bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virulence and antibiotic-resistance genes in Enterococcus faecalis associated with streptococcosis disease in fish
Authors: Akter Tasmina , Haque Md. Najmul , Ehsan Rakib , Paul Sulav Indra , Foysal Md. Javed , Tay Alfred Chin Yen , Islam Md. Tofazzal , Rahman Md. Mahbubur 
Published: January 2023

AbstractEnterococcus faecalis is associated with streptococcosis like infection in fish. A whole-genome sequence study was conducted to investigate the virulence factor and antibiotic-resistance genes in three fish pathogenic E. faecalis. Genomic DNA was extracted from three strains of E. faecalis isolated from streptococcosis infected Nile tilapia (strains BF1B1 and BFFF11) and Thai sarpunti (strain BFPS6). The whole genome sequences of these three strains were performed using a MiSeq sequencer (Illumina, Inc.). All three strains conserved 69 virulence factor such as genes associated with protection against oxidative stress, bacterial cell wall synthesis, gelatinase toxin, multiple biofilm-associated genes and capsule producing genes. Moreover, 39 antibiotic-resistance genes against sixteen major groups of antibiotics were identified in the genome sequences of all three strains. The most commonly used antibiotic Tetracycline resistance genes were found only in BFPS6 strain, whereas, Bacteriocin synthesis genes were identified in both BFFF11 and BFPS6 strain. Phylogenetic analysis revealed that strains BF1B1 and BFFF1 form a different cluster than BFPS6. This is one of the first whole-genome sequence study of fish pathogenic E. faecalis, unfold new information on the virulence factor and Antibiotic resistance genes linked to pathogenicity in fish.
Training drives turnover rates in racehorse proximal sesamoid bones
Authors: Shaffer Sarah K. , Stover Susan M. , Fyhrie David P. 
Published: January 2023

AbstractFocal bone lesions are often found prior to clinically relevant stress-fractures. Lesions are characterized by low bone volume fraction, low mineral density, and high levels of microdamage and are hypothesized to develop when bone tissue cannot sufficiently respond to damaging loading. It is difficult to determine how exercise drives the formation of these lesions because bone responds to mechanical loading and repairs damage. In this study, we derive steady-state rate constants for a compartment model of bone turnover using morphometric data from fractured and non-fractured racehorse proximal sesamoid bones (PSBs) and relate rate constants to racing-speed exercise data. Fractured PSBs had a subchondral focus of bone turnover and microdamage typical of lesions that develop prior to fracture. We determined steady-state model rate constants at the lesion site and an internal region without microdamage using bone volume fraction, tissue mineral density, and microdamage area fraction measurements. The derived undamaged bone resorption rate, damage formation rate, and osteoid formation rate had significant robust regression relationships to exercise intensity (rate) variables, layup (time out of exercise), and exercise 2–10 months before death. However, the direction of these relationships varied between the damaged (lesion) and non-damaged regions, reflecting that the biological response to damaging-loading differs from the response to non-damaging loading.
Duration between aneurysm rupture and treatment and its association with outcome in aneurysmal subarachnoid haemorrhage
Authors: Hostettler Isabel C. , Lange Nicole , Schwendinger Nina , Frangoulis Samira , Hirle Theresa , Trost Dominik , Gempt Jens , Kreiser Kornelia , Wostrack Maria , Meyer Bernhard 
Published: January 2023

AbstractTimely treatment of aneurysmal subarachnoid haemorrhage (aSAH) is key to prevent further rupture and poor outcome. We evaluated complications and outcome adjusting for time from haemorrhage to treatment. Retrospective analysis of aSAH patients admitted between 2006 and 2020. Data was collected using standardized case report forms. We compared risk factors using multivariable logistic regression. We included 853 patients, 698 (81.8%) were treated within 24 h. Patients with higher Hunt and Hess grades were admitted and treated significantly faster than those with lower grades (overall p-value < 0.001). Fifteen patients (1.8%) rebled before intervention. In the multivariable logistic analysis adjusting for timing, Barrow Neurological Institute score and intracerebral haemorrhage were significantly associated with rebleeding (overall p-value 0.006; OR 3.12, 95%CI 1.09–8.92, p = 0.03, respectively) but timing was not. Treatment > 24 h was associated with higher mortality and cerebral infarction in only the subgroup of lower grades aSAH (OR 3.13, 1.02–9.58 95%CI, p-value = 0.05; OR 7.69, 2.44–25.00, p-value < 0.001, respectively). Therefore treatment > 24 h after rupture is associated with higher mortality and cerebral infarction rates in lower grades aSAH. Delay in treatment primarily affects lower grade aSAH patients. Patients with lower grade aSAH ought to be treated with the same urgency as higher-grade aSAH.
Correlations between COVID-19 and dengue obtained via the study of South America, Africa and Southeast Asia during the 2020s
Authors: Bergero Paula , Schaposnik Laura P. , Wang Grace 
Published: January 2023

