bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutralization of hepatitis B virus with vaccine-escape mutations by hepatitis B vaccine with large-HBs antigen
Authors: Washizaki Ayaka , Murayama Asako , Murata Megumi , Kiyohara Tomoko , Yato Keigo , Yamada Norie , Aly Hussein Hassan , Tanaka Tomohisa , Moriishi Kohji , Nishitsuji Hironori , Shimotohno Kunitada , Goh Yasumasa , Ishii Ken J. , Yotsuyanagi Hiroshi , Muramatsu Masamichi , Ishii Koji , Takahashi Yoshimasa , Suzuki Ryosuke , Akari Hirofumi , Kato Takanobu 
Published: September 2022

AbstractAlthough the current hepatitis B (HB) vaccine comprising small-HBs antigen (Ag) is potent and safe, attenuated prophylaxis against hepatitis B virus (HBV) with vaccine-escape mutations (VEMs) has been reported. We investigate an HB vaccine consisting of large-HBsAg that overcomes the shortcomings of the current HB vaccine. Yeast-derived large-HBsAg is immunized into rhesus macaques, and the neutralizing activities of the induced antibodies are compared with those of the current HB vaccine. Although the antibodies induced by the current HB vaccine cannot prevent HBV infection with VEMs, the large-HBsAg vaccine-induced antibodies neutralize those infections. The HBV genotypes that exhibited attenuated neutralization via these vaccines are different. Here, we show that the HB vaccine consisting of large-HBsAg is useful to compensate for the shortcomings of the current HB vaccine. The combined use of these HB vaccines may induce antibodies that can neutralize HBV strains with VEMs or multiple HBV genotypes.
Huntington’s disease age at motor onset is modified by the tandem hexamer repeat in TCERG1
Authors: Lobanov Sergey V. , McAllister Branduff , McDade-Kumar Mia , Landwehrmeyer G. Bernhard , Orth Michael , Rosser Anne E. ,   REGISTRY Investigators of the European Huntington’s disease network, Paulsen Jane S. ,   PREDICT-HD Investigators of the Huntington Study Group, Lee Jong-Min , MacDonald Marcy E. , Gusella James F. , Long Jeffrey D. , Ryten Mina , Williams Nigel M. , Holmans Peter , Massey Thomas H. , Jones Lesley 
Published: September 2022

AbstractHuntington’s disease is caused by an expanded CAG tract in HTT. The length of the CAG tract accounts for over half the variance in age at onset of disease, and is influenced by other genetic factors, mostly implicating the DNA maintenance machinery. We examined a single nucleotide variant, rs79727797, on chromosome 5 in the TCERG1 gene, previously reported to be associated with Huntington’s disease and a quasi-tandem repeat (QTR) hexamer in exon 4 of TCERG1 with a central pure repeat. We developed a method for calling perfect and imperfect repeats from exome-sequencing data, and tested association between the QTR in TCERG1 and residual age at motor onset (after correcting for the effects of CAG length in the HTT gene) in 610 individuals with Huntington’s disease via regression analysis. We found a significant association between age at onset and the sum of the repeat lengths from both alleles of the QTR (p = 2.1 × 10−9), with each added repeat hexamer reducing age at onset by one year (95% confidence interval [0.7, 1.4]). This association explained that previously observed with rs79727797. The association with age at onset in the genome-wide association study is due to a QTR hexamer in TCERG1, translated to a glutamine/alanine tract in the protein. We could not distinguish whether this was due to cis-effects of the hexamer repeat on gene expression or of the encoded glutamine/alanine tract in the protein. These results motivate further study of the mechanisms by which TCERG1 modifies onset of HD.
Diagnostic differentiation between asthma and COPD in primary care using lung function testing
Authors: Bouwens Jelle D. M. , Bischoff Erik W. M. A. , in ’t Veen Johannes C. C. M. , Schermer Tjard R. 
Published: September 2022

