for the physiological function of PrPC.
Experimental and computational chemical studies on the corrosion inhibitive properties of carbonitrile compounds for carbon steel in aqueous solutions
Authors: Fouda Abd El-Aziz S. , El-Askalany Abdelmonem H. , Molouk Ahmed F. S. , Elsheikh Niveen S. , Abousalem Ashraf S. 
Published: November 2021

AbstractThe present work aims to study 6-amino-4-aryl-2-oxo-1-phenyl-1,2-dihydropyridine-3,5-dicarbonitrile derivatives namely: 6-Amino-2-oxo-1,4-diphenyl-1,2-dihydropyridine-3,5-dicarbonitrile (PdC-H), 6-Amino-2-oxo-1-phenyl-4-(p-tolyl)-1,2-dihydropyridine-3,5-dicarbonitrile (PdC-Me) and 6-Amino-4-(4-hydroxyphenyl)-2-oxo-1-phenyl-1,2-dihydropyridine-3,5-dicarbonitrile (PdC-OH) as corrosion inhibitors to provide protection for carbon steel in a molar hydrochloric acid medium. Chemical measurements such as (weight loss) and electrochemical techniques such as (Potentiodynamic polarization, electrochemical impedance spectroscopy, and Electron frequency modulation) were applied to characterize the inhibitory properties of the synthesized derivatives. The adsorption of these derivatives on the carbon steel surface was confirmed by Attenuated Total Refraction Infrared (ATR-IR), Atomic Force Microscope (AFM), and X-ray Photoelectron Spectroscopy (XPS). Our findings revealed that the tested derivatives have corrosion inhibition power, which increased significantly from 75.7 to 91.67% on the addition of KI (PdC-OH:KI = 1:1) to inhibited test solution with PdC-OH derivative at 25 °C. The adsorption process on the metal surface follows the Langmuir adsorption model. XPS analysis showed that the inhibitor layer consists of an iron oxide/hydroxide mixture in which the inhibitor molecules are incorporated. Computational chemical theories such as DFT calculations and Mont Carlo simulation have been performed to correlate the molecular properties of the investigated inhibitors with experimental efficiency. The theoretical speculation by Dmol3 corroborates with the results from the experimental findings.
Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade
Authors: Yagi-Utsumi Maho , Aoki Kazuhiro , Watanabe Hiroki , Song Chihong , Nishimura Seiji , Satoh Tadashi , Yanaka Saeko , Ganser Christian , Tanaka Sae , Schnapka Vincent , Goh Ean Wai , Furutani Yuji , Murata Kazuyoshi , Uchihashi Takayuki , Arakawa Kazuharu , Kato Koichi 
Published: November 2021

AbstractAnhydrobiosis, one of the most extensively studied forms of cryptobiosis, is induced in certain organisms as a response to desiccation. Anhydrobiotic species has been hypothesized to produce substances that can protect their biological components and/or cell membranes without water. In extremotolerant tardigrades, highly hydrophilic and heat-soluble protein families, cytosolic abundant heat-soluble (CAHS) proteins, have been identified, which are postulated to be integral parts of the tardigrades’ response to desiccation. In this study, to elucidate these protein functions, we performed in vitro and in vivo characterizations of the reversible self-assembling property of CAHS1 protein, a major isoform of CAHS proteins from Ramazzottius varieornatus, using a series of spectroscopic and microscopic techniques. We found that CAHS1 proteins homo-oligomerized via the C-terminal α-helical region and formed a hydrogel as their concentration increased. We also demonstrated that the overexpressed CAHS1 proteins formed condensates under desiccation-mimicking conditions. These data strongly suggested that, upon drying, the CAHS1 proteins form oligomers and eventually underwent sol–gel transition in tardigrade cytosols. Thus, it is proposed that the CAHS1 proteins form the cytosolic fibrous condensates, which presumably have variable mechanisms for the desiccation tolerance of tardigrades. These findings provide insights into molecular strategies of organisms to adapt to extreme environments.
The ability of physical activity in reducing mortality risks and cardiovascular loading and in extending life expectancy in patients with COPD
Authors: Shu Chin-Chung , Lee June-Han , Tsai Min-Kuang , Su Ta-Chen , Wen Chi Pang 
Published: November 2021