AbstractA dramatic increase in the number of outbreaks of dengue has recently been reported, and climate change is likely to extend the geographical spread of the disease. In this context, this paper shows how a neural network approach can incorporate dengue and COVID-19 data as well as external factors (such as social behaviour or climate variables), to develop predictive models that could improve our knowledge and provide useful tools for health policy makers. Through the use of neural networks with different social and natural parameters, in this paper we define a Correlation Model through which we show that the number of cases of COVID-19 and dengue have very similar trends. We then illustrate the relevance of our model by extending it to a Long short-term memory model (LSTM) that incorporates both diseases, and using this to estimate dengue infections via COVID-19 data in countries that lack sufficient dengue data.
Entropy analysis for a novel peristaltic flow in a curved heated endoscope: an application of applied sciences
Authors: Nadeem Sohail , Akhtar Salman , Saleem Anber , Akkurt Nevzat , Almutairi Shahah , Ghazwani Hassan Ali , Eldin Sayed M. 
Published: January 2023

AbstractEntropy interpretation with a descriptive heat generation analysis is carried out for the heated flow between two homocentric and sinusoidally fluctuating curved tubes. A novel peristaltic endoscope is considered for the first time inside a curved tube with evaluation of heat transfer and entropy. This flexible and novel endoscope with peristaltic locomotion is more efficient for endoscopy of complex mechanical structures and it is more comfortable for patients undergoing the endoscopy of a human organs. A comprehensive mathematical model is developed that also completely evaluates the heat transfer analysis for this novel endoscope. Certain and systematic computations are performed with the help of Mathematica software and exact mathematical as well as graphical solutions are obtained. Entropy has a lower rate that is almost zero entropy in the central region of these two curved tubes, but maximum entropy is noted near the sinusoidally deformable walls of both the endoscope and channel.
Comparative proteomic analysis identified proteins and the phenylpropanoid biosynthesis pathway involved in the response to ABA treatment in cotton fiber development
Authors: Yang Yong , Lai Wenjie , Long Lu , Gao Wei , Xu Fuchun , Li Ping , Zhou Shihan , Ding Yuanhao , Hu Haiyan 
Published: January 2023

AbstractAbscisic acid (ABA) is a plant hormone that plays an important role in cotton fiber development. In this study, the physiological changes and proteomic profiles of cotton (Gossypium hirsutum) ovules were analyzed after 20 days of ABA or ABA inhibitor (ABAI) treatment. The results showed that compared to the control (CK), the fiber length was significantly decreased under ABA treatment and increased under ABAI treatment. Using a tandem mass tags-based quantitative technique, the proteomes of cotton ovules were comprehensively analyzed. A total of 7321 proteins were identified, of which 365 and 69 differentially accumulated proteins (DAPs) were identified in ABA versus CK and ABAI versus CK, respectively. Specifically, 345 and 20 DAPs were up- and down-regulated in the ABA group, and 65 and 4 DAPs were up- and down-regulated in the ABAI group, respectively. The DAPs in the ABA group were mainly enriched in the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis and flavonoid secondary metabolism, whereas the DAPs in the ABAI group were mainly enriched in the indole alkaloid biosynthesis and phenylpropanoid biosynthesis pathways. Moreover, 9 proteins involved in phenylpropanoid biosynthesis were upregulated after ABA treatment, suggesting that this pathway might play important roles in the response to ABA, and 3 auxin-related proteins were upregulated, indicating that auxin might participate in the regulation of fiber development under ABAI treatment.
Posttraumatic stress disorder and diabetes-related outcomes in patients with type 1 diabetes
Authors: Lunkenheimer Frederike , Eckert Alexander J. , Hilgard Dörte , Köth Daniel , Kulzer Bernhard , Lück Ursula , Lüdecke Blanca , Müller Antonia , Baumeister Harald , Holl Reinhard W. 
Published: January 2023

