bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semiautomated approach focused on new genomic information results in time and effort- efficient reannotation of negative exome data
Authors: Ferrer Alejandro , Duffy Patrick , Olson Rory J. , Meiners Michael A. , Schultz-Rogers Laura , Macke Erica L. , Safgren Stephanie , Morales-Rosado Joel A. , Cousin Margot , Oliver Gavin R. , Rider David , Williams Megan , Pichurin Pavel N. , Deyle David R. , Morava Eva , Gavrilova Ralitza H , Dhamija Radhika , Wierenga Klass J. , Lanpher Brendan C. , Babovic-Vuksanovic Dusica , Kaiwar Charu , Vitek Carolyn R. , McAllister Tammy M. , Wick Myra J. , Schimmenti Lisa A. , Lazaridis Konstantinos N. , Vairo Filippo Pinto e , Klee Eric W. 
Published: July 2023

Abstract
Introduction:
Most rare disease patients (75 − 50%) undergoing genomic sequencing remain unsolved, often due to lack of information about variants identified. Data review over time can leverage novel information regarding disease-causing variants and genes, increasing this diagnostic yield. However, time and resource constraints have limited reanalysis of genetic data in clinical laboratories setting. We developed RENEW, (REannotation of NEgative WES/WGS) an automated reannotation procedure that uses relevant new information in on-line genetic databases to enable rapid review of genetic findings.
Methods
We tested RENEW in an unselected cohort of 1,066 undiagnosed cases from the Mayo Clinic Center for Individualized Medicine using new information in ClinVar, HGMD and OMIM between the date of previous analysis/testing and April of 2022.
Results
5,741 variants prioritized by RENEW were rapidly reviewed by variant interpretation specialists. Mean analysis time was approximately 20 seconds per variant (32 hours total time). Reviewed cases were classified as: 879 (93.0%) undiagnosed, 63 (6.6%) putatively diagnosed, and 4 (0.4%) definitively diagnosed.
Discussion
New strategies are needed to enable efficient review of genomic findings in unsolved cases. We report on a fast and practical approach to address this need and improve overall diagnostic success in patient testing through a recurrent reannotation process.
Crosstalk between glial Cx43 and neuronal Panx1 and P2X7 receptors modulate presynaptic homeostatic plasticity
Authors: Rafael Alberto , Tizzoni Marina , Justet Cristian , Cairus Andrea , Abudara Verónica , Vitureira Nathalia 
Published: July 2023

Abstract
The emerging role of glial cells in the modulation of neuronal excitability and synaptic strength is a growing field in neuroscience. An increased number of studies indicate that gliotransmission is mediated by both the classical Ca2+-dependent release and the non-vesicular route mediated by connexin and pannexin hemichannels. Recent reports highlighted the role of gliotransmission in the homeostatic adjustment of synaptic strength. In particular, glial-derived ATP arises as a key mediator in this process. However, very little is known about the glial non-vesicular ATP-release pathway and how this ATP could participate in the modulation of synaptic strength. Here we investigated the functional changes occurring in the presynaptic terminal and the role of the purinergic signaling, connexin43 and pannexin1 hemichannels in this process. By using hippocampal dissociated cultures, we show that glial connexin43-dependent ATP release triggers the homeostatic adjustment of presynaptic remodeling and function upon chronic activity silencing. Notably, activated neuronal P2X7Rs play an essential role in this process by mediating the entrance of Ca2+ to the presynaptic cell; our data also suggest that the functional crosstalk between neuronal P2X7Rs and pannexin1 hemichannels is required for the compensatory adjustment of presynaptic function. Interestingly, we show that neuronal permeability is regulated during chronic inactivity and, in particular, we found that neuronal pannexin1 hemichannels are gradually opened, increasing their activity upon 12h of neuronal inactivity. Hence, our results show for the first time the glial-dependent changes occurring in the presynaptic terminal upon chronic activity silencing and highlight the role of the interaction between presynaptic P2X7Rs and pannexin1 in the homeostatic adjustment of presynaptic strength.
Primate-specific isoform of Nedd4-1 regulates substrate binding via Ser/Thr phosphorylation and 14-3-3 binding
Authors: Kefalas George , Rotin Daniela 
Published: July 2023