AbstractAsthma and COPD are defined as different disease entities, but in practice patients often show features of both diseases making it challenging for primary care clinicians to establish a correct diagnosis. We aimed to establish the added value of spirometry and more advanced lung function measurements to differentiate between asthma and COPD. A cross-sectional study in 10 Dutch general practices was performed. 532 subjects were extensively screened on respiratory symptoms and lung function. Two chest physicians assessed if asthma or COPD was present. Using multivariable logistic regression analysis we assessed the ability of three scenarios (i.e. only patient history; diagnostics available to primary care; diagnostics available only to secondary care) to differentiate between the two conditions. Receiver operator characteristics (ROC) curves and area under the curve (AUC) were calculated for each scenario, with the chest physicians’ assessment as golden standard. Results showed that 84 subjects were diagnosed with asthma, 138 with COPD, and 310 with no chronic respiratory disease. In the scenario including only patient history items, ROC characteristics of the model showed an AUC of 0.84 (95% CI 0.78–0.89) for differentiation between asthma and COPD. When adding diagnostics available to primary care (i.e., pre- and postbronchodilator spirometry) AUC increased to 0.89 (95% CI 0.84–0.93; p = 0.020). When adding more advanced secondary care diagnostic tests AUC remained 0.89 (95% CI 0.85–0.94; p = 0.967). We conclude that primary care clinicians’ ability to differentiate between asthma and COPD is enhanced by spirometry testing. More advanced diagnostic tests used in hospital care settings do not seem to provide a better overall diagnostic differentiation between asthma and COPD in primary care patients.
Long-term cardiac pathology in individuals with mild initial COVID-19 illness
Authors: Puntmann Valentina O. , Martin Simon , Shchendrygina Anastasia , Hoffmann Jedrzej , Ka Mame Madjiguène , Giokoglu Eleni , Vanchin Byambasuren , Holm Niels , Karyou Argyro , Laux Gerald S. , Arendt Christophe , De Leuw Philipp , Zacharowski Kai , Khodamoradi Yascha , Vehreschild Maria J. G. T. , Rohde Gernot , Zeiher Andreas M. , Vogl Thomas J. , Schwenke Carsten , Nagel Eike 
Published: September 2022

AbstractCardiac symptoms are increasingly recognized as late complications of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in previously well individuals with mild initial illness, but the underlying pathophysiology leading to long-term cardiac symptoms remains unclear. In this study, we conducted serial cardiac assessments in a selected population of individuals with Coronavirus Disease 2019 (COVID-19) with no previous cardiac disease or notable comorbidities by measuring blood biomarkers of heart injury or dysfunction and by performing magnetic resonance imaging. Baseline measurements from 346 individuals with COVID-19 (52% females) were obtained at a median of 109 days (interquartile range (IQR), 77–177 days) after infection, when 73% of participants reported cardiac symptoms, such as exertional dyspnea (62%), palpitations (28%), atypical chest pain (27%) and syncope (3%). Symptomatic individuals had higher heart rates and higher imaging values or contrast agent accumulation, denoting inflammatory cardiac involvement, compared to asymptomatic individuals. Structural heart disease or high levels of biomarkers of cardiac injury or dysfunction were rare in symptomatic individuals. At follow-up (329 days (IQR, 274–383 days) after infection), 57% of participants had persistent cardiac symptoms. Diffuse myocardial edema was more pronounced in participants who remained symptomatic at follow-up as compared to those who improved. Female gender and diffuse myocardial involvement on baseline imaging independently predicted the presence of cardiac symptoms at follow-up. Ongoing inflammatory cardiac involvement may, at least in part, explain the lingering cardiac symptoms in previously well individuals with mild initial COVID-19 illness.
Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)
Authors: Fayaz Humara , Tyagi Sandhya , Wani Aijaz A. , Pandey Renu , Akhtar Sabina , Bhat Mohd Ashraf , Chitikineni Annapurna , Varshney Rajeev Kumar , Thudi Mahendar , Kumar Upendra , Mir Reyazul Rouf 
Published: September 2022

