bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Cutaneous Features of Patients Infected With SARS-CoV-2 Hospitalized for Pneumonia: A Cross-sectional Study
Authors: Mascitti Hélène , Bonsang Benjamin , Dinh Aurélien , Assan Florence , Perronne Véronique , Leblanc Thibault , Duran Clara , Bouchand Frédérique , Matt Morgan , Le Gal Aurélie , N’guyen Van Thanh Julia , Lanore Aymeric , Jacob Louis , Kiavue Nicolas , Siméon Soline , Bessis Simon , de Truchis Pierre , Landowski Stéphanie , Davido Benjamin , Moreau Frédérique , Rameix-Welti Marie-Anne , Gault Elyanne , Gaillard Jean-Louis , Roux Anne-Laure , Sivadon-Tardy Valérie , Salomon Elsa , El Sayed Faten , Carlier Robert , Emile Jean-François , Perronne Christian , Bourgault-Villada Isabelle 
Published: October 2020

Abstract

Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a current pandemic worldwide. This virus can reach all organs and disturbs the immune system, leading to a cytokine storm in severe forms. We aimed to report cutaneous features among coronavirus disease 2019 (COVID-19) hospitalized patients.

Methods
We performed a cross-sectional study on 1 given day among all patients hospitalized in acute care for COVID-19 and included all patients with cutaneous features. Follow-up 48 hours later was obtained.

Results
Among 59 adult patients hospitalized on the day of the study in an infectious diseases ward for SARS-CoV-2 infection who were confirmed by molecular assay and/or radiological findings (computed tomography scan), 40 were included. Several cutaneous manifestations were found: macular exanthema (80%), face edema (32%), livedo (13%), urticarial rash (8%), purpura (5%), oral lichenoid lesions (33%), and conjunctivitis (18%). Cutaneous biopsy was performed in 17 patients. Histological findings showed mast cell hyperplasia (100%), superficial perivascular infiltrate of lymphocytes (94%), and superficial edema (47%) consistent with capillary leak.

Conclusions
Various dermatological signs can be encountered during COVID-19. A macular rash was the most frequent. All cutaneous features could be related to a vascular leak process.
Randomized Trial Evaluating the Neurotoxicity of Dolutegravir/Abacavir/Lamivudine and Its Reversibility After Switching to Elvitegravir/Cobicistat/Emtricitabine/Tenofovir Alafenamide: GESIDA 9016
Authors: Perez Valero Ignacio , Cabello Alfonso , Ryan Pablo , De La Fuente-Moral Sara , Santos Ignacio , Vivancos Maria Jesus , Gonzalez Alicia , Gorgolas Miguel , Cuevas Guillermo , Diaz De Santiago Alberto , Cano Joanna , Rua Guadalupe , Yllescas Maria , González García Juan Julian 
Published: October 2020

Abstract

Background
Despite evidence shown of dolutegravir (DTG)-related neurotoxicity, which may be more common when combined with abacavir (ABC), its reversibility has not been explored in a clinical trial.

Methods
We conducted a randomized, multicenter, open-label, pilot trial to evaluate the reversibility of patient-reported neuropsychiatric symptoms, developed or worsened on DTG/ABC/lamivudine (DTG/ABC/3TC), in virologically suppressed patients switched to cobicistat-boosted-elvitegravir/emtricitabine/tenofovir-alafenamide (EVG/COBI/FTC/TAF). Participants were randomized to immediate switch (baseline) or to defer switch (week 4), and then all completed 24 weeks of follow up on EVG/COBI/FTC/TAF. At each visit, participants completed Pittsburgh Sleep Quality Index (PSQI) and Hospital Anxiety and Depression (HAD) scales and were interviewed about 11 neuropsychiatric symptoms potentially related with DTG through a questionnaire. At baseline and at the end of follow up, they also performed neurocognitive testing. Our primary objective was to compare changes in neuropsychiatric symptoms and PSQI and HAD scales between arms at week 4. Secondary objectives were to evaluate changes in neuropsychiatric symptoms and PSQI and HAD scales at weeks 4, 12, and 24 after switching to EVG/COBI/FTC/TAF and in neurocognitive performance and magnetic resonance imaging biomarkers at end of follow up.