AbstractMental comorbidities in patients with type 1 diabetes mellitus (T1D) are common, and can have a negative impact on acute blood glucose levels and long-term metabolic control. Information on the association of T1D and comorbid posttraumatic stress disorder (PTSD) with diabetes-related outcomes is limited. The aim was to examine the associations between a clinical diagnosis of PTSD and diabetes-related outcomes in patients with T1D. Patients with T1D and comorbid documented PTSD from the DPV database (n = 179) were compared to a group with T1D without PTSD (n = 895), and compared to a group with T1D without comorbid mental disorder (n = 895) by matching demographics (age, gender, duration of diabetes, therapy and migration background) 1:5. Clinical diabetes-related outcomes {body mass index (BMI), hemoglobin A1c (hbA1c), daily insulin dose, diabetic ketoacidosis (DKA), hypoglycemia, number of hospital admissions, number of hospital days} were analyzed, stratified by age groups (≤ 25 years vs. > 25 years). Patients with comorbid PTSD aged ≤ 25 years compared with patients without PTSD or patients without mental disorders had significantly higher HbA1c (8.71 vs. 8.30 or 8.24%), higher number of hospital admissions (0.94 vs. 0.44 or 0.32 per year) and higher rates of DKA (0.10 vs. 0.02 or 0.01 events/year). Patients with comorbid PTSD aged ≤ 25 years compared with patients without PTSD had significantly higher BMI (0.85 vs. 0.59) and longer hospital stays (15.89 vs.11.58 days) than patients without PTSD. Patients with PTSD > 25 years compared with patients without PTSD or without any mental comorbidities had significantly fewer hospital admissions (0.49 vs. 0.77 or 0.69), but a longer hospital length of stay (20.35 vs. 11.58 or 1.09 days). We found that PTSD in younger patients with T1D is significantly related to diabetes outcome. In adult patients with T1D, comorbid PTSD is associated with fewer, but longer hospitalizations. Awareness of PTSD in the care of patients with T1D should be raised and psychological intervention should be provided when necessary.
Engineering of Chinese hamster ovary cells for co-overexpressing MYC and XBP1s increased cell proliferation and recombinant EPO production
Authors: Latorre Yesenia , Torres Mauro , Vergara Mauricio , Berrios Julio , Sampayo Maria Molina , Gödecke Natasha , Wirth Dagmar , Hauser Hansjörg , Dickson Alan J. , Altamirano Claudia 
Published: January 2023

AbstractImproving the cellular capacity of Chinese hamster ovary (CHO) cells to produce large amounts of therapeutic proteins remains a major challenge for the biopharmaceutical industry. In previous studies, we observed strong correlations between the performance of CHO cells and expression of two transcription factors (TFs), MYC and XBP1s. Here, we have evaluated the effective of overexpression of these two TFs on CHO cell productivity. To address this goal, we generated an EPO-producing cell line (CHOEPO) using a targeted integration approach, and subsequently engineered it to co-overexpress MYC and XBP1s (a cell line referred to as CHOCXEPO). Cells overexpressing MYC and XBP1s increased simultaneously viable cell densities and EPO production, leading to an enhanced overall performance in cultures. These improvements resulted from the individual effect of each TF in the cell behaviour (i.e., MYC-growth and XBP1s-productivity). An evaluation of the CHOCXEPO cells under different environmental conditions (temperature and media glucose concentration) indicated that CHOCXEPO cells increased cell productivity in high glucose concentration. This study showed the potential of combining TF-based cell engineering and process optimisation for increasing CHO cell productivity.
Virtual screening and molecular dynamics simulations provide insight into repurposing drugs against SARS-CoV-2 variants Spike protein/ACE2 interface
Authors: Pirolli Davide , Righino Benedetta , Camponeschi Chiara , Ria Francesco , Di Sante Gabriele , De Rosa Maria Cristina 
Published: January 2023

AbstractAfter over two years of living with Covid-19 and hundreds of million cases worldwide there is still an unmet need to find proper treatments for the novel coronavirus, due also to the rapid mutation of its genome. In this context, a drug repositioning study has been performed, using in silico tools targeting Delta Spike protein/ACE2 interface. To this aim, it has been virtually screened a library composed by 4388 approved drugs through a deep learning-based QSAR model to identify protein–protein interactions modulators for molecular docking against Spike receptor binding domain (RBD). Binding energies of predicted complexes were calculated by Molecular Mechanics/Generalized Born Surface Area from docking and molecular dynamics simulations. Four out of the top twenty ranking compounds showed stable binding modes on Delta Spike RBD and were evaluated also for their effectiveness against Omicron. Among them an antihistaminic drug, fexofenadine, revealed very low binding energy, stable complex, and interesting interactions with Delta Spike RBD. Several antihistaminic drugs were found to exhibit direct antiviral activity against SARS-CoV-2 in vitro, and their mechanisms of action is still debated. This study not only highlights the potential of our computational methodology for a rapid screening of variant-specific drugs, but also represents a further tool for investigating properties and mechanisms of selected drugs.
Arbuscular mycorrhizal fungi associated with maize plants during hydric deficit
Authors: Santana Letícia Rezende , da Silva Lais Noamy , Tavares Germanna Gouveia , Batista Priscila Ferreira , Cabral Juliana Silva Rodrigues , Souchie Edson Luiz 
Published: January 2023