AbstractFor chronic obstructive pulmonary disease (COPD), the role of physical activity in reducing COPD mortality and heart loading and in extending life expectancy remains unclear. Participants in comprehensive medical screening were recruited with spirometry on everyone. We analyzed physical activity volume calculated from intensity, duration and frequency of self-reported exercise history. Deaths were identified from the National Death File. The impacts of physical activity on mortality, heart rate and life expectancy were analyzed. Among the cohort of 483,603 adults, 32,535 had spirometry-determined COPD, indicating an adjusted national prevalence of 11.4% (male) and 9.8% (female). On the average, COPD increased all-cause mortality with a hazard ratio of 1.44 and loss of 6.0 years in life expectancy. Almost two thirds (65%) of the causes of deaths were extra-pulmonary, such as cardiovascular disease, diabetes, cancer and kidney diseases. In addition, COPD was associated with increases in heart rate proportionate to its severity, which led to higher mortality. Participants with COPD who were fully active physically could reduce mortality and have improved heart rates as compared with those without physical activity. In addition, their life expectancy could be extended close to those of the no COPD but inactive cohort. Fully active physical activity can help patients with COPD overcome most of the mortality risks, decrease heart rate, and achieve a life expectancy close to that of patients without COPD. The effectiveness of physical activity on COPD is facilitated by its systemic nature beyond lung disease.
COVID-19 vaccine acceptance among adults in four major US metropolitan areas and nationwide
Authors: El-Mohandes Ayman , White Trenton M. , Wyka Katarzyna , Rauh Lauren , Rabin Kenneth , Kimball Spencer H. , Ratzan Scott C. , Lazarus Jeffrey V. 
Published: November 2021

AbstractThis study assesses attitudes towards COVID-19 vaccination and the predictive value of COVID-VAC, a novel scale, among adults in the four largest US metropolitan areas and nationally. A 36-item survey of 6037 Americans was conducted in mid-April 2021. The study reports factors for COVID-19 vaccine acceptance among: (1) already vaccinated; (2) unvaccinated but willing to accept a vaccine; and (3) unvaccinated and unwilling to vaccinate. More than 20% were unwilling to vaccinate, expressing concerns about vaccine efficacy and safety and questioning the disease’s severity. Poverty, working outside of the home and conservative political views are predictors of unwillingness. Conversely, those who either personally tested positive for COVID-19, or had a family member who did so, were more likely to accept vaccination. Majorities of all respondents supported vaccination mandates for employees and university students. Respondents preferred to receive vaccines in their doctor´s office. Lower income and conservative ideology, but not race, were strongly associated with vaccine unwillingness. The predictive value of COVID-VAC was demonstrated. While vaccination mandates are likely to be accepted, additional effective, targeted interventions to increase vaccine uptake are needed urgently.
Aeromagnetic and digital elevation model constraints on the structural framework of southern margin of the Middle Niger Basin, Nigeria
Authors: Salawu Naheem Banji 
Published: November 2021

AbstractHigh resolution aeromagnetic anomaly and topographic data using enhancement filtering techniques have resulted in better understanding of the nature of structures at the margins of the Middle Niger Basin. Due to the lack of structural data, the gold deposits within the margins of the Middle Niger Basin were variably excavated, leading to land degradation. The newly-produced structural map highly constrained the mineralization, which makes the study area and its periphery safe for gold exploration. Structural map has been produced from the integration of derivative maps to assess the pattern of surface and subsurface structural features within the studied area. The structural map unravels structural features with major and minor structural trends, in addition to a prominent crustal partitioning, characterized by the Ifewara shear zone. These structural features correlate very well with known gold mineralized locations and also predict new zones for structurally controlled gold and associated mineralization. The structural patterns are directly related with tectonic episodes in the basement. In fact, the Ifewara shear zone appears more pronounced on the total gradient and 3-D Euler deconvolution maps, which reveal various lineaments within the shear zone. The topographic maps (digital elevation model) clearly shows the surface morphology of the region under study while the resulting shaded-relief map reveal the continuity of the deduced magnetic lineaments that coincide with the valleys of River Niger which exploits zones of weakness from the lineaments. The results suggest high sensitivity of fluvial network to deduced lineaments with possible significant implication for alluvial gold mineralization.
Aerial high-throughput phenotyping of peanut leaf area index and lateral growth
Authors: Sarkar Sayantan , Cazenave Alexandre-Brice , Oakes Joseph , McCall David , Thomason Wade , Abbott Lynn , Balota Maria 
Published: November 2021