Results
Thirty-eight participants were included. Study arms were similar at baseline. At week 4, neuropsychiatric symptoms and PSQI and HAD scores remained unchanged in participants receiving DTG/ABC/3TC and improved significantly in participants receiving EVG/COBI/FTC/TAF. These significant improvements were also observed at weeks 4, 12, and 24 after all participants switched to EVG/COBI/FTC/TAF. In addition, global neurocognitive performance improved (NPZ-7) after switching to EVG/COBI/FTC/TAF.

Conclusions
Neuropsychiatric symptoms in patients on DTG/ABC/3TC could resolve or improve after switching to EVG/COBI/FTC/TAF.
Toxoplasmosis among cancer patients undergoing chemotherapy: a population study based on the serological, molecular and epidemiological aspects
Authors: Hosseini Seyed Abdollah , Sharif Mehdi , Sarvi Shahabeddin , Janbabai Ghasem , Keihanian Shahrbanoo , Abediankenari Saeid , Gholami Sara , Amouei Afsaneh , Javidnia Javad , Saberi Reza , Shekarriz Ramin , Daryani Ahmad 
Published: October 2020

Abstract

Background
Toxoplasmosis is highly prevalent in northern Iran and immunocompromised individuals are more susceptible to this infection. The present study aimed to determine the seroprevalence, parasitism and genetic diversity of Toxoplasma gondii among patients with cancer undergoing chemotherapy in northern Iran.

Methods
A total of 350 serum samples obtained from cancer patients were collected from laboratory centers in northern Iran. Immunodiagnosis and DNA detection were accomplished by ELISA and PCR. Thereafter, multiplex-nested PCR-restriction fragment length polymorphism was used for the genotyping of T. gondii.

Results
In general, out of 350 patients, 264 (75.4%) and 9 (2.57%) cases were positive for anti-T. gondii IgG and IgM, respectively. Moreover, 19 (5.43%) samples contained T. gondii DNA. From 19 positive samples, 10 high-quality samples with sharp and non-smear bands were selected to determine the genotypes of T. gondii. Accordingly, the samples were classified as genotype #1 (type II clonal; n=4, 40%), genotype #2 (type III clonal; n=3, 30%), genotype #10 (type I clonal; n=2, 20%) and genotype #27 (type I variant; n=1, 10%).

Conclusions
As evidenced by the results, due to the high prevalence of T. gondii, cancer patients in northern Iran are at serious risk of severe toxoplasmosis and its complications. Therefore, oncologists need to regard this critical health problem as a matter requiring urgent attention.
Some morphologically distinguishable hypotrich ciliates share identical 18S rRNA gene sequences – taxonomic insights from a case study onOxytrichaspecies (Protista, Ciliophora)
Authors: Fan Xinpeng , Yao Shunli , Luo Xiaotian , Dong Tianyao , Xu Yuan , Chen Lingyun , Bourland William , Zhao Yan , Huang Jie 
Published: October 2020

AbstractModern taxonomic studies of ciliated protozoa require both morphological and molecular data. One dilemma is how to distinguish morphologically similar species with few nucleotide differences in the widely used marker, the 18S rRNA gene. In the present study, two Oxytricha species were morphologically documented using light and electron microscopy. The mitochondrial cytochrome c oxidase subunit I (COI) gene and a fragment of the rRNA gene covering the 18S-ITS1-5.8S-ITS2-28S rRNA gene regions were sequenced. Phylogenetic analyses of all available Oxytricha granulifera-related populations were performed to reveal the internal relationships of this group. We described a new species, Oxytricha atypica sp. nov., distinguished from its congeners by having seven postoral ventral cirri resulting from the additional fragmentation of anlage V during ontogenesis. Although their 18S rRNA genes differ by only one nucleotide, divergence of the COI gene is as high as 11.8% between O. atypica and the closely related species, O. granulifera. All but one of the COI nucleotide substitutions were synonymous. We documented the highly conserved nature of the 18S rRNA gene in the morphospecies of Oxytricha. Based on these findings, we speculate that O. granulifera contains cryptic species or morphospecies needing further characterization, and new insights for the taxonomy of hypotrich ciliates are also discussed.
The first known riodinid ‘cuckoo’ butterfly reveals deep-time convergence and parallelism in ant social parasites
Authors: Kaminski Lucas A , Volkmann Luis , Callaghan Curtis J , DeVries Philip J , Vila Roger 
Published: October 2020

