bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-sectional study to assess the efficacy of SARS-CoV-2 vaccination in patients with monoclonal gammopathies
Authors: Abella Eugenia , Trigueros Macedonia , Pradenas Edwards , Muñoz-Lopez Francisco , Garcia-Pallarols Francesc , Ben Azaiz Ben Lahsen Randa , Trinité Benjamin , Urrea Victor , Marfil Silvia , Rovirosa Carla , Puig Teresa , Grau Eulàlia , Chamorro Anna , Toledo Ruth , Font Marta , Palacín Dolors , Lopez-Segui Francesc , Carrillo Jorge , Prat Nuria , Mateu Lourdes , Clotet Bonaventura , Blanco Julià , Massanella Marta ,   KING cohort extension and CoronAVI@S studies
Published: January 2022

SummarySARS-CoV-2 vaccination is the most effective strategy to protect patients with haematologic malignancies against severe COVID-19, but primary vaccine responses are less effective in this population. Here, we characterized the humoral responses following 3 months after mRNA-based vaccines in patients at different stages of the same plasma cell diseases, including monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM) and multiple myeloma on first line therapy (MM), compared to a healthy control population matched by sex and age. We observed that plasmas from uninfected MM patients after 3 months post-vaccine have lower SARS-CoV-2 specific IgG and IgA antibodies and decreased neutralization capacity compared with MGUS and SMM individuals, and a group of healthy controls. Importantly, we detected significantly higher plasma neutralization capacity in MM individuals who recovered from COVID-19 compared to their uninfected counterparts, highlighting that hybrid immunity elicit stronger immune responses even in this immunocompromised population. In contrast to MM group, no differences in the vaccine-induced humoral response were observed between uninfected MGUS, SMM and healthy individuals. In conclusion, a booster vaccine dose is recommended in uninfected MM patients to develop an adequate and effective humoral response to SARS-CoV-2 vaccine.
Gene-based polygenic risk scores analysis of alcohol use disorder in African Americans
Authors: Lai Dongbing , Schwantes-An Tae-Hwi Linus , Abreu Marco , Chan Grace , Hesselbrock Victor , Kamarajan Chella , Liu Yunlong , Meyers Jacquelyn L. , Nurnberger John I , Plawecki Martin H. , Wetherill Leah , Schuckit Marc , Zhang Pengyue , Edenberg Howard J. , Porjesz Bernice , Agrawal Arpana , Foroud Tatiana 
Published: January 2022

ABSTRACTGenome-wide association studies (GWAS) in admixed populations such as African American (AA) have limited sample sizes, resulting poor performance of polygenic risk scores (PRS). Based on the observations that many disease-causing genes are shared between AA and European ancestry (EA) populations, and some disease-causing variants are located within boundaries of these genes, we proposed a novel gene-based PRS method (PRSgene) by using variants located in these shared disease-causing genes. Using AA GWAS of alcohol use disorder (AUD) from the Million Veteran Program and EA GWAS of problematic alcohol use as the discovery datasets, we identified 858 variants from 410 genes that were AUD-related in both AA and EA. PRSgenecalculated using these variants were significantly associated with AUD in three AA cohorts (P-values: 7.61E-05-6.27E-03; Betas: 0.15-0.21) and outperformed PRS calculated using all variants (P-values: 7.28E-03-0.16; Betas: 0.06-0.18). PRSgenewas also associated with AUD in an EA cohort (P-value=0.02, Beta=0.11). In AA, individuals in the highest PRSgenedecile had an Odds Ratio of 1.76 (95% CI: 1.32-2.34) to develop AUD compared to those in the lowest decile. The 410 genes were enriched in 54 Gene Ontology biological processes, including ethanol oxidation and processes involving synaptic system, which are known to be AUD-related. Additionally, 26 genes were targets of drugs to treat AUD or other diseases, but may be repurposed to treat AUD. Our study demonstrated that our gene-based PRS had improved performance in evaluating AUD risk in AA and provided new insight into identification of AUD genes.
Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex
Authors: Foucher Anne-Emmanuelle , Touat-Todeschini Leila , Juarez-Martinez Ariadna B. , Laroussi Hamida , Karczewski Claire , Acajjaoui Samira , Soler-López Montserrat , Cusack Stephen , Mackereth Cameron D. , Verdel André , Kadlec Jan 
Published: January 2022