AbstractLeaf area index (LAI) is the ratio of the total one-sided leaf area to the ground area, whereas lateral growth (LG) is the measure of canopy expansion. They are indicators for light capture, plant growth, and yield. Although LAI and LG can be directly measured, this is time consuming. Healthy leaves absorb in the blue and red, and reflect in the green regions of the electromagnetic spectrum. Aerial high-throughput phenotyping (HTP) may enable rapid acquisition of LAI and LG from leaf reflectance in these regions. In this paper, we report novel models to estimate peanut (Arachis hypogaeaL.) LAI and LG from vegetation indices (VIs) derived relatively fast and inexpensively from the red, green, and blue (RGB) leaf reflectance collected with an unmanned aerial vehicle (UAV). In addition, we evaluate the models’ suitability to identify phenotypic variation for LAI and LG and predict pod yield from early season estimated LAI and LG. The study included 18 peanut genotypes for model training in 2017, and 8 genotypes for model validation in 2019. The VIs included the blue green index (BGI), red-green ratio (RGR), normalized plant pigment ratio (NPPR), normalized green red difference index (NGRDI), normalized chlorophyll pigment index (NCPI), and plant pigment ratio (PPR). The models used multiple linear and artificial neural network (ANN) regression, and their predictive accuracy ranged from 84 to 97%, depending on the VIs combinations used in the models. The results concluded that the new models were time- and cost-effective for estimation of LAI and LG, and accessible for use in phenotypic selection of peanuts with desirable LAI, LG and pod yield.
Association of a simple SACAF score with bystander witnessed sudden death due to ventricular tachyarrhythmias in a multicenter cohort
Authors: Wu Mei-Yao , Wen Ming-Shien , Chen Mien-Cheng , Tsai Chia-Ti , Wu Tsu-Juey , Lee Wei-Chieh , Lin Yen-Nien , Chang Shih-Sheng , Chang Kuan-Cheng 
Published: November 2021

AbstractOut-of-hospital cardiac arrest (OHCA) remains a major threat to public health worldwide. OHCA patients presenting initial shockable ventricular tachycardia/ventricular fibrillation (VT/VF) rhythm have a better survival rate. We sought to develop a simple SACAF score to discriminate VT/VF from non-VT/VF OHCAs based on the Taiwan multicenter hospital-based registry database. We analyzed the in- and pre-hospital data, including demographics, baseline comorbidities, response times, automated external defibrillator information, and the 12-lead ECG recording closest to the OHCA event in bystander-witnessed OHCA patients. Among the 461 study patients, male sex (OR 2.54, 95% CI = 1.32–4.88, P = 0.005), age ≤ 65 years (OR 2.78, 95% CI = 1.64–4.70, P < 0.001), cardiovascular diseases (OR 2.97, 95% CI = 1.73–5.11, P < 0.001), and atrial fibrillation (AF) (OR 2.36, 95% CI = 1.17–4.76, P = 0.017) were independent risk factors for VT/VF OHCA (n = 81) compared with non-VT/VF OHCA (n = 380). A composite SACAF score was developed (male Sex, Age ≤ 65 years, Cardiovascular diseases, and AF) and compared with the performance of a modified CHA2DS2-VASc score (Cardiovascular diseases, Hypertension, Age ≥ 75 years, Diabetes, previous Stroke, Vascular disease, Age 65–74 years, female Sex category). The area under the receiver operating characteristic curve (AUC) of the SACAF was 0.739 (95% CI = 0.681–0.797, P < 0.001), whereas the AUC of the modified CHA2DS2-VASc was 0.474 (95% CI = 0.408–0.541, P = 0.464). A SACAF score of ≥ 2 was useful in discriminating VT/VF from non-VT/VF OHCAs with a sensitivity of 0.75 and a specificity of 0.60. In conclusion, the simple SACAF score appears to be useful in discriminating VT/VF from non-VT/VF bystander-witnessed OHCAs and the findings may also shed light on future mechanistic evaluation.
Genetic fusion of P450 BM3 and formate dehydrogenase towards self-sufficient biocatalysts with enhanced activity
Authors: Kokorin Arsenij , Parshin Pavel D. , Bakkes Patrick J. , Pometun Anastasia A. , Tishkov Vladimir I. , Urlacher Vlada B. 
Published: November 2021

AbstractFusion of multiple enzymes to multifunctional constructs has been recognized as a viable strategy to improve enzymatic properties at various levels such as stability, activity and handling. In this study, the genes coding for cytochrome P450 BM3 from B. megaterium and formate dehydrogenase from Pseudomonas sp. were fused to enable both substrate oxidation catalyzed by P450 BM3 and continuous cofactor regeneration by formate dehydrogenase within one construct. The order of the genes in the fusion as well as the linkers that bridge the enzymes were varied. The resulting constructs were compared to individual enzymes regarding substrate conversion, stability and kinetic parameters to examine whether fusion led to any substantial improvements of enzymatic properties. Most noticeably, an activity increase of up to threefold was observed for the fusion constructs with various substrates which were partly attributed to the increased diflavin reductase activity of the P450 BM3. We suggest that P450 BM3 undergoes conformational changes upon fusion which resulted in altered properties, however, no NADPH channeling was detected for the fusion constructs.
Visuo-proprioceptive integration and recalibration with multiple visual stimuli
Authors: Debats Nienke B. , Heuer Herbert , Kayser Christoph 
Published: November 2021