AbstractThe objective of this study was to verify the physiological behavior and development of maize plants under hydric deficit inoculated with the AMF Rhizophagus clarus and Claroideoglomus etunicatum and the commercial inoculant ROOTELLA BR in nonsterilized soil as a strategy to mitigate the effects of drought in the crop. Corn seeds were grown and inoculated with R. clarus, C. etunicatum and the commercial inoculant ROOTELLA BR separately at sowing. The plants were grown in a greenhouse and submitted to water deficit in stage V3, keeping the pots at 20% field capacity for 10 days. The first analyses were performed, followed by reirrigation for 2 days, and the analyses were performed again. The experiment was a double factorial, with 2 water treatments (irrigated and water deficit) × 4 inoculation treatments (control, ROOTELLA BR, R. clarus, C. etunicatum) × 5 replicates per treatment, totaling 40 vessels. The results indicate that the plants were able to recover favorably according to the physiological data presented. It is noted that in inoculated plants, there was no damage to the photosynthetic apparatus. These data demonstrate that AMF contribute greatly to better plant recovery after a dry period and a new irrigation period. Inoculation with AMF favors postwater stress recovery in plants.
Hypoxia inducible factor-1α promotes trichogenic gene expression in human dermal papilla cells
Authors: Seo Jieun , Yan Lei , Kageyama Tatsuto , Nanmo Ayaka , Chun Yang-Sook , Fukuda Junji 
Published: January 2023

AbstractDermal papilla cells (DPCs) play critical roles in hair follicle development, but the underlying mechanisms that contribute to hair regeneration have yet to be fully elucidated, particularly in terms of alterations in androgenetic alopecia patients. In this study, we demonstrated that hypoxia-inducible factor-1α (HIF-1α) is suppressed in scalp tissues of androgenetic alopecia patients and potentially associated with hair follicle development. Using RT-qPCR and western blot, we found that mRNA and protein levels of trichogenic genes, LEF1 and versican (VCAN), were attenuated in HIF-1α knockdown DPCs. Under an in vivo mimicked environment in a three-dimensional spheroid culture, HIF-1α-suppressed DPCs downregulated the expression of hair induction-related genes. Finally, treatment with a HIF-1α activator resulted in the elevated expression of trichogenic genes in DPCs. This study highlights the importance of dermal HIF-1α expression in regulating trichogenic genes and provides a promising therapeutic target and a fundamental tissue engineering approach for hair loss treatment.
Tyrosine-targeted covalent inhibition of a tRNA synthetase aided by zinc ion
Authors: Qiao Hang , Xia Mingyu , Cheng Yiyuan , Zhou Jintong , Zheng Li , Li Wei , Wang Jing , Fang Pengfei 
Published: January 2023

AbstractAminoacyl-tRNA synthetases (AARSs), a family of essential protein synthesis enzymes, are attractive targets for drug development. Although several different types of AARS inhibitors have been identified, AARS covalent inhibitors have not been reported. Here we present five unusual crystal structures showing that threonyl-tRNA synthetase (ThrRS) is covalently inhibited by a natural product, obafluorin (OB). The residue forming a covalent bond with OB is a tyrosine in ThrRS active center, which is not commonly modified by covalent inhibitors. The two hydroxyl groups on the o-diphenol moiety of OB form two coordination bonds with the conserved zinc ion in the active center of ThrRS. Therefore, the β-lactone structure of OB can undergo ester exchange reaction with the phenolic group of the adjacent tyrosine to form a covalent bond between the compound and the enzyme, and allow its nitrobenzene structure to occupy the binding site of tRNA. In addition, when this tyrosine was replaced by a lysine or even a weakly nucleophilic arginine, similar bonds could also be formed. Our report of the mechanism of a class of AARS covalent inhibitor targeting multiple amino acid residues could facilitate approaches to drug discovery for cancer and infectious diseases.
The long noncoding RNA Meg3 mediates TLR4-induced inflammation in experimental obstructive nephropathy
Authors: Yiu Wai Han , Lok Sarah W.Y. , Xue Rui , Chen Jiaoyi , Lai Kar Neng , Lan Hui Yao , Tang Sydney C.W. 
Published: January 2023