AbstractTo eliminate specific or aberrant transcripts, eukaryotic cells use nuclear RNA-targeting complexes that deliver them to the exosome for degradation. S. pombe MTREC complex, and its human counterpart PAXT, are key players in this mechanism. Red1 and hZFC3H1 function as scaffolds of these respective complexes. Here, we present an NMR structure of a helix-turn-helix domain of Red1 in complex with the N-terminus of Iss10 and show this interaction is required for proper cellular growth and meiotic mRNA degradation. We also report a crystal structure of a Red1-Ars2 complex that explains the mutually exclusive interactions of hARS2 with various “ED/EGEI/L” motif-possessing RNA regulators such as hZFC3H1, hFLASH or hNCBP3. Finally, we show that both Red1 and hZFC3H1 homo-dimerize via their coiled-coil regions indicating that MTREC and PAXT likely function as dimers. Our results, combining structures of three Red1 binding interfaces with in vivo studies, provide mechanistic insights into conserved features of MTREC/PAXT architecture.
Hedgehog regulation of epithelial cell state and morphogenesis in the larynx
Authors: Ramachandran Janani , Zhou Weiqiang , Bardenhagen Anna E. , Nasr Talia , Zorn Aaron M. , Ji Hongkai , Vokes Steven A. 
Published: January 2022

AbstractThe larynx enables speech while regulating swallowing and respiration. Larynx function hinges on the laryngeal epithelium which originates as part of the anterior foregut and undergoes extensive remodeling to separate from the esophagus and form vocal folds that interface with the adjacent trachea. Here we find that Sonic hedgehog (SHH) is essential for epithelial integrity in the larynx as well as the anterior foregut. During larynx-esophageal separation, lowShhexpression marks specific domains of actively remodeling epithelium that undergo an epithelial to mesenchymal transition (EMT) characterized by the induction of N-Cadherin and movement of cells out of the epithelial layer. Consistent with a role for SHH signaling in regulating this process,Shhmutants undergo an abnormal EMT throughout the anterior foregut and larynx, marked by a cadherin switch, movement out of the epithelial layer and cell death. Unexpectedly,Shhmutant epithelial cells are replaced by a new population ofPax-1expressing cells that form a rudimentary epithelium. These findings have important implications for interpreting the etiology of HH- dependent birth defects within the foregut. We propose that SHH signaling has a default role in maintaining epithelial identity throughout the anterior foregut and that regionalized reductions in SHH trigger epithelial remodeling.
Molecular basis of broad neutralization against SARS-CoV-2 variants including Omicron by a human antibody
Authors: Ju Bin , Zheng Qingbing , Guo Huimin , Fan Qing , Li Tingting , Song Shuo , Sun Hui , Shen Senlin , Zhou Xinrong , Cheng Lin , Xue Wenhui , Cui Lingyan , Zhou Bing , Ge Xiangyang , Wang Haiyan , Wang Miao , Li Shaowei , Xia Ningshao , Zhang Zheng 
Published: January 2022

AbstractOmicron, a newly emerging SARS-CoV-2 variant, carried a large number of mutations in the spike protein leading to an unprecedented evasion from many neutralizing antibodies (nAbs). Here, we performed a head-to-head comparison of Omicron with other existing highly evasive variants in terms of their reduced sensitivities to antibodies, and found that Omicron variant is significantly more evasive than Beta and Mu variants. Of note, some key mutations occur in the conserved epitopes identified previously, especially in the binding sites of Class 4 nAbs, contributing to the increased Ab evasion. We also reported a broadly nAb (bnAb), VacW-209, which effectively neutralized all tested SARS-CoV-2 variants and even SARS-CoV. Finally, we determined six cryo-electron microscopy structures of VacW-209 complexed with the spike ectodomains of wild-type, Delta, Mu, C.1.2, Omicron, and SARS-CoV, and revealed the molecular basis of the broadly neutralizing activities of VacW-209 against SARS-CoV-2 variants. Overall, Omicron has once again raised the alarm over virus variation with significantly compromised neutralization. BnAbs targeting more conserved epitopes among variants will continue to play a key role in pandemic control and prevention.One sentence summaryStructural and functional analyses reveal that a human antibody named VacW-209 confers broad neutralization against SARS-CoV-2 variants including Omicron by recognizing a highly conserved epitope.
NRP1 and furin as putative mediators of SARS-CoV-2 entry into human brain cells
Authors: Kumar Ashutosh , Narayan Ravi K. , Kumar Sujeet , Pareek Vikas , Kumari Chiman , Jha Rakesh K. , Prasoon Pranav 
Published: January 2022