Abstract
Nedd4 (Nedd4-1) is an E3 ubiquitin ligase involved in crucial biological processes such as growth factor receptor signaling. While canonical Nedd4-1 comprises a C2-WW(4)-HECT domain architecture, alternative splicing produces non-canonical isoforms that are poorly characterized. Here we characterized Nedd4-1(NE), a primate-specific isoform of Nedd4-1 that contains a large N-terminal Extension (NE) that replaces most of the C2 domain. We show that Nedd4-1(NE) mRNA is ubiquitously expressed in human tissues and cell lines. Moreover, we found that Nedd4-1(NE) is more active than the canonical Nedd4-1 isoform, likely due to the absence of a C2 domain-mediated autoinhibitory mechanism. Additionally, we identified two Thr/Ser phosphoresidues in the NE region that act as binding sites for 14-3-3 proteins, and show that phosphorylation on these sites reduces substrate binding. Finally, we show that the NE region can act as a binding site for the RPB2 subunit of RNA polymerase II, a unique substrate of Nedd4-1(NE) but not the canonical Nedd4-1. Taken together, our results demonstrate that alternative splicing of the ubiquitin ligase Nedd4-1 can produce isoforms that differ in their catalytic activity, binding partners and substrates, and mechanisms of regulation.
An innovative mobile application (CAITOM ® ) for assessment of oral and maxillofacial trauma
Authors: de Souza Glaciele Maria , de Oliveira Gabriel Narcisio Vieira , Lacerda Allysson Steve Mota , Falci Saulo Gabriel Moreira 
Published: July 2023

Abstract

The use of technological resources, such as mobile applications, in the health area has become a growing reality that aims to improve service delivery from diagnosis to prognosis with greater practicality.
Background/ Aim: present an epidemiological survey of victims of maxillofacial trauma and the technological development of a checklist for auxiliary diagnostic evaluation of these patients.
Methods: A questionnaire was used to study the epidemiological profile of victims of maxillofacial trauma. For the development of the mobile application, a previously developed and validated checklist was used. This application developed was called CAITOM® (Checklist for Initial Assessment of Oral and Maxillofacial Trauma).
Result: The epidemiological profile found in this study is similar to those found in literature wherein victims of facial trauma are male, with age in the second or third decade of life, without marital bond, lower income and low education, rural workers, and victims of traffic accidents. Concurrently with this investigation, the Caitom® was designed for the Android system. Its layout is simple and intuitive so that any professional with knowledge of specific technical terms can use it. Through Caitom® the professional has a screenplay to help him in the initial assessment of victims of maxillofacial trauma.
Conclusion: It is estimated that the use of CAITOM® can practically systematize the diagnostic evaluation of patients with oral and maxillofacial trauma.
Identification of Clinically Relevant Patient Endotypes in Traumatic Brain Injury Using Latent Class Analysis
Authors: Qiu Hongbo , Zador Zsolt , Lannon Melissa , Farrokhyar Forough , Duda Taylor , Sharma Sunjay 
Published: July 2023

Abstract

Traumatic brain injury (TBI) is a complex condition where heterogeneity impedes the advancement of care. Understanding the diverse presentations of TBI is crucial for personalized medicine. Our study aimed to identify clinically relevant patient endotypes in TBI using latent class analysis based on comorbidity data. We used the Medical Information Mart for Intensive Care III database, which includes 2,629 adult TBI patients. We identified five stable endotypes characterized by specific comorbidity profiles: Heart Failure and Arrhythmia, Healthy, Renal Failure with Hypertension, Alcohol Abuse, and Hypertension. Each endotype had distinct clinical characteristics and outcomes: The Heart Failure and Arrhythmia endotype had lower survival rates than the Renal Failure with Hypertension despite featuring less comorbidities overall. Patients in the Hypertension endotype had higher rates of neurosurgical intervention but shorter stays in contrast to the Alcohol Abuse endotype which had lower rates of neurosurgical intervention but significantly longer hospital stays. Both endotypes had high overall survival rates comparable to the Healthy endotype. Logistic regression models showed that endotypes improved the predictability of survival compared to individual comorbidities alone. This study validates clinical endotypes as an approach to addressing heterogeneity in TBI, and demonstrates the potential of this methodology in other complex conditions.
Characterization of changes in annual urban air temperature with special reference to the city of Modena: Comparison between regression models and proposal for a new index to evaluate relationship between environmental variables.
Authors: Morlini Isabella , Albertson Sean , Orlandini Stefano 
Published: July 2023