AbstractMutualistic interactions between butterflies and ants can evolve into complex social parasitism. ‘Cuckoo’ caterpillars, known only in the Lycaenidae, use multimodal mimetic traits to achieve social integration into ant societies. Here, we present the first known ‘cuckoo’ butterfly in the family Riodinidae. Aricoris arenarum remained in taxonomic limbo for &gt; 80 years, relegated to nomen dubium and misidentified as Aricoris gauchoana. We located lost type material, designated lectotypes and documented the morphology and natural history of the immature stages. The multifaceted life cycle of A. arenarum can be summarized in three phases: (1) females lay eggs close to honeydew-producing hemipterans tended by specific Camponotus ants; (2) free-living caterpillars feed on liquids (honeydew and ant regurgitations); and (3) from the third instar onward, the caterpillars are fed and tended by ants as ‘cuckoos’ inside the ant nest. This life cycle is remarkably similar to that of the Asian lycaenid Niphanda fusca, despite divergence 90 Mya. Comparable eco-evolutionary pathways resulted in a suite of ecomorphological homoplasies through the ontogeny. This study shows that convergent interactions can be more important than phylogenetic proximity in shaping functional traits of social parasites.
Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps
Authors: Zhou Xiaogen , Li Yang , Zhang Chengxin , Zheng Wei , Zhang Guijun , Zhang Yang 
Published: October 2020

ABSTRACTProgress in cryo-electron microscopy (cryo-EM) has provided the potential for large-size protein structure determination. However, the solution rate for multi-domain proteins remains low due to the difficulty in modeling inter-domain orientations. We developed DEMO-EM, an automatic method to assemble multi-domain structures from cryo-EM maps through a progressive structural refinement procedure combining rigid-body domain fitting and flexible assembly simulations with deep neural network inter-domain distance profiles. The method was tested on a large-scale benchmark set of proteins containing up to twelve continuous and discontinuous domains with medium-to-low-resolution density maps, where DEMO-EM produced models with correct inter-domain orientations (TM-score >0.5) for 98% of cases and significantly outperformed the state-of-the-art methods. DEMO-EM was applied to SARS-Cov-2 coronavirus genome and generated models with average TM-score/RMSD of 0.97/1.4Å to the deposited structures. These results demonstrated an efficient pipeline that enables automated and reliable large-scale multi-domain protein structure modeling with atomic-level accuracy from cryo-EM maps.
Abnormal antibodies to self-carbohydrates in SARS-CoV-2 infected patients
Authors: Butler Dorothy L. , Gildersleeve Jeffrey C. 
Published: October 2020

AbstractSARS-CoV-2 is a deadly virus that is causing the global pandemic coronavirus disease 2019 (COVID-19). Our immune system plays a critical role in preventing, clearing, and treating the virus, but aberrant immune responses can contribute to deleterious symptoms and mortality. Many aspects of immune responses to SARS-CoV-2 are being investigated, but little is known about immune responses to carbohydrates. Since the surface of the virus is heavily glycosylated, pre-existing antibodies to glycans could potentially recognize the virus and influence disease progression. Furthermore, antibody responses to carbohydrates could be induced, affecting disease severity and clinical outcome. In this study, we used a carbohydrate antigen microarray with over 800 individual components to profile serum anti-glycan antibodies in COVID-19 patients and healthy control subjects. In COVID-19 patients, we observed abnormally high IgG and IgM antibodies to numerous self-glycans, including gangliosides,N-linked glycans, LacNAc-containing glycans, blood group H, and sialyl Lewis X. Some of these anti-glycan antibodies are known to play roles in autoimmune diseases and neurological disorders, which may help explain some of the unusual and prolonged symptoms observed in COVID-19 patients. The detection of antibodies to self-glycans has important implications for using convalescent serum to treat patients, developing safe and effective SARS-CoV-2 vaccines, and understanding the risks of infection. In addition, this study provides new insight into the immune responses to SARS-CoV-2 and illustrates the importance of including host and viral carbohydrate antigens when studying immune responses to viruses.
Biofilm Formation and Virulence ofShigella flexneriis Modulated by pH of Gastrointestinal Tract
Authors: Chiang I-Ling , Wang Yi , Fujii Satoru , Muegge Brian D. , Lu Qiuhe , Stappenbeck Thaddeus 
Published: October 2020