ABSTRACTCOVID-19 has prominent neurological manifestations including psychiatric symptoms, indicating significant synaptic pathology. Surprisingly, existing evidence suggests negligible expression of the key SARS-CoV-2 host cell entry mediators ACE2 and TMPRSS2 in human brain, which complicates understanding of the pathomechanisms of the neuropsychiatric manifestations in COVID-19. Recent studies suggested that an alternative host-cell entry receptor, NRP1, can mediate entry of furin cleaved SARS-CoV-2 spike proteins into the host cells. However, the role of NRP1 and furin in mediating SARS-CoV-2 entry in human brain cells has been least explored and remains a lacuna in the literature. We performed an in silico analysis of the transcriptomic and proteomic expressions of SARS-CoV-2 host-cell entry receptors and associated tissue proteases in human brain tissue, using the publically available databases. Based on the expression analysis, SARS-CoV-2 entry in human brain cells is likely to be mediated through NRP1 and furin.Graphical Abstract
Probing the proton release by Photosystem II in the S1 to S2 high-spin transition
Authors: Boussac Alain , Sugiura Miwa , Sellés Julien 
Published: January 2022

AbstractThe stoichiometry and kinetics of the proton release were investigated during each transition of the S-state cycle in Photosystem II (PSII) from Thermosynechococcus elongatus containing either a Mn4CaO5 (PSII/Ca) or a Mn4SrO5 (PSII/Sr) cluster. The measurements were done at pH 6.0 and pH 7.0 knowing that, in PSII/Ca at pH 6.0 and pH 7.0 and in PSII/Sr at pH 6.0, the flash-induced S2-state is in a low-spin configuration (S2LS) whereas in PSII/Sr at pH 7.0, the S2-state is in a high-spin configuration (S2HS) in half of the centers. Two measurements were done; the time-resolved flash dependent i) absorption of either bromocresol purple at pH 6.0 or neutral red at pH 7.0 and ii) electrochromism in the Soret band of PD1 at 440 nm. The fittings of the oscillations with a period of four indicate that one proton is released in the S1 to S2HS transition in PSII/Sr at pH 7.0. It has previously been suggested that the proton released in the S2LS to S3 transition would be released in a S2LSTyrZ● → S2HSTyrZ● transition before the electron transfer from the cluster to TyrZ● occurs. The release of a proton in the S1TyrZ● →S2HSTyrZ transition would logically imply that this proton release is missing in the S2HSTyrZ● to S3TyrZ transition. Instead, the proton release in the S1 to S2HS transition in PSII/Sr at pH 7.0 was mainly done at the expense of the proton release in the S3 to S0 and S0 to S1 transitions. However, at pH 7.0, the electrochromism of PD1 seems larger in PSII/Sr when compared to PSII/Ca in the S3 state. This points to the complex link between proton movements in and immediately around the Mn4 cluster and the mechanism leading to the release of protons into the bulk.
Doderlin: Isolation and Characterization of a Broad-Spectrum Antimicrobial Peptide from Lactobacillus acidophilus
Authors: da Silva Bruna S. , Díaz-Roa Andrea , Yamane Erica S. , Hayashi Mirian A. F. , da Silva Junior Pedro Ismael 
Published: January 2022

