bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management of Tessier Type 3 Cleft With a Novel Reverse Palatal Expander
Authors: Kim Erinn N. , Moss Whitney D. , Yamashiro Duane K. , Tuncer Fatma B. , Siddiqi Faizi A. 
Published: August 2021

Abstract
The purpose of this clinical report is to present the novel management of a type Tessier 3 cleft which was treated using a palatal expander in reverse fashion to reapproximate the craniofacial skeleton allowing for closure of the palate and soft tissue of the cleft. Reapproximation of the bony component of the cleft was achieved without osteotomies and allowed for easier and earlier realignment of the bony and soft tissue components of the cleft. To our knowledge, this is the first use of reverse palatal expansion in the treatment of type 3 Tessier cleft. Reverse palatal expansion made management of this cleft more straightforward and should be considered as a useful adjunct in the management of wide facial clefts.
Forehead Flap Templates for Nasal Reconstruction Digitally Developed From 2D and 3D Images
Authors: Fishman Zachary , Whyne Cari M. , Fialkov Jeffery A. 
Published: August 2021

Abstract
The forehead flap is the gold standard procedure for nasal reconstruction to address a partial or complete rhinectomy. Traditionally, the three-dimensional (3D) nasal defect is manually templated intraoperatively to design the two-dimensional (2D) flap shape on intact morphology. In this clinical study, digital preoperative planning is used to template with computer-assisted design and manufacturing. Preoperative digital templates were implemented for 3 representative patients (1 in Supplementary Digital Content, http://links.lww.com/SCS/D60). This includes designs for a hemi-rhinectomy case from 3D mirroring, a partial total rhinectomy case generated from a 3D scan, and a total rhinectomy case generated from a 3D morphable model based on a prepathology 2D photo. Digital unwrapping flattened the patient's 3D nasal geometry designs to 2D skin flap shapes. Finally, the 2D designs were printed as traceable intraoperative templates at a 1:1 scale. This clinical study demonstrates the application of digital 3D preoperative templating to improve workflow for nasal reconstruction.
Adverse events following COVID-19 virus vaccination in Japanese young population: The first cross-sectional study conducted by a questionnaire survey after the first-time-injection
Authors: Suehiro Marie , Okubo Shinya , Nakajima Kensuke , Kanda Kosuke , Hayakawa Masanobu , Oiso Shigeru , Kabashima Tsutomu , Fujita Hideaki , Ando Yukio , Muro Takahiro 
Published: August 2021

AbstractA cross-sectional study was conducted to clarify the adverse events of COVID-19 vaccines in Japanese young population.The proportion of participants with adverse events at the vaccination site (immediately or within 30 minutes after vaccination) was 0.5%, and anaphylaxis occurred in one female student (0.03%).We analyzed 1,877 data obtained from a questionnaire survey of 1,993 vaccinated individuals. Eighty-two percent of participants complained of local adverse events. Injection site pain was the most common local adverse event (71%). Systemic adverse events occurred in 48% of participants. The most common adverse event was myalgia (34%).A multivariable logistic regression model was used to determine risk factors.Local adverse events were associated with sex (female) and allergy history, with odds ratios (ORs) (95% confidence interval [CI]) of 2.15 (1.69-2.73) and 1.73 (1.10-2.74), respectively. Systemic adverse events were associated with sex (female), age (<20 years old), allergy history, and history of adverse events with previous medications, with ORs (95% CI) of 2.49 (2.03-3.06), 1.80 (1.44-2.24), 1.39 (1.03-1.89), and 1.53 (1.02-2.29).The results of this study clarified for the first time that age less than 20 years is a risk factor for systemic adverse events from the COVID-19 Vaccine Moderna Intramuscular Injection. This information will give impacts on considering adverse events and its mechanisms in mRNA vaccination.
Cytocapsular Tube-Based Precise Cancer Diagnosis in Colon Cancers
Authors: Yi Tingfang , Wagner Gerhard , Ganshirt Stephen 
Published: August 2021

