bluuebunny/crossref_metadata_2025_split huggingface dataset:
Untargeted metabolomic analyses support the main phylogenetic groups of the common plant-associated Alternaria fungi isolated from grapevine (Vitis vinifera)
Authors: Molnár Anna , Knapp Dániel G. , Lovas Miklós , Tóth Gergő , Boldizsár Imre , Váczy Kálmán Zoltán , Kovács Gábor M. 
Published: November 2023

AbstractAlternaria, a cosmopolitan fungal genus is a dominant member of the grapevine (Vitis vinifera) microbiome. Several Alternaria species are known to produce a variety of secondary metabolites, which are particularly relevant to plant protection and food safety in field crops. According to previous findings, the majority of Alternaria species inhabiting grapevine belong to Alternaria sect. Alternaria. However, the phylogenetic diversity and secondary metabolite production of the distinct Alternaria species has remained unclear. In this study, our aim was to examine the genetic and metabolic diversity of endophytic Alternaria isolates associated with the above-ground tissues of the grapevine. Altogether, 270 Alternaria isolates were collected from asymptomatic leaves and grape clusters of different grapevine varieties in the Eger wine region of Hungary. After analyses of the nuclear ribosomal DNA internal transcribed spacer (ITS) and RNA polymerase second largest subunit (rpb2) sequences, 170 isolates were chosen for further analyses. Sequences of the Alternaria major allergen gene (Alt a 1), endopolygalacturonase (endoPG), OPA10-2, and KOG1058 were also included in the phylogenetic analyses. Identification of secondary metabolites and metabolite profiling of the isolates were performed using high-performance liquid chromatography (HPLC)–high-resolution tandem mass spectrometry (HR-MS/MS). The multilocus phylogeny results revealed two distinct groups in grapevine, namely A. alternata and the A. arborescens species complex (AASC). Eight main metabolites were identified in all collected Alternaria isolates, regardless of their affiliation to the species and lineages. Multivariate analyses of untargeted metabolites found no clear separations; however, a partial least squares-discriminant analysis model was able to successfully discriminate between the metabolic datasets from isolates belonging to the AASC and A. alternata. By conducting univariate analysis based on the discriminant ability of the metabolites, we also identified several features exhibiting large and significant variation between A. alternata and the AASC. The separation of these groups may suggest functional differences, which may also play a role in the functioning of the plant microbiome.
Exploring pineapple peel hydrolysate as a sustainable carbon source for xylitol production
Authors: Nasoha Nur Zahidah , Luthfi Abdullah Amru Indera , Roslan Muhammad Faizuddin , Hariz Hikmah Bajunaid , Bukhari Nurul Adela , Manaf Shareena Fairuz Abdul 
Published: November 2023

AbstractThis study explores utilizing pineapple peel (PP) hydrolysate as a promising carbon source for xylitol production, covering scopes from the pre-treatment to the fermentation process. The highest xylose concentration achieved was around 20 g/L via mild acid hydrolysis (5% nitric acid, 105 °C, 20-min residence time) with a solid loading of 10%. Two sets fermentability experiments were carried out of varying pH levels in synthetic media that includes acetic acid as the main inhibitors and hydrolysate supplemented with diverse nitrogen source. The results revealed that pH 7 exhibited the highest xylitol production, yielding 0.35 g/g. Furthermore, urea was found to be a highly promising and cost-effective substitute for yeast extract, as it yielded a comparable xylitol production of 0.31 g/g with marginal difference of only 0.01 g/g compared to yeast extract further highlights the viability of urea as the preferred option for reducing xylitol production cost. The absence of a significant difference between the synthetic media and hydrolysate, with only a marginal variance of 0.35 to 0.32 g/g, implies that acetic acid is indeed the primary constraint in xylitol production using PP hydrolysate. The study sheds light on PP biomass's potential for xylitol production, aligning economic benefits with environmental sustainability and waste management.
Deep learning-based prediction of the retinal structural alterations after epiretinal membrane surgery
Authors: Kim Joseph , Chin Hee Seung 
Published: November 2023