ABSTRACTLactobacillus acidophilus are Gram-positive bacteria distributed in diverse environments, and as being a component of the normal microbiota of gastrointestinal and urogenital tract, being relevant to humans. Classified as lactic acid bacteria, due to the pro-duction of lactic acid, Lactobacillus can also produce antimicrobial peptides (AMPs), which is a compound synthesized by all forms of life aiming for protecting themselves from threats and to increase their competitivity to survive in a specific environment. AMPs are molecules capable of inhibiting the growth of microorganisms and, due to the indiscriminate use of conventional antibiotics and the emergence of multi-resistant bacteria, they have become an alternative, not only for treating multi-resistant infections, but also for probiotic product confection and food conservation. Considering the rampant rise of resistance, the present study aimed to isolate and characterize antimicrobial peptides from Lactobacillus acidophilus extracts. Samples were obtained from Lactobacillus acid extract supernatant which was pre-fractionated on disposable cartridges, followed by a high-performance liquid chromatography (HPLC). The collected fractions were evaluated in a liquid growth inhibition assay where eight fractions antimicrobial activity were obtained. One of them was selected for further characterization by mass spectrometry (MS), due to its antimicrobial activity against Candida albicans and conclusive results in mass spectrometry analysis. This molecule was identified as a peptide having a molecular mass of 1788.01 Da, peptide sequence NEPTHLLKAFSKAGFQ, and named Doderlin. Interestingly, antimicrobial molecules isolated from L. acidophilus have already been described previously, but few reports in the literature describe an AMP effective against C. albicans as reported here. The results obtained suggest that this newly discovered molecule have a biological property with potential to be applied in pharmaceutical and food companies in the fight against contamination and/or for treating infections caused by microorganisms.IMPORTANCEDoderlin, this newly discovered molecule have a biological property with potential to be applied in pharmaceutical and food companies in the fight against contamination and/or for treating infections caused by microorganisms.
The developmental origin and the specification of the adrenal cortex in humans and cynomolgus monkeys
Authors: Cheng Keren , Seita Yasunari , Moriwaki Taku , Noshiro Kiwamu , Sakata Yuka , Hwang Young Sun , Torigoe Toshihiko , Saitou Mitinori , Tsuchiya Hideaki , Iwatani Chizuru , Hosaka Masayoshi , Ohkouchi Toshihiro , Watari Hidemichi , Umazume Takeshi , Sasaki Kotaro 
Published: January 2022

ABSTRACTDevelopment of the adrenal cortex, a vital endocrine organ, originates in the adrenogonadal primordium, a common progenitor for both the adrenocortical and gonadal lineages in rodents. In contrast, we find that in humans and cynomolgus monkeys, the adrenocortical lineage originates in a temporally and spatially distinct fashion from the gonadal lineage, arising earlier and more anteriorly within the coelomic epithelium. The adrenal primordium arises from adrenogenic coelomic epithelium via an epithelial-to- mesenchymal-like transition, which then progresses into the steroidogenic fetal zone via both direct and indirect routes. Notably, we find that adrenocortical and gonadal lineages exhibit distinct HOX codes, suggesting distinct anterior-posterior regionalization. Together, our assessment of the early divergence of these lineages provides a molecular framework for understanding human adrenal and gonadal disorders.One Sentence SummarySpecification of the adrenal cortex occurs in adrenogenic coelomic epithelium independent of gonadogenesis in humans and cynomolgus monkeys
High prevalence of long-term olfactory disorders in healthcare workers after COVID-19: a case-control study
Authors: Frasnelli Johannes , Tognetti Arnaud , Winter Anja L. , Thunell Evelina , Olsson Mats J. , Greilert Nina , Olofsson Jonas K. , Havervall Sebastian , Thålin Charlotte , Lundström Johan N. 
Published: January 2022

AbstractBackgroundMore than a year after recovering from COVID-19, a large proportion of individuals, many of whom work in the healthcare sector, still report olfactory dysfunctions. However, olfactory dysfunction was common already before the COVID-19 pandemic, making it necessary to also consider the existing baseline prevalence of olfactory dysfunction. To establish the adjusted prevalence of COVID-19 related olfactory dysfunction, we assessed smell function in healthcare workers who had contracted COVID-19 during the first wave of the pandemic using psychophysical testing.MethodsParticipants were continuously tested for SARS-CoV-2 IgG antibodies since the beginning of the pandemic. To assess the baseline rate of olfactory dysfunction in the population and to control for the possibility of skewed recruitment of individuals with prior olfactory dysfunction, consistent SARS-CoV-2 IgG naïve individuals were tested as a control group.ResultsFifteen months after contracting COVID-19, 37% of healthcare workers demonstrated a quantitative reduction in their sense of smell, compared to only 20% of the individuals in the control group. Fifty-one percent of COVID-19-recovered individuals reported qualitative symptoms, compared to only 5% in the control group. In a follow-up study 2.6 years after COVID-19 diagnosis, 24% of all tested recovered individuals still experienced parosmia.ConclusionsIn summary, 65% of healthcare workers experienced parosmia/hyposmia 15 months after contracting COVID-19. When compared to a control group, the prevalence of olfactory dysfunction in the population increased by 41 percentage points. Parosmia symptoms were still lingering two-and-a half years later in 24% of SARS-CoV-2 infected individuals. Given the amount of time between infection and testing, it is possible that the olfactory problems may not be fully reversible in a plurality of individuals.
Finite-difference wave-propagation models for dispersive media: impact of space-time discretization
Authors: Zygiridis Theodoros , Kantartzis Nikolaos 
Published: January 2022