Abstract
Kidney inflammation contributes to the progression of chronic kidney disease (CKD). Modulation of Toll-like receptor 4 (TLR4) signaling is a potential therapeutic strategy for this pathology, but the regulatory mechanisms of TLR4 signaling in kidney tubular inflammation remains unclear. Here, we demonstrated that tubule-specific deletion of TLR4 in mice conferred protection against obstruction-induced kidney injury, with reduction in inflammatory cytokine production, macrophage infiltration and kidney fibrosis. Transcriptome analysis revealed a marked down-regulation of long noncoding RNA (lncRNA) Meg3 in the obstructed kidney from tubule-specific TLR4 knockout mice compared with wild-type control. Meg3 was also induced by lipopolysaccharide in tubular epithelial cells via a p53-dependent signaling pathway. Silencing of Meg3 suppressed LPS-induced cytokine production of CCL-2 and CXCL-2 and the activation of p38 MAPK pathway in vitro and ameliorated kidney fibrosis in mice with obstructive nephropathy. Together, these findings identify a proinflammatory role of lncRNA Meg3 in CKD and suggest a novel regulatory pathway in TLR4-driven inflammatory responses in tubular epithelial cells.
Lexical and Morphosyntactic Profiles of Autistic Youth With Minimal or Low Spoken Language Skills
Authors: Butler Lindsay K. , Shen Lue , Chenausky Karen V. , La Valle Chelsea , Schwartz Sophie , Tager-Flusberg Helen 
Published: January 2023

Purpose:
Autistic youth who are minimally or low verbal are underrepresented in research leaving little to no evidence base for supporting them and their families. To date, few studies have examined the types of words and word combinations these individuals use. The purpose of this study was to take a strengths-based approach to outline descriptive profiles of autistic youth who use few words and elucidate the lexical and morphosyntactic features of their spoken language.

Method:
We analyzed language samples from 49 autistic youth ages 6–21 years who used fewer than 200 words. Systematic Analysis of Language Transcripts was used to investigate the relationship between number of different words (NDW) and proportion of nouns and verbs (vs. other word classes), mean length of utterance in morphemes (MLUm), and the frequency of early developing morphosyntactic structures. We used linear regression to quantify the relationship between NDW and lexical and morphosyntactic features.

Results:
Proportion of nouns and verbs produced did not increase significantly in those with higher NDW. Conversely, MLUm and the frequency of early developing morphosyntactic structures increased significantly in those with higher NDW.

Conclusions:
Youth with higher NDW did not produce more nouns and verbs, suggesting lexical profiles that are not aligned with spoken vocabulary level. Youth with higher NDW had higher MLUm and more early morphosyntactic forms, suggesting that morphosyntactic profiles align with spoken vocabulary level. We discuss the implications for improving clinical services related to spoken language.
MILP‐based security evaluation for AEGIS/Tiaoxin‐346/Rocca
Authors: Shiraya Takuro , Takeuchi Nobuyuki , Sakamoto Kosei , Isobe Takanori 
Published: January 2023

AbstractIn this paper, the security of Advanced Encryption Standard‐based authenticated encryption schemes, including AEGIS family, Tiaoxin‐346, and Rocca by mixed integer linear programming tools is examined. Specifically, for the initialisation phase of AEGIS, Tiaoxin‐346, and Rocca, the security against differential attacks and integral attacks is evaluated by estimating the lower bounds for the number of active S‐boxes and utilising division property, respectively. In addition to the estimations of initialisation phases, the security of the encryption phases of AEGIS, Tiaoxin‐346, and Rocca against distinguishing attacks on keystream is evaluated by exploiting integral properties. As a result, the authors show that the initialisation phases of AEGIS‐128/128L/256, Tiaoxin‐346, and Rocca are secure against differential attacks after 4/3/6, 5, and 6 rounds, respectively. Regarding integral attacks, the distinguisher is found on 6/6/7, 15, and 7 rounds in the initialisation phases of AEGIS‐128/128L/256, Tiaoxin‐346, and Rocca, respectively. Additionally, the integral distinguisher is presented on 2/2/4, 4, and 4 rounds in the encryption phases of AEGIS‐128/128L/256, Tiaoxin‐346, and Rocca, respectively. As far as it is known, this study’s results are the first distinguishing attacks on the keystream on AEGIS, Tiaoxin‐346, and Rocca without relying on weak keys.