AbstractChickpea is the most important nutrient-rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with a Axiom(®)50K CicerSNP array and trait phenotyped in two different environments for four seed micronutrients (Zn, Cu, Fe and Mn). The trait data and high-throughput 50K SNP genotypic data were used for the genome-wide association study (GWAS). The study led to the discovery of genes/QTLs for seed Zn, Cu, Fe and Mn, concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all four micronutrient concentrations (P ≤ 0.05). The mean concentrations of seed Zn, Cu, Fe and Mn pooled over the 2 years were 45.9 ppm, 63.8 ppm 146.1 ppm, and 27.0 ppm, respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 marker-trait associations (MTAs), 5 were stable (consistently identified in different environments), 6 were major (explaining more than 15% of the phenotypic variation for an individual trait) and 3 were both major and stable MTAs. A set of 6 MTAs, MTAs (3 for Mn, 2 for Fe, and 1 for Cu) reported by us during the present study have been also reported in the same/almost same genomic regions in earlier studies and therefore declared as validated MTAs. The stable, major and validated MTAs identified during the present study will prove useful in future chickpea molecular breeding programs aimed at enhancing the seed nutrient density of chickpea.
Potential of ESBL-producing Escherichia coli selection in bovine feces after intramammary administration of first generation cephalosporins using in vitro experiments
Authors: Speksnijder David C. , Hopman Nonke E. M. , Kusters Nina E. , Timmerman Arjen , Swinkels Jantijn M. , Penterman Pleun A. A. , Krömker Volker , Bradley Andrew J. , Botteldoorn Nadine , Gehring Ronette , Zomer Aldert L. 
Published: September 2022

AbstractSelection and spread of Extended Spectrum Beta-Lactamase (ESBL) -producing Enterobacteriaceae within animal production systems and potential spillover to humans is a major concern. Intramammary treatment of dairy cows with first-generation cephalosporins is a common practice and potentially selects for ESBL-producing Enterobacteriaceae, although it is unknown whether this really occurs in the bovine fecal environment. We aimed to study the potential effects of intramammary application of cephapirin (CP) and cefalonium (CL) to select for ESBL-producing Escherichia coli in the intestinal content of treated dairy cows and in manure slurry, using in vitro competition experiments with ESBL and non-ESBL E. coli isolates. No selection of ESBL-producing E. coli was observed at or below concentrations of 0.8 µg/ml and 4.0 µg/ml in bovine feces for CP and CL, respectively, and at or below 8.0 µg/ml and 4.0 µg/ml, respectively, in manure slurry. We calculated that the maximum concentration of CP and CL after intramammary treatment with commercial products will not exceed 0.29 µg/ml in feces and 0.03 µg/ml in manure slurry. Therefore, the results of this study did not find evidence supporting the selection of ESBL-producing E. coli in bovine feces or in manure slurry after intramammary use of commercial CP or CL-containing products.
A cross-sectional study of clinical, dermoscopic, histopathological, and molecular patterns of scalp melanoma in patients with or without androgenetic alopecia
Authors: Porto Ana Carolina , Pinto Blumetti Tatiana , Calsavara Vinícius Fernando , Tardin Torrezan Giovana , Andrade de Paula Cláudia Alessandra , Lellis Rute , Pedreira Duprat Neto João , Carraro Dirce Maria , Casagrande Tavoloni Braga J. 
Published: September 2022

AbstractScalp melanoma (SM) has a worse prognosis than melanoma in other locations likely because of late diagnosis due to hair coverage, difficulties in interpreting dermoscopy findings, and its unique molecular profile. We aimed to describe the clinical, histopathological, molecular, and dermoscopic patterns of SM and its relation to androgenetic alopecia/elastosis at the tumor site. Through a retrospective cross-sectional study, we identified all SM diagnosed at the A.C.Camargo Cancer Center between 2008 and 2018. In all, 48 SM were analyzed: 45.8% of which exhibited moderate/severe androgenetic alopecia and 54.1% exhibited elastosis. Androgenetic alopecia/elastosis at the site of the SM was associated with older age (p < 0.001), chronic sun damage (p < 0.001), lentigo maligna subtype (p = 0.029), and photodamaged dermoscopic pattern (p < 0.001). Additionally, 41 cases were evaluated with a 14-gene panel: 53.7% displayed mutations and 46.3% were wild-type. BRAF mutations were most common (77%), with BRAF V600K being more frequent (50%) than BRAF V600E (31.2%). The NF1 gene was evaluated in 40 samples, of which 20% exhibited mutations. SM presents differently in areas covered by hair compared to in areas with androgenetic alopecia. Patients without alopecia may have higher Breslow thickness due to late diagnosis because of hair concealment. The high frequency of detrimental mutations can also explain the poor prognosis of SM.
Measurement of focal light spot at single-photon level with silicon photomultipliers
Authors: Yang Yaxian , Zhang Guoqing , Zhang Chen , Cao Xinyue , Liu Lina , Li Lianbi , Han Xiaoxiang 
Published: September 2022