AbstractShigellainfections remain a major public health issue in developing countries. One model ofShigellapathogenesis suggests that the microfold epithelial cells in the small intestine are the preferred initial site of infection. However, a growing body of evidence supports an alternative model wherebyShigellaprimarily infects a much wider range of epithelial cells that reside primarily within the colon. Here, we investigated whether the luminal pH difference between the small intestine and colon could provide evidence in support of either model ofShigella flexneripathogenesis. As virulence factors leading to cellular invasion are linked to biofilms inS. flexneri, we examined the effect of pH onS. flexneri’s ability to form and maintain adherent biofilms when induced by deoxycholate. We showed that a basic pH inhibited formation and dispersed pre-assembled mature biofilms while an acidic pH (similar to the colonic environment) did not have either of these effects. To further elucidate this phenomenon at the molecular level, we probed the transcriptomes of biofilms andS. flexnerigrown in different pH conditions. We identified specific amino acid metabolic pathways (cysteine and arginine) that were enriched in the bacteria that formed the biofilms, but decreased upon pH increase. We then utilized a type III secretion system reporter strain to show that increasing pH reduced deoxycholate-induced virulence ofS. flexneriin a dose dependent manner. Taken together, these experiments support a model wherebyShigellainfection is favored in the colon because of the local pH differences in these organs.
Psychological Well-being and Demographic Factors can Mediate Soundscape Pleasantness and Eventfulness: A large sample study
Authors: Erfanian Mercede , Mitchell Andrew , Aletta Francesco , Kang Jian 
Published: October 2020

AbstractSoundscape studies aim to consider the holistic human perception of a sound environment, including both the physical phenomena and how these are mediated by internal factors: the mechanisms underpinning the interactions between these two aspects are not well understood. This study aims to assess the influence of psychological well-being and demographic factors including age, gender, occupation status, and education levels on the dimensions of the soundscape circumplex, i.e., Pleasantness and Eventfulness. Data was collected in eleven urban locations in London through a large-scale (N=1134) soundscape survey according to the ISO 12913-2 technical specifications and incorporating the WHO-5 well-being index. Linear mixed-effects modelling applying backwards-step feature selection was used to model the interactions between internal factors including psychological well-being, age, gender, occupation status, education levels and the soundscape Pleasantness and Eventfulness, while accounting for the random effects of the survey location. The findings suggest that internal factors account for approximately 1.4% of the variance for Pleasantness and 3.9% for Eventfulness, while the influence of the locations accounted for approximately 34% and 14%, respectively. Psychological well-being is positively associated with perceived Pleasantness, while there is a negative association with Eventfulness only for males. Occupation status, in particular retirement as a proxy of age and gender, was identified as a significant factor for both dimensions. These findings offer empirical grounds for developing theories of the interaction between internal factors and soundscape formation whilst highlighting the importance of the location, namely: the context.
Chronic exposure of ErbB TKIs inhibits DRA expression and activity through an ERK/Elk-1/CREB/AP-1 dependent pathway
Authors: Yang Hong , Lin Ru-Xian , Sarker Rafiquel , Donowitz Mark 
Published: October 2020

AbstractDiarrhea is the major side effect of first- and second-generation ErbB tyrosine kinase inhibitors (TKI), the mechanism of which remains incompletely understood. The current studies were carried out over the time frame that ErbB TKIs usually initiate diarrhea. We report in Caco-2/bbe cells that exposure of ErbB TKIs, but not non-ErbB TKIs for six days at clinically-relevant concentrations significantly reduced the expression of DRA and inhibited apical Cl-/HCO3-exchange activity. The ErbB TKIs decreased DRA expression through an ERK/Elk-1/CREB/AP-1 dependent pathway. The blockade of ERK phosphorylation by ErbB TKIs decreased the phosphorylation of Elk-1 and the amount of total and p-CREB, and reduced the expression of C-Fos, which is part of the AP-1 complex that maintain DRA expression. Altogether, our studies demonstrate that ErbB TKIs decrease expression and activity of DRA, which occurs over the time frame that these drugs clinically cause diarrhea, and since DRA is part of the intestinal neutral NaCl absorptive process, the reduced absorption is likely to represent a major contributor to the ErbB TKI-associated diarrhea.
Non-rodent mammalian zygotes assemble dual spindles despite the presence of paternal centrosomes
Authors: Schneider Isabell , de Ruijter-Villani Marta , Hossain M. Julius , Stout Tom A. E. , Ellenberg Jan 
Published: October 2020