AbstractTo generate and evaluate synthesized postoperative OCT images of epiretinal membrane (ERM) based on preoperative OCT images using deep learning methodology. This study included a total 500 pairs of preoperative and postoperative optical coherence tomography (OCT) images for training a neural network. 60 preoperative OCT images were used to test the neural networks performance, and the corresponding postoperative OCT images were used to evaluate the synthesized images in terms of structural similarity index measure (SSIM). The SSIM was used to quantify how similar the synthesized postoperative OCT image was to the actual postoperative OCT image. The Pix2Pix GAN model was used to generate synthesized postoperative OCT images. Total 60 synthesized OCT images were generated with training values at 800 epochs. The mean SSIM of synthesized postoperative OCT to the actual postoperative OCT was 0.913. Pix2Pix GAN model has a possibility to generate predictive postoperative OCT images following ERM removal surgery.
Analysis of factors of willingness to adopt intelligent construction technology in highway construction enterprises
Authors: Zhou Zhi-chao , Su Yi-kun , Zheng Zhi-zhe , Wang Yi-lin 
Published: November 2023

AbstractThis study aims to investigate the factors that influence the willingness of highway construction enterprises in China to adopt intelligent construction technology. Based on the existing literature, a TOSE framework was proposed, and four dimensions and 15 hypothesized influencing factors were identified through expert interviews. By using a combination of PLS-SEM and ANN, 513 survey data were analyzed to determine the linear and non-linear relationships of the influencing factors on the willingness to adopt. The results showed that all 14 hypothesized factors had varying degrees of positive or negative effects on the willingness to adopt, except for organizational culture, which was found to have no significant impact. Specifically, technology cost was found to be the most influential negative factor, while market demand and organizational structure were the most influential positive factors. The findings of this study have important reference value for decision makers and participants in highway construction enterprises, as well as other construction companies when considering the adoption of smart construction technologies. The originality of this research lies in the novel application of the TOSE framework to investigate smart construction technology adoption, and the combined use of PLS-SEM and ANN to examine both linear and nonlinear relationships between variables for the first time.
Predictors of intracranial hemorrhage in neonatal patients on extracorporeal membrane oxygenation
Authors: Wood Sara , Iacobelli Riccardo , Kopfer Sarah , Lindblad Caroline , Thelin Eric Peter , Fletcher-Sandersjöö Alexander , Broman Lars Mikael 
Published: November 2023

AbstractExtracorporeal membrane oxygenation (ECMO) is a life-supportive treatment in neonatal patients with refractory lung and/or heart failure. Intracranial hemorrhage (ICH) is a severe complication and reliable predictors are warranted. The aims of this study were to explore the incidence and possible predictors of ICH in ECMO-treated neonatal patients. We performed a single-center retrospective observational cohort study. Patients aged ≤ 28 days treated with ECMO between 2010 and 2018 were included. Exclusion criteria were ICH, ischemic stroke, cerebrovascular malformation before ECMO initiation or detected within 12 h of admission, ECMO treatment < 12 h, or prior treatment with ECMO at another facility > 12 h. The primary outcome was a CT-verified ICH. Logistic regression models were employed to identify possible predictors of the primary outcome. Of the 223 patients included, 29 (13%) developed an ICH during ECMO treatment. Thirty-day mortality was 59% in the ICH group and 16% in the non-ICH group (p < 0.0001). Lower gestational age (p < 0.01, odds ratio (OR) 0.96; 95%CI 0.94–0.98), and higher pre-ECMO lactate levels (p = 0.017, OR 1.1; 95%CI 1.01–1.18) were independently associated with increased risk of ICH-development. In the clinical setting, identification of risk factors and multimodal neuromonitoring could help initiate steps that lower the risk of ICH in these patients.
Introducing the Muzzammil classification for spoke wheel injuries in children to enhance injury assessment and treatment in developing countries
Authors: Muzzammil Muhammad , Minhas Muhammad Saeed , Yaqoob Uzair , Shah Syed Ghulam Mujtaba , Jahanzeb Syed , Qadir Abdul , Fazlani Sohail Ahmed , Jabbar Saadia 
Published: November 2023