AbstractFocal spot (light spot) at single-photon level have important applications in many fields. This report demonstrates a method for measuring focal spot size at the single-photon level indirectly. This method utilizes Silicon Photomultiplier (SiPM) as the single-photon sensitive detectors, combined with a nano-positioning stage. The approach involves one- or two-dimensional space scanning and a deconvolution operation, which enable evaluations of the size and spatial distribution of the focal spot formed by a single-photon-level pulsed laser. The results indicate that the average full width at half maximum of the focal spot is about 0.657 μm, which is close to the nominal resolution of the objective lens of the microscope (i.e. 0.42 μm). The proposed method has two key advantages: (1) it can measure focal spot at the single-photon level, and (2) the focal spot can easily be aligned with the detector because the array area of the Geiger mode avalanche photodiode (Gm-APD) cells in SiPM is usually on the order of square millimeter, and there is no need to put an optical slit, knife edge, or pinhole in front of the detector. The method described herein is applicable in weak focal spot detection related fields.
Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris
Authors: Tayşi Nurbanu , Kaymaz Yasin , Ateş Duygu , Sari Hatice , Toker Cengiz , Tanyolaç M. Bahattin 
Published: September 2022

AbstractLens is a member of the Papilionoideae subfamily of Fabaceae and is generally used as a source of vegetable protein as part of human diets in many regions worldwide. Chloroplast (cp) genomes are highly active genetic components of plants and can be utilized as molecular markers for various purposes. As one of the wild lentil species, the Lens ervoides cp genome has been sequenced for the first time in this study using next-generation sequencing. The de novo assembly of the cp genome resulted in a single 122,722 bp sequence as two separate coexisting structural haplotypes with similar lengths. Results indicated that the cp genome of L. ervoides belongs to the inverted repeat lacking clade. Several noteworthy divergences within the coding regions were observed in ndhB, ndhF, rbcL, rpoC2, and ycf2 genes. Analysis of relative synonymous codon usage showed that certain genes, psbN, psaI, psbI, psbE, psbK, petD, and ndhC, preferred using biased codons more often and therefore might have elevated expression and translation efficiencies. Overall, this study exhibited the divergence level between the wild-type and cultured lentil cp genomes and pointed to certain regions that can be utilized as distinction markers for various goals.
Optical thin film coated organic nonlinear crystal for efficient terahertz wave generation
Authors: Uchida Hirohisa , Kawauchi Tetsuya , Otake Gemma , Koyama Chisa , Takeya Kei , Tripathi Saroj R. 
Published: September 2022

AbstractIn the process of terahertz (THz) wave generation via optical rectification of infrared femtosecond pulses in a non-linear optical crystal, the power of terahertz wave is directly proportional to the square of the optical pump power. Therefore, high power terahertz wave can be generated using a high power femtosecond laser provided that the crystal has both high laser induced damage threshold and optical non-linear coefficient. However, a significant amount of pump power is lost in this process due to the Fresnel’s reflection at the air-crystal boundary. In this paper, we numerically and experimentally demonstrate that the coat of optical thin film called Cytop on the 4-N, N-dimethylamino-4’-N’-methyl-stilbazolium tosylate (DAST) crystal effectively reduces the reflection loss of pump power, thereby increasing the THz wave emission efficiency of the DAST crystal. We found that the average power of THz wave emitted by the thin film coated crystal is about 28% higher than the THz power emitted by the uncoated crystal when an equal amount of laser power is used. The thin film coated DAST crystals can be used not only in terahertz measurement systems but also in optical devices such as modulators and waveguides.
Single-base resolution methylomes of somatic embryogenesis in Theobroma cacao L. reveal epigenome modifications associated with somatic embryo abnormalities
Authors: Garcia Claudia , Furtado de Almeida Alex-Alan , Costa Marcio , Britto Dahyana , Correa Fabio , Mangabeira Pedro , Silva Lidiane , Silva Jose , Royaert Stefan , Marelli Jean-Philippe 
Published: September 2022