AbstractTo organize the plethora of sensory signals from our environment into a coherent percept, our brain relies on the processes of multisensory integration and sensory recalibration. We here asked how visuo-proprioceptive integration and recalibration are shaped by the presence of more than one visual stimulus, hence paving the way to study multisensory perception under more naturalistic settings with multiple signals per sensory modality. We used a cursor-control task in which proprioceptive information on the endpoint of a reaching movement was complemented by two visual stimuli providing additional information on the movement endpoint. The visual stimuli were briefly shown, one synchronously with the hand reaching the movement endpoint, the other delayed. In Experiment 1, the judgments of hand movement endpoint revealed integration and recalibration biases oriented towards the position of the synchronous stimulus and away from the delayed one. In Experiment 2 we contrasted two alternative accounts: that only the temporally more proximal visual stimulus enters integration similar to a winner-takes-all process, or that the influences of both stimuli superpose. The proprioceptive biases revealed that integration—and likely also recalibration—are shaped by the superposed contributions of multiple stimuli rather than by only the most powerful individual one.
Metacyclogenesis defects and gene expression hallmarks of histone deacetylase 4-deficient Trypanosoma cruzi cells
Authors: Picchi-Constante Gisele Fernanda Assine , Guerra-Slompo Eloise Pavão , Tahira Ana Carolina , Alcantara Monica Visnieski , Amaral Murilo Sena , Ferreira Arthur Schveitzer , Batista Michel , Batista Cassiano Martin , Goldenberg Samuel , Verjovski-Almeida Sergio , Zanchin Nilson Ivo Tonin 
Published: November 2021

AbstractTrypanosoma cruzi—the causative agent of Chagas disease—like other kinetoplastids, relies mostly on post-transcriptional mechanisms for regulation of gene expression. However, trypanosomatids undergo drastic changes in nuclear architecture and chromatin structure along their complex life cycle which, combined with a remarkable set of reversible histone post-translational modifications, indicate that chromatin is also a target for control of gene expression and differentiation signals in these organisms. Chromatin-modifying enzymes have a direct impact on gene expression programs and DNA metabolism. In this work, we have investigated the function of T. cruzi histone deacetylase 4 (TcHDAC4). We show that, although TcHDAC4 is not essential for viability, metacyclic trypomastigote TcHDAC4 null mutants show a thin cell body and a round and less condensed nucleus located very close to the kinetoplast. Sixty-four acetylation sites were quantitatively evaluated, which revealed H2AT85ac, H4K10ac and H4K78ac as potential target sites of TcHDAC4. Gene expression analyses identified three chromosomes with overrepresented regions of differentially expressed genes in the TcHDAC4 knockout mutant compared with the wild type, showing clusters of either up or downregulated genes. The adjacent chromosomal location of some of these genes indicates that TcHDAC4 participates in gene expression regulation during T. cruzi differentiation.
Symmetry-protected solitons and bulk-boundary correspondence in generalized Jackiw–Rebbi models
Authors: Oh Chang-geun , Han Sang-Hoon , Cheon Sangmo 
Published: November 2021

AbstractWe investigate the roles of symmetry and bulk-boundary correspondence in characterizing topological edge states in generalized Jackiw–Rebbi (JR) models. We show that time-reversal (T), charge-conjugation (C), parity (P), and discrete internal field rotation ($$Z_n$$

Z
n

) symmetries protect and characterize the various types of edge states such as chiral and nonchiral solitons via bulk-boundary correspondence in the presence of the multiple vacua. As two representative models, we consider the JR model composed of a single fermion field having a complex mass and the generalized JR model with two massless but interacting fermion fields. The JR model shows nonchiral solitons with the $$Z_2$$

Z
2

rotation symmetry, whereas it shows chiral solitons with the broken $$Z_2$$

Z
2

rotation symmetry. In the generalized JR model, only nonchiral solitons can emerge with only $$Z_2$$

Z
2

rotation symmetry, whereas both chiral and nonchiral solitons can exist with enhanced $$Z_4$$

Z
4

rotation symmetry. Moreover, we find that the nonchiral solitons have C, P symmetries while the chiral solitons do not, which can be explained by the symmetry-invariant lines connecting degenerate vacua. Finally, we find the symmetry correspondence between multiply-degenerate global vacua and solitons such that T, C, P symmetries of a soliton inherit from global minima that are connected by the soliton, which provides a novel tool for the characterization of topological solitons.