Abstract
It is commonly recognized that the observed increase in global mean annual air temperature is strongly related to the increase in global CO2 concentration C, and that both these variables are related to global development. It remains, however, unclear the degree to which local mean annual urban air temperature T is affected by local variables such as annual precipitation depth P and urban area extent A. This study assumes that A is a proxy of local development and C is a proxy of global development and investigates the commingled effects of A, P, and C on T by using long-term annual data observed over the years 1881–2019 from the Modena Observatory in Italy. Linear relationships between T, C and A are found to be spurious since all these series have a monotonic increasing trend with time. Parametric analytic models like logistic functions are found to lack flexibility. Smoothing splines can only give insights into the strength of the relationships but not on their shape defining the functional relationship between variables. Advanced nonlinear models like generalized additive models, instead, are found to combine flexibility in a parametric form, and appear therefore to be suitable models for explaining the complex relationships between A, P, and C on T. The different models are evaluated using traditional goodness of fit statistics like R2, BIC, AIC and a new index of relation IR which is introduced to jointly evaluate the goodness-of-fit of relationships between variables that may either be dependent or independent.
Diversity of Heading date 1 (Hd1) gene that conditioning flowering time in traditional tropical japonica and traditional indica rice from Thailand
Authors: Prathepha Preecha 
Published: July 2023

Abstract

The traditional rice cultivars are genetic resources in breeding programs that possess variable of DNA sequence of genes, but variants of gene of these resources have been limited in Thailand. Therefore, DNA sequence variation of the heading date 1 (Hd1) gene was explored in these rice cultivars collected from north (tropical japonica rice) and northeastern (indica rice) regions of the country. Results from re-sequencing of the Hd1 gene identified 3 non-synonymous SNPs in coding sequence (exon2) and there are four SNPs in noncoding sequence of the gene. First nonsynonymous SNP, AGT/GGT leading to amino acid sequence changes in Hd1 protein at position 339 of 407 residues. The allele S (AGT:Serine) of Hd1 gene were dominant in tropical japonica rice in northern region. Whereas the allele G (GGT:Glycine) was mostly found in indica rice from northeastern region. In addition, two traditional cultivars from the northern, a premature stop codon at exon2 was identified. Furthermore, 2 others nonsynonymous SNPs was distributed in both populations, including allele S (AGC:Serine) was dominant in tropical japonica rice, while the allele A (AGA:Arginine) were mostly found in indica rice. The muations may affect Hd1 gene structures and may contribute to intraspecific flowering time adaptations.
Plasma Modification of Graphene Nanoplatelets Surfaces
Authors: Johnson Tyler , Wang Keliang , Fan Qi Hua , Lee Andre 
Published: July 2023

Abstract
Atmospheric plasma processing, which combines the efficacy of chemical processes and the safety of physical processes, has been used to modify the surface characteristic of graphite-based materials. In this work, two distinct plasma source gases, C4F8 and O2, with the addition of a rotary reactor were used. The effectiveness to modify the basal plane of intercalated graphite nanoplatelets (GnP) was investigated with various analytical techniques and the visual observation of the dispersion of these plasma-treated GnP in solvents was also reported. It is shown that this low-temperature plasma processing technique can be used to successfully modify the GnP surface without significantly changing the intrinsic structure of the GnP, which is desirable in many applications. With the C4F8 plasma treatment, the immersion characteristics in solvents can be tuned and the functional groups present on the surface can be tailored to produce desired bonding environments. This surface chemistry tunability is expected to provide the needed functionalities in creating graphene-containing composite materials.
Turing cationic antimicrobial peptide KR-12 into Self-assembled nanobiotics with potent bacterial killing and LPS neutralizing activities
Authors: Lei Ruyi , Sun Yaqi , Zhu Tao , Yang Chujun , Zhu Zhiqiang , Li Dejian , Yang Yunqing , Hao Liman , Li Yang , Wu Shuijing , Cui Hongwei , Jiang Yuming , Xie Jiafeng , Pei Hui , Li Jiye , Mao Yujing , Lan Chao , Zhu Changju , Fang Xiangming 
Published: July 2023