Purpose
The computational accuracy and performance of finite-difference time-domain (FDTD) methods are affected by the implementation of approximating derivative formulae in diverse ways. This study aims to focus on FDTD models featuring material dispersion with negligible losses and investigates two specific aspects that, until today, are usually examined in the context of non-dispersive media only. These aspects pertain to certain abnormal characteristics of coarsely resolved electromagnetic waves and the selection of the proper time-step size, in the case of a high-order discretization scheme.

Design/methodology/approach
Considering a Lorentz medium with negligible losses, the propagation characteristics of coarsely resolved waves is examined first, by investigating thoroughly the numerical dispersion relation of a typical discretization scheme. The second part of the study is related to the unbalanced space-time errors in FDTD schemes with dissimilar space-time approximation orders. The authors propose a remedy via the suitable choice of the time-step size, based on the single-frequency minimization of an error expression extracted, again, from the scheme’s numerical dispersion formula.

Findings
Unlike wave propagation in free space, there exist two parts of the frequency spectrum where waves in a Lorentz medium experience non-physical attenuation and display non-changing propagation constants, due to coarse discretization. The authors also show that an optimum time-step size can be determined, in the case of the (2,4) FDTD scheme, which minimizes the selected error formula at a specific frequency point, promoting more efficient implementations.

Originality/value
Unique characteristics displayed by discretized waves, which have been known for non-dispersive media, are examined and verified for the first time in the case of dispersive materials, thus completing the comprehension of the space-time discretization impact on simulated quantities. In addition, the closed-form formula of the optimum time-step enables the efficient implementation of the (2,4) FDTD method, minimizing the detrimental influence of the low-order temporal integration.
An introduction to the parabolic equation method for electromagnetic wave propagation in tunnels
Authors: Rasool Hafiz Faiz , Qureshi Muhammad Ali , Aziz Abdul , Akhtar Zain Ul Abiden , Khan Usman Ali 
Published: January 2022

Purpose
The purpose of this paper is to provide a brief introduction of the finite difference based parabolic equation (PE) modeling to the advanced engineering students and academic researchers.

Design/methodology/approach
A three-dimensional parabolic equation (3DPE) model is developed from the ground up for modeling wave propagation in the tunnel via a rectangular waveguide structure. A discussion of vector wave equations from Maxwell’s equations followed by the paraxial approximations and finite difference implementation is presented for the beginners. The obtained simulation results are compared with the analytical solution.

Findings
It is shown that the alternating direction implicit finite difference method (FDM) is more efficient in terms of accuracy, computational time and memory than the explicit FDM. The reader interested in maximum details of individual contributions such as the latest achievements in PE modeling until 2021, basic PE derivation, PE formulation’s approximations, finite difference discretization and implementation of 3DPE, can learn from this paper.

Research limitations/implications
For the purpose of this paper, a simple 3DPE formulation is presented. For simplicity, a rectangular waveguide structure is discretized with the finite difference approach as a design problem. Future work could use the PE based FDM to study the possibility of utilization of meteorological techniques, including the effects of backward traveling waves as well as making comparisons with the experimental data.

Originality/value
The proposed work is directly applicable to typical problems in the field of tunnel propagation modeling for both national commercial and military applications.
A comparative study of organizational commitment process in the private and public sectors
Authors: Boukamcha Fayçal 
Published: January 2022

Purpose
The purpose of this paper is to shed light on the motivational process that leads to commitment development in the private and public sectors. It has been suggested that employee’s commitment is mainly predicted by job satisfaction and motivational factors such as internal communication, training, structural empowerment, incentive systems, transformational leadership and person–organization fit.

Design/methodology/approach
A comparative approach, between a set of private and public organizations, was undertaken. A survey was conducted on two random samples of workers belonging to both types of organizations.

Findings
The findings report a set of similarities and discrepancies between the private and the public organizations in terms of motivational factors that lead to job satisfaction and employees’ commitment.

Originality/value
This research brings additional value to the comparative literature on organizational analysis. It is one of the scarce comparative research in the North African context that deal with motivational factors at private and public workplaces.