AbstractColorectal (colon) cancer ranks second in terms of cancer lethality worldwide. It is estimated that approximately 1.93 million new colorectal (colon) cancer cases and approximate one million colorectal cancer deaths occur worldwide in 2020 alone. Cancer metastasis is a major source of cancer lethality. Mechanisms underlying colorectal cancer metastases are long-term obscure. Recently, a new organelle associated with aggressive cancer cells, dubbed cytocapsular tube, was recognized to conduct cancer cell metastases in tissues in vivo. Here, we investigated the roles of cytocapsular tubes in colon cancer metastasis in 9 subtypes of colon cancers with original clinical colon cancer tissues, paracancer tissues of colon cancer, and metastatic colon cancers in multiple other tissues and organs. We found that colon cancer metastasized via cytocapsular tubes and their networks in clinical tissues in vivo. Furthermore, we applied the cytocapsular tube analyses in precise cancer diagnosis in clinical colon cancers and obtained better outcomes in clinical colon cancer management.
Systemic and mucosal IgA responses are variably induced in response to SARS-CoV-2 mRNA vaccination and are associated with protection against subsequent infection
Authors: Sheikh-Mohamed Salma , Isho Baweleta , Chao Gary Y.C. , Zuo Michelle , Cohen Carmit , Lustig Yaniv , Nahass George R. , Salomon-Shulman Rachel E. , Blacker Grace , Fazel-Zarandi Mahya , Rathod Bhavisha , Colwill Karen , Jamal Alainna , Li Zhijie , de Launay Keelia Quin , Takaoka Alyson , Garnham-Takaoka Julia , Patel Anjali , Fahim Christine , Paterson Aimee , Li Angel Xinliu , Haq Nazrana , Barati Shiva , Gilbert Lois , Green Karen , Mozafarihashjin Mohammad , Samaan Philip , Budylowski Patrick , Siqueira Walter L. , Mubareka Samira , Ostrowski Mario , Rini James M. , Rojas Olga L. , Weissman Irving L. , Tal Michal Caspi , McGeer Allison , Regev-Yochay Gili , Straus Sharon , Gingras Anne-Claude , Gommerman Jennifer L. 
Published: August 2021

AbstractAlthough SARS-CoV-2 infects the upper respiratory tract, we know little about the amount, type, and kinetics of antibodies (Ab) generated at this site in response to intramuscular COVID-19 vaccination, and whether these Ab protect against subsequent “breakthrough” infections. We collected longitudinal serum and saliva samples from participants receiving two doses of mRNA COVID-19 vaccines over a 6-month period and measured the relative level of anti-Spike and anti-Receptor Binding Domain (RBD) Ab. We detected anti-Spike/RBD IgG and IgA and associated secretory component in the saliva of most participants receiving 1 dose of mRNA vaccine. Administration of a second dose of mRNA boosted the IgG but not the IgA response, with only 30% of participants remaining positive for IgA at this timepoint. At 6 months post-dose 2, these participants exhibited greatly diminished anti-Spike/RBD IgG and IgA levels concomitant with a reduction in neutralizing activity in the saliva, although the level of secretory component associated anti-Spike was less susceptible to decay. Examining two prospective cohorts of subjects that were monitored for infections post-vaccination, we found that participants who were subsequently infected with SARS-CoV-2 had lower levels of vaccine-induced serum anti-Spike/RBD IgA at 2-4 weeks post-dose 2 compared to participants who did not experience an infection, whereas IgG levels were comparable between groups. These data emphasize the importance of developing COVID-19 vaccines that elicit a durable IgA response.One-Sentence SummaryOur study delves into whether intra-muscular mRNA vaccination regimes confer a local IgA response in the oral cavity and whether the IgA response is associated with protection against breakthrough infection.
Aspergillosis and Mucormycosis in COVID-19 Patients; a Systematic Review and Meta-analysis
Authors: Afzal Saira , Nasir Mehreen 
Published: August 2021