AbstractMotorbike spoke wheel injuries (SWIs) among children are a notable public health concern, especially in low and middle-income regions. The primary objective of this study is to comprehensively examine the patterns of motorbike spoke wheel injuries (SWIs) in children. Additionally, the study introduces a novel classification system for these injuries. The implementation of this classification system aims to streamline the management of SWIs, making it more efficient and facilitating the development of standardized treatment protocols. This prospective observational study was conducted in the Accident and Emergency Department from January 2019 to 2021. Children < 14 years of age of either gender with foot and ankle injury due to motorbike spoke wheels as passengers and presenting within 3 days were included. The motorbike SWI was assessed for its location and classified by a new classification as Class I, Soft tissue injury without skin loss; Class II, Skin loss of more than 1 cm without underlying tissue involvement; Class III, Skin loss with underlying tissue involvement, this class is further divided on basis of underlying soft-tissue involvement; Class IV: mangled foot/toe. Management plan and outcome were noted. In our study158 children suffering from SWI were registered with a mean age of 6.2 ± 5.4 years, 127 (80.37%) males and 31 (19.62%) females. Class I injury was seen in 18 (11.39%) patients, class II in 69 (43.67%), and class III in 68 (43.03%) patients. Class III injuries were further subcategorized as follows: IIIT (Tendon) injuries, which accounted for 32 cases (20.25%); IIIB (Bone) injuries, with 29 cases (18.35%); and IIINV (Neurovascular) injuries, identified in 7 cases (4.43%). Class IV injuries were observed in 3 (1.8%) children. The flap was needed in 33 (20.88%) patients. There were no complications like flap necrosis or graft rejection. In this current study, a new classification system specific for a motorbike SWI has been introduced along with its application on children presenting at tertiary care hospital’s emergency department. The application of the proposed classification will enable universal management guidelines for SWIs, especially in the Ino-Pak region where SWIs are common.
Abnormal basic visual processing functions in binocular fusion disorders
Authors: Benhaim-Sitbon Laura , Lev Maria , Polat Uri 
Published: November 2023

AbstractHeterophoria is a common type of binocular fusion disorder that consists of a latent eye misalignment with potential consequences on daily activities such as reading or working on a computer (with CVS). Crowding, a type of contextual modulation, can also impair reading. Our recent studies found an abnormal pattern of low-level visual processing with larger perceptive fields (PF) in heterophoria. The PF is the fundamental processing unit of human vision and both masking and crowding depend on its size. We investigated how heterophoria would impact the PF’s size via a lateral masking experiment and consequently affect the foveal crowding at different letter-spacings (the crowding zone). More specifically, we explored the relationship between crowding, lateral masking, the PF’s size, and the amount of heterophoria. The binocular horizontal PF’s size was larger with heterophoric subjects, in agreement with our previous study. We found a stronger crowding and an extended crowding zone associated with slower response times; this shows that the processing of letter identification under both crowded and uncrowded conditions requires more processing effort in heterophoric individuals. In agreement with previous studies, we found a correlation between the crowding zone and the PF’s size; each was strongly correlated with the amount of phoria. These findings resemble those involving the PF size and the extended crowding found at the fovea in amblyopia and young children. We suggest that these findings could help explain the inter-observers’ variability found in the masking literature, and the reading difficulties often encountered in subjects with high heterophoria.
Antithyroid drug-induced leukopenia and G-CSF administration: a long-term cohort study
Authors: Kamitani Fumika , Nishioka Yuichi , Koizumi Miyuki , Nakajima Hiroki , Kurematsu Yukako , Okada Sadanori , Kubo Shinichiro , Myojin Tomoya , Noda Tatsuya , Imamura Tomoaki , Takahashi Yutaka 
Published: November 2023