AbstractPropagation by somatic embryogenesis in Theobroma cacao has some issues to be solved, as many morphologically abnormal somatic embryos that do not germinate into plants are frequently observed, thus hampering plant production on a commercial scale. For the first time the methylome landscape of T. cacao somatic embryogenesis was examined, using whole-genome bisulfite sequencing technique, with the aim to understand the epigenetic basis of somatic embryo abnormalities. We identified 873 differentially methylated genes (DMGs) in the CpG context between zygotic embryos, normal and abnormal somatic embryos, with important roles in development, programmed cell death, oxidative stress, and hypoxia induction, which can help to explain the morphological abnormalities of somatic embryos. We also identified the role of ethylene and its precursor 1-aminocyclopropane-1-carboxylate in several biological processes, such as hypoxia induction, cell differentiation and cell polarity, that could be associated to the development of abnormal somatic embryos. The biological processes and the hypothesis of ethylene and its precursor involvement in the somatic embryo abnormalities in cacao are discussed.
Uncertainty propagation in pore water chemical composition calculation using surrogate models
Authors: Sochala Pierre , Chiaberge Christophe , Claret Francis , Tournassat Christophe 
Published: September 2022

AbstractPerformance assessment in deep geological nuclear waste repository systems necessitates an extended knowledge of the pore water chemical conditions prevailing in host-rock formations. In the last two decades, important progress has been made in the experimental characterization and thermodynamic modeling of pore water speciation, but the influence of experimental artifacts and uncertainties of thermodynamic input parameters are seldom evaluated. In this respect, we conducted an uncertainty propagation study in a reference geochemical model describing the pore water chemistry of the Callovian-Oxfordian clay formation. Nineteen model input parameters were perturbed, including those associated to experimental characterization (leached anions, exchanged cations, cation exchange selectivity coefficients) and those associated to generic thermodynamic databases (solubilities). A set of 13 quantities of interest were studied by the use of polynomial chaos expansions built non-intrusively with a least-squares forward stepwise regression approach. Training and validation sets of simulations were carried out using the geochemical speciation code PHREEQC. The statistical results explored the marginal distribution of each quantity of interest, their bivariate correlations as well as their global sensitivity indices. The influence of the assumed distributions for input parameters uncertainties was evaluated by considering two parametric domain sizes.
Assessing wastewater-based epidemiology for the prediction of SARS-CoV-2 incidence in Catalonia
Authors: Joseph-Duran Bernat , Serra-Compte Albert , Sàrrias Miquel , Gonzalez Susana , López Daniel , Prats Clara , Català Martí , Alvarez-Lacalle Enric , Alonso Sergio , Arnaldos Marina 
Published: September 2022

AbstractWhile wastewater-based epidemiology has proven a useful tool for epidemiological surveillance during the COVID-19 pandemic, few quantitative models comparing virus concentrations in wastewater samples and cumulative incidence have been established. In this work, a simple mathematical model relating virus concentration and cumulative incidence for full contagion waves was developed. The model was then used for short-term forecasting and compared to a local linear model. Both scenarios were tested using a dataset composed of samples from 32 wastewater treatment plants and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) incidence data covering the corresponding geographical areas during a 7-month period, including two contagion waves. A population-averaged dataset was also developed to model and predict the incidence over the full geography. Overall, the mathematical model based on wastewater data showed a good correlation with cumulative cases and allowed us to anticipate SARS-CoV-2 incidence in one week, which is of special relevance in situations where the epidemiological monitoring system cannot be fully implemented.