AbstractFungal infections have increased in number since the onset of this lethal pandemic. The aim of this study is to assess risk factors and case fatality in COVID-19 cases with aspergillosis or mucormycosis. Systematic review and meta-analysis was done according to PRISMA guidelines. Data bases used were Google scholar, Pakmedinet, PUBMED and MEDLINE. 21 case reports and case series of mucormycosis in COVID-19 patients were identified and mean age was 56.3 years (36 males and 12 females). The most common comorbidity was diabetes and site was Rhino orbital mucormycosis. Case fatality of 48 combined cases was calculated to be 52%. 19 articles of aspergillosis were included. Diabetes was the most common comorbidity in cases. The number of male cases were more than females. Incidence of aspergillosis in critically sick COVID-19 patients was calculated to be 9.3%. Case fatality was calculated to be 51.2%. Screening can be a beneficial tool for decreasing the morbidity and mortality.
SARS-CoV-2-specific Humoral and Cell-mediated Immune Responses after Immunization with Inactivated COVID-19 Vaccine in Kidney Transplant Recipients (CVIM 1 Study)
Authors: Bruminhent Jackrapong , Sethaudom Chavachol , Chaumdee Pongsathon , Boongird Sarinya , Kiertiburanakul Sasisopin , Malathum Kumthorn , Nongnuch Arkom , Phuphuakrat Angsana , Jirasiritham Sopon , Janphram Chitimaporn , Thotsiri Sansanee , Upama Supparat , Assanatham Montira ,   Ramathibodi Transplant Infectious Diseases (RTID) Study Group
Published: August 2021

AbstractImmunogenicity following inactivated SARS-CoV-2 vaccination among solid organ transplant recipients has not been assessed. Seventy-five patients (37 kidney transplant [KT] recipients and 38 non-transplant controls) received two doses, at 4-week intervals, of an inactivated whole-virus SARS-CoV-2 vaccine. SARS-CoV-2-specific humoral (HMI) and cell-mediated immunity (CMI) were measured before, 4 weeks post-first dose, and 2 weeks post-second dose. The median age of KT recipients was 50 years (IQR, 42–54) and 89% were receiving calcineurin inhibitors/mycophenolate/corticosteroid regimens. The median time since transplant was 4.5 years (IQR, 2–9.5). Among 35 KT patients, anti-RBD IgG titer after vaccination was not significantly different to baseline, but was significantly lower than in controls (7.8 [95%CI 0.2–15.5] vs 2,691 [95%CI 1,581–3,802], p<0.001) as well as the percentage of surrogate virus neutralizing antibody inhibition (2 [95% CI −1-6] vs 71 [95%CI 61–81], p<0.001). However, the mean of SARS-CoV-2 mixed peptides-specific T-cell responses measured by enzyme-linked immunospot assays was significantly increased compared with baseline (66 [95%CI 36–99] vs. 34 [95%CI 19–50] T-cells/106PBMCs, p=0.02) and comparable to that in controls. Our findings revealed weak HMI and marginal CMI responses in fully vaccinated KT recipients receiving inactivated SARS-CoV-2 vaccine. (Thai Clinical Trials Registry, TCTR20210226002).
Tear antibodies to SARS-CoV-2: implications for transmission
Authors: Selva Kevin J. , Davis Samantha K. , Haycroft Ebene R. , Lee Wen Shi , Lopez Ester , Reynaldi Arnold , Davenport Miles P. , Kent Helen E. , Juno Jennifer A. , Chung Amy W. , Kent Stephen J. 
Published: August 2021

AbstractObjectivesSARS-CoV-2 can be transmitted by aerosols and the ocular surface may be an important route of transmission. Little is known about protective antibody responses to SARS-CoV-2 in tears after infection or vaccination. We analysed SARS-CoV-2 specific IgG and IgA responses in human tears after either COVID-19 infection or vaccination.MethodsWe recruited 16 subjects with COVID-19 infection an average of 7 months previously and 15 subjects before and 2 weeks after Comirnaty (Pfizer-BioNtech) vaccination. Plasma, saliva and basal tears were collected. Pre-pandemic plasma, saliva and basal tears from 11 individuals were included as healthy controls. Antibody responses to 5 SARS-CoV-2 antigens were measured via multiplex.ResultsIgG antibodies to Spike and Nucleoprotein were detected in tears, saliva and plasma from subjects with prior SARS-CoV-2 infection in comparison to uninfected controls. While RBD-specific antibodies were detected in plasma, minimal RBD-specific antibodies were detected in tears and saliva. In contrast, high levels of IgG antibodies to Spike and RBD, but not Nucleoprotein, were induced in tears, saliva and plasma of subjects receiving 2 doses of the Comirnaty vaccine. Increased levels of IgA1 and IgA2 antibodies to SARS-CoV-2 antigens were detected in plasma following infection or vaccination, but were unchanged in tears and saliva.ConclusionBoth infection and vaccination induce SARS-CoV-2-specific IgG antibodies in tears. RBD-specific IgG antibodies in tears were induced by vaccination but were not present 7 months post-infection. This suggests neutralising antibodies may be low in the tears late following infection.
Exploring polygenic-environment and residual-environment interactions for depressive symptoms within the UK Biobank
Authors: Gillett Alexandra C. , Jermy Bradley S. , Lee S. Hong , Pain Oliver , Howard David M. , Hagenaars Saskia P. , Hanscombe Ken B. , Coleman Jonathan R. I. , Lewis Cathryn M. 
Published: August 2021