AbstractAlthough antithyroid drug (ATD)-induced agranulocytosis is a significant concern, its risks associated with long-term use and re-administration are not fully elucidated. Therefore, we performed this study to determine the incidence of ATD-induced leukopenia and G-CSF administration using administrative claims database. Retrospective cohort study. This study was performed using the DeSC Japanese administrative claims database. A total of 12,491 patients with newly diagnosed Graves’ disease (GD) who received methimazole or propylthiouracil between April 2014, and February 2021 among 3.44 million patients in the database were included in the study. We measured the six-year incidence of leukopenia and granulocyte colony-stimulating factor (G-CSF) administration. The incidence of leukopenia and G-CSF administration was 1.34% (168 patients) and 0.30% (38 patients), respectively. Leukopenia had a dose-dependent and biphasic incidence. The incidence of leukopenia and G-CSF administration was 37.2 (0.7%) and 8.0 (0.2%) per 1000 person-years during the first 72 days of ATD initiation, whereas it was 3.1 and 0.7 per 1000 person-years during the subsequent 6 years, respectively. The incidence of both outcomes was comparable between first administration and re-administration of ATD. The incidence of ATD-induced leukopenia and G-CSF administration was high in the first 72 days, with a reduced risk for at least 6 years thereafter. The incidence was similar between first administration and re-administration. ATD, a standard therapy, is often administered for a long period; therefore, our findings can guide the treatment of GD.
Q-RAI data-independent acquisition for lipidomic quantitative profiling
Authors: Chang Jing Kai , Teo Guoshou , Pewzner-Jung Yael , Cuthbertson Daniel J. , Futerman Anthony H. , Wenk Markus R. , Choi Hyungwon , Torta Federico 
Published: November 2023

AbstractUntargeted lipidomics has been increasingly adopted for hypothesis generation in a biological context or discovery of disease biomarkers. Most of the current liquid chromatography mass spectrometry (LC–MS) based untargeted methodologies utilize a data dependent acquisition (DDA) approach in pooled samples for identification and MS-only acquisition for semi-quantification in individual samples. In this study, we present for the first time an untargeted lipidomic workflow that makes use of the newly implemented Quadrupole Resolved All-Ions (Q-RAI) acquisition function on the Agilent 6546 quadrupole time-of-flight (Q-TOF) mass spectrometer to acquire MS2 spectra in data independent acquisition (DIA) mode. This is followed by data processing and analysis on MetaboKit, a software enabling DDA-based spectral library construction and extraction of MS1 and MS2 peak areas, for reproducible identification and quantification of lipids in DIA analysis. This workflow was tested on lipid extracts from human plasma and showed quantification at MS1 and MS2 levels comparable to multiple reaction monitoring (MRM) targeted analysis of the same samples. Analysis of serum from Ceramide Synthase 2 (CerS2) null mice using the Q-RAI DIA workflow identified 88 lipid species significantly different between CerS2 null and wild type mice, including well-characterized changes previously associated with this phenotype. Our results show the Q-RAI DIA as a reliable option to perform simultaneous identification and reproducible relative quantification of lipids in exploratory biological studies.
Addition of soluble fiber to standard purified diets is important for gut morphology in mice
Authors: von Süßkind-Schwendi Marietta , Dötsch Andreas , Haberland Vivien , Ferrario Paola , Krüger Ralf , Louis Sandrine , Döring Maik , Graf Daniela 
Published: November 2023

AbstractPurified diets (PD) increase standardization and repeatability in rodent studies but lead to differences in the phenotype of animals compared to grain-based “chow” diets. PD contain less fiber and are often devoid of soluble fiber, which can impact gut health. Thus, the aim of the present study was to modify the PD AIN93G by addition of soluble fiber, to promote more natural gut development as seen with chow diets. One hundred twenty male C57BL/6J mice were fed over 12 weeks either a chow diet, AIN93G or one of three modified AIN93G with increased fiber content and different ratios of soluble fiber to cellulose. Gut health was assessed through histological and immunohistochemical parameters and gut barrier gene expression. Gut microbiota composition was analyzed and its activity characterized through short chain fatty acid (SCFA) quantification. Feeding AIN93G led to tissue atrophy, a less diverse microbiota and a lower production of SCFA compared to chow diet. The addition of soluble fiber mitigated these effects, leading to intermediate colon and caecum crypt lengths and microbiota composition compared to both control diets. In conclusion, the addition of soluble fibers in PDs seems essential for gut morphology as well as a diverse and functional gut microbiome.
Development, characterization, and consumer acceptance evaluation of thermally stable capsule beads containing mixed extracts of green tea and turmeric
Authors: Singh Kanjana , Adhikari Benu , Low Julia , Brennan Margaret Anne , Newman Lisa , Brennan Charles Stephen , Utama-ang Niramon 
Published: November 2023