AbstractThe first mitosis of the mammalian embryo must partition the parental genomes contained in two pronuclei. In rodent zygotes, sperm centrosomes are degraded and, instead, acentriolar microtubule organizing centers and microtubule self-organization guide the assembly of two separate spindles around the genomes. In non-rodent mammals, including human or bovine, centrosomes are inherited from the sperm and have been widely assumed to be active. Whether non-rodent zygotes assemble a single centrosomal spindle around both genomes, or follow the dual spindle self-assembly pathway is unclear. To address this, we investigated spindle assembly in bovine zygotes by systematic immunofluorescence and real-time light-sheet microscopy. We show that two independent spindles form around the parental genomes despite the presence of centrosomes, which had little effect on spindle structure and were only loosely connected to the two spindles. We conclude that the dual spindle assembly pathway is conserved in non-rodent mammals. This could explain whole parental genome loss frequently observed in blastomeres of human IVF embryos.SummaryThis study investigates spindle assembly during the first embryonic division in bovine zygotes that, like human, inherit centrosomes from the sperm. It shows that two independent microtubule arrays form by self-organization around parental genomes with only loosely connected centrosomes.
Beyond broadband: towards a spectral decomposition of EEG microstates
Authors: Férat Victor , Seeber Martin , Michel Christoph M. , Ros Tomas 
Published: October 2020

AbstractOriginally applied to alpha oscillations in the 1970s, MS analysis has since been used to decompose mainly broadband EEG signals (e.g. 1-40 Hz). We hypothesized that MS decomposition within separate, narrow frequency bands could provide more fine-grained information for capturing the spatio-temporal complexity of multichannel EEG. In this study using a large open-access dataset (n=203), we decomposed EEG recordings into 4 classical frequency bands (delta, theta, alpha, beta) in order to compare their individual MS segmentations using mutual information as well as traditional MS measures (e.g. mean duration, time coverage). Firstly, we confirmed that MS topographies were spatially equivalent across all frequencies, matching the canonical broadband maps (A, B, C, D). Interestingly however, we observed strong informational independence of MS temporal sequences between spectral bands, together with significant divergence in traditional MS measures. For example, relative to broadband, alpha/beta band dynamics displayed greater time coverage of maps A & B, while map D was more prevalent in delta/theta bands. Moreover, by using a frequency-specificMS taxonomy (e.g. θA, αC), we were able to predict the eyes-open vs closed-behavioural state significantly better using alpha-band MS features compared with broadband ones (80% vs 73% accuracy). Overall, our findings demonstrate the value and validity of spectrally-specific MS analyses, which may prove useful for identifying new neural mechanisms in fundamental research and/or for biomarker discovery in clinical populations.
Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro
Authors: Schloer Sebastian , Brunotte Linda , Mecate-Zambrano Angeles , Zheng Shuyu , Tang Jing , Ludwig Stephan , Rescher Ursula 
Published: October 2020

ABSTRACTThe SARS-COV-2 pandemic and the global spread of coronavirus disease 2019 (COVID-19) urgently calls for efficient and safe antiviral treatment strategies. A straightforward approach to speed up drug development at lower costs is drug repurposing. Here we investigated the therapeutic potential of targeting the host- SARS-CoV-2 interface via repurposing of clinically licensed drugs and evaluated their use in combinatory treatments with virus- and host-directed drugs. We tested the antiviral potential of repurposing the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS-CoV-2 particles in the polarized Calu-3 cell culture model and evaluated the added benefit of a combinatory use of these host-directed drugs with remdesivir, an inhibitor of viral RNA polymerase. Drug treatments were well-tolerated and potent impaired viral replication was observed with all drug treatments. Importantly, both itraconazole-remdesivir and fluoxetine-remdesivir combinations inhibited the production of infectious SARS-CoV-2 particles > 90% and displayed synergistic effects in commonly used reference models for drug interaction. Itraconazole-Remdesivir and Fluoxetine-Remdesivir combinations are promising therapeutic options to control SARS-CoV-2 infection and severe progression of COVID-19.