AbstractSubstantial advances have been made in identifying genetic contributions to depression, but little is known about how the effect of genes can be modulated by the environment, creating a gene-environment interaction. Using multivariate reaction norm models (MRNMs) within the UK Biobank (N=61294-91644), we investigate whether the polygenic and residual variation of depressive symptoms are modulated by 25 a-priori selected covariate traits: 12 environmental variables, 5 biomarkers and polygenic risk scores for 8 mental health disorders. MRNMs provide unbiased polygenic-covariate interaction estimates for a quantitative trait by controlling for outcome-covariate correlations and residual-covariate interactions. Of the 25 selected covariates, 11 significantly modulate depressive symptoms, but no single interaction explains a large proportion of phenotypic variation. Results are dominated by residual-covariate interactions, suggesting that covariate traits (including neuroticism, childhood trauma and BMI) typically interact with unmodelled variables, rather than a genome-wide polygenic score, to influence depressive symptoms. Only average sleep duration has a polygenic-covariate interaction explaining a demonstrably non-zero proportion of the variability in depressive symptoms. This effect is small, accounting for only 1.22% (95% CI [0.54,1.89]) of variation. The presence of an interaction highlights a specific focus for intervention, but the negative results here indicate a limited contribution from polygenic-environment interactions.
SARS-CoV-2 viral load monitoring by extraction-free testing of saliva
Authors: Qiu Yue , Lu Ling , Gao Dexiang , McGrath Patrick , Han Chann , Kogut Igor , Blomquist Bob , Yao Xin , Zevallos Jose P. , Harry Brian L. , Lu Shi-Long 
Published: August 2021

AbstractReal-time quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) remains the foundation of SARS-CoV-2 testing due to its accessibility, scalability, and superior assay performance. Variability in specimens and methods prevent standardization of RT-qPCR assays and reliable quantitative reporting to assess viral load. We developed an extraction-free RT-qPCR assay for detection of SARS-CoV-2 in saliva and monitored viral load until convalescence in COVID-19 patients. Comparison of 231 matched anterior nares swab and saliva specimens demonstrated that extraction-free testing of saliva has equivalent analytical and clinical assay performance compared to testing of RNA extracts from either anterior nares or saliva specimens. Analysis of specimen pairs revealed higher viral loads in the nasal cavity compared to the oral cavity, although this difference did not impact clinical sensitivity for COVID-19. Extraction-free testing of a combination specimen consisting of both nasal swab and saliva is also demonstrated. Assessment of viral load by RT-qPCR and parallel digital droplet PCR (ddPCR) revealed that cycle threshold (Ct) values less than approximately 30 correlated well with viral load, whereas Ct values greater than 30 correspond to low viral loads <10 copies/µL. Therefore, extraction-free saliva testing maximizes testing efficiency without compromising assay performance and approximates viral loads >10 copies/µL. This technology can facilitate high-throughput laboratory testing for SARS-CoV-2, monitor viral load in individual patients, and assess efficacy of therapies for COVID-19.
Reactivation of transposable elements following hybridization in fission yeast
Authors: Tusso Sergio , Suo Fang , Liang Yue , Du Li-Lin , Wolf Jochen B.W. 
Published: August 2021

AbstractHybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this ‘genomic shock hypothesis’ in the fission yeast Schizosaccharomyces pombe. In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. Sequence analysis of active full-length elements, as well as solo-LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo-LTRs prior to the split of the Sp and Sk lineages. Most full-length elements were inserted more recently after hybridization. With the exception of a single full-length element with signs of positive selection, both solo-LTRs, and in particular, full-length elements carried signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increased with the degree of genomic admixture. This study gives a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements and provides evidence for the ‘genomic shock hypothesis’.
pamlr: a toolbox for analysing animal behaviour using pressure, acceleration, temperature, magnetic and light data in R
Authors: Dhanjal-Adams Kiran L. , Willener Astrid S. T. , Liechti Felix 
Published: August 2021