AbstractThe aim of this study was to investigate the ability of shell (coating) formulations comprised of alginate and glucono delta lactone (GDL) to encapsulate a mixture of green tea and turmeric extracts. Three concentrations of alginate and GDL were used at 0.5%, 0.75%, and 1%, w/v and their solid ratio was varied using a factorial design. A response surface model was applied to optimize the retention of catechin and curcuminoid contents, to determine encapsulation efficiency, and to minimize undesirable flavor and taste. Increasing the concentration of alginate and GDL significantly increased the retention of catechin and curcuminoid contents, encapsulation efficiency, and consumer acceptance (p < 0.05). The encapsulating solution containing 1% of each alginate and GDL performed the best against each criterion. The thermal treatment carried out at the boiling point of water for 15 min had a significant impact on the retention of catechin and curcuminoid content which, in the thermally-treated beads, was 5.15 and 3.85 times higher than unencapsulated, respectively. The consumer acceptance of the encapsulated beads after thermal treatment was higher than that of the unencapsulated formulations as they exhibited lesser pungent flavor and bitterness. The innovative process of thermally stable microencapsulation can produce anti-cancer activity compounds involved in functional food industrial sectors.
Development of mechanically-consistent coarse-grained molecular dynamics model: case study of mechanics of spider silk
Authors: Momeni Bashusqeh S. , Pugno N. M. 
Published: November 2023

AbstractUnderstanding mechanics of spider silk holds immense importance due to its potential to drive innovation in the development of materials with exceptional mechanical characteristics suited for a wide range of applications. Coarse-grained (CG) molecular simulations plays a particularly valuable role in this endeavor, allowing for the efficient investigation of spider silk’s mechanical properties. Our research is centered on the examination of spider silk, which comprises major ampullate silk protein (MaSp1). To achieve this, we developed a CG molecular dynamics model. Our investigation began with a focus on MaSp1 chains subjected to uniaxial tensile load, with comparisons made between the CG model results and all-atom simulations. Subsequently, we extended our simulations to encompass more extensive systems, including fully-ordered MaSp1 bundles undergoing uniaxial static stretching. Through comparison with existing literature, we assess how well the CG model reproduces the mechanical properties of spider silk in highly ordered structures. Furthermore, we explored a scenario where MaSp1 bundles were randomly positioned and stretched, providing valuable insights into silk behavior when the initial structure lacks order. Another simulation involved random positioning, but with some degree of orientation in the loading direction, allowing for a closer examination of the initial structure’s influence.
Comprehensive antibody and cytokine profiling in hospitalized COVID-19 patients in relation to clinical outcomes in a large Belgian cohort
Authors: Ruytinx Pieter , Vandormael Patrick , Fraussen Judith , Pieters Zoë , Thonissen Stef , Hellings Niels , Stinissen Piet , Callebaut Ina , Penders Joris , Vanhove Karolien , Kieffer Davy , Rummens Jean-Luc , Valkenborgh Tom , Messiaen Peter , Stessel Björn , Mesotten Dieter , Somers Veerle 
Published: November 2023

AbstractThe immune response in patients with Coronavirus Disease 2019 (COVID-19) is highly variable and is linked to disease severity and mortality. However, antibody and cytokine responses in the early disease stage and their association with disease course and outcome are still not completely understood. In this large, multi-centre cohort study, blood samples of 434 Belgian COVID-19 hospitalized patients with different disease severities (ranging from asymptomatic/mild to critically ill) from the first wave of the COVID-19 pandemic were obtained. Baseline antibody and cytokine responses were characterized and associations with several clinical outcome parameters were determined. Anti-spike immunoglobulin (Ig)G and IgM levels were elevated in patients with a more severe disease course. This increased baseline antibody response however was associated with decreased odds for hospital mortality. Levels of the pro-inflammatory cytokines IL-6, IP-10 and IL-8, the anti-inflammatory cytokine IL-10 and the antiviral cytokines IFN-α, IFN-β and IFN-λ1 were increased with disease severity. Remarkably, we found significantly lower levels of IFN-λ2,3 in critically ill patients compared to patients of the moderate and severe disease category. Finally, levels of IL-8, IL-6, IP-10, IL-10, IFN-α, IFN-β, IFN-γ and IFN-λ1 at baseline were positively associated with mortality, whereas higher IFN-λ2,3 levels were negatively associated with mortality.