AbstractLight-level geolocators have revolutionised the study of animal behaviour. However, lacking precision, they cannot be used to infer behaviour beyond large-scale movements. Recent technological developments have allowed the integration of barometers, magnetometers, accelerometers and thermometers into geolocator tags, offering new insights into the behaviour of species which were previously impossible to tag.Here, we introduce an R toolbox for identifying behavioural patterns from multisensor geolocator tags, with functions specifically designed for data visualisation, calibration, classification and error estimation. Some functions are also tailored for identifying specific behavioural patterns in birds (most common geolocators-tagged species), but are flexible for other applications.Finally, we highlight opportunities for applying this toolbox to other species beyond birds, the behaviours they might identify and their potential applications beyond behavioural analyses.Data archivingCurrently, the package is on github and will be submitted to CRAN after review. The supporting code (package manual) for this paper is also on https://kiranlda.github.io/PAMLrManual/index.html, but will later be hosted by the Swiss Ornithological Institute.Summarypamlr: a toolbox for analysing animal behaviour using pressure, acceleration, temperature, magnetic and light data in R
Multitask group Lasso for Genome Wide association Studies in diverse populations
Authors: Nouira Asma , Azencott Chloé-Agathe 
Published: August 2021

Genome-Wide Association Studies, or GWAS, aim at finding Single Nucleotide Polymorphisms (SNPs) that are associated with a phenotype of interest. GWAS are known to suffer from the large dimensionality of the data with respect to the number of available samples. Other limiting factors include the dependency between SNPs, due to linkage disequilibrium (LD), and the need to account for population structure, that is to say, confounding due to genetic ancestry.We propose an efficient approach for the multivariate analysis of multi-population GWAS data based on a multitask group Lasso formulation. Each task corresponds to a subpopulation of the data, and each group to an LD-block. This formulation alleviates the curse of dimensionality, and makes it possible to identify disease LD-blocks shared across populations/tasks, as well as some that are specific to one population/task. In addition, we use stability selection to increase the robustness of our approach. Finally, gap safe screening rules speed up computations enough that our method can run at a genome-wide scale.To our knowledge, this is the first framework for GWAS on diverse populations combining feature selection at the LD-groups level, a multitask approach to address population structure, stability selection, and safe screening rules. We show that our approach outperforms state-of-the-art methods on both a simulated and a real-world cancer datasets.
Regulus infers signed regulatory networks in few samples from regions and genes activities
Authors: Louarn Marine , Collet Guillaume , Barré Ève , Fest Thierry , Dameron Olivier , Siegel Anne , Chatonnet Fabrice 
Published: August 2021

MotivationTranscriptional regulation is performed by transcription factors (TF) binding to DNA in context-dependent regulatory regions and determines the activation or inhibition of gene expression. Current methods of transcriptional regulatory networks inference, based on one or all of TF, regions and genes activity measurements require a large number of samples for ranking the candidate TF-gene regulation relations and rarely predict whether they are activations or inhibitions. We hypothesize that transcriptional regulatory networks can be inferred from fewer samples by (1) fully integrating information on TF binding, gene expression and regulatory regions accessibility, (2) reducing data complexity and (3) using biology-based logical constraints to determine the global consistency of the candidate TF-gene relations and qualify them as activations or inhibitions.ResultsWe introduce Regulus, a method which computes TF-gene relations from gene expressions, regulatory region activities and TF binding sites data, together with the genomic locations of all entities. After aggregating gene expressions and region activities into patterns, data are integrated into a RDF endpoint. A dedicated SPARQL query retrieves all potential relations between expressed TF and genes involving active regulatory regions. These TF-region-gene relations are then filtered using a logical consistency check translated from biological knowledge, also allowing to qualify them as activation or inhibition. Regulus compares favorably to the closest network inference method, provides signed relations consistent with public databases and, when applied to biological data, identifies both known and potential new regulators. Altogether, Regulus is devoted to transcriptional network inference in settings where samples are scarce and cell populations are closely related. Regulus is available at https://gitlab.com/teamDyliss/regulus