Abstract
Gram-negative sepsis has become one of major increasing medical burdens globally, which is subjected to growing antibiotic resistance problem and the relatively delayed development of new antibiotics. LL-37, the only type of Cathelicidin identified in humans, has diverse biological activities including direct bactericidal action, regulation of inflammation and LPS-neutralization. The KR-12 peptide is the smallest portion of LL-37 with antibacterial action, which has been shown that could be modified into more effective antimicrobials. Here, we synthesize two myristoylated derivatives of KR-12, Myr-KR-12N and Myr-KR-12C, which can spontaneously form nanoparticles when mixed with deionized water. We show that myristoylated KR-12 derivatives possess a broad-spectrum and more powerful bactericidal activity through interrupting the membranes of bacteria. Myr-KR-12N rescues mice from lethal sepsis induced by E. coli, even more potent rescuing activity than meropenem. We also demonstrate that myristoylated KR-12 nanobiotic can significantly bind with LPS and inhibit the inflammation in vitro and Myr-KR-12N rescue mice from LPS-induced sepsis in vivo, even more potent rescuing activity than polymyxin B. Toxic experiments indicate that neither Myr-KR-12N nor Myr-KR-12C nanobiotics exhibits meaningful hemolytic activity, liver and kidney injury. We thus developed a novel nanobiotic with dual bactericidal and LPS-neutralization properties, which may provide good insights for clinical translation of antimicrobial peptides and the creation of new antibiotics.
Carbothermal Reduction of SiO2 using different coal
Authors: Li Fei , Yang Kaixin , Fu Wangwang , Wang Dahui 
Published: July 2023

Abstract
In this study, the carbon thermal reduction of agglomerate composed of pure silica and carbon was studied at 1898 K, 1923 K, and 1948 K. The main product of this reaction is silicon carbide. Compare the reduction effects of four types of coal from different industrial silicon enterprises on the analysis of pure silica, and explore the application of different coal in silicon production. C4 coal has high SiO reactivity, while C1 coal has low SiO reactivity. An increase in temperature will reduce the reaction matching degree of coal and increase the amount of SiO gas escaping. C4 coal has a high and stable reaction matching degree, and the reaction rate is less affected by temperature, making it the best coal among the four types to produce SiC.
Dietary Patterns and Common Diseases in Chinese Elderly: Exploring Associations and Providing Guidance for Personalized Interventions
Authors: Tian Zheng , He Jingchun , Li Yimiao , Zhang Zhijun , Zhang Nan , Wang Lan 
Published: July 2023

Abstract
Background: Specific dietary patterns significantly ameliorate or worsen the risk of certain diseases. However, the relationship between multiple geriatric diseases and dietary patterns remains unclear and the dietary patterns in the current literature may not apply to the Chinese elderly population. This study sought to analyze the major dietary patterns of the Chinese elderly in a large sample population and explore the association between these dietary patterns and 16 prevalent diseases to guide dietary interventions for geriatric populations.
Methods: CLHLS 2018 were analyzed in the present study. 13 types of food and 16 common diseases were extracted from the CLHLS database. Principal component analysis was employed to identify the main dietary patterns of the Chinese elderly, and binary logistic regression models were used to analyze the associations between these dietary patterns and the 16 common diseases.
Results: Four main dietary patterns were identified in the Chinese elderly population: Egg-Milk Pattern, Salt-preserved vegetable-Nut Pattern, Vegetable-Fruit Pattern, and Fish-Meat Pattern. Higher scores for the Egg-Milk Pattern were associated with a greater risk of heart disease, stroke or cardiovascular disease, respiratory disease, glaucoma, prostate tumor, and Parkinson's disease in older adults (p<0.05). Higher scores for Salt-preserved vegetable-Nut Pattern correlated with a greater risk of hypertension, heart disease, and uterine tumors and a lower risk of rheumatism or rheumatoid disease in older adults (P<0.05). The higher scores of the Vegetable-Fruit Pattern were associated with a lower risk of heart disease in older adults (p<0.05). Finally, higher scores of the Fish-Meat Pattern correlated with a lower risk of heart disease, stroke, and cardiovascular disease and a greater risk of rheumatic or rheumatoid disease in older adults (p<0.05).
Conclusions: Much heterogeneity surrounds the recommended dietary patterns for common diseases in elderly patients. A Salt-preserved vegetable-nut pattern is recommended for rheumatic diseases, while vegetable-fruit and fish-meat patterns are recommended for heart disease. Patients with stroke or cardiovascular disease are recommended to adopt the fish-meat pattern. However, the same dietary pattern may have contrasting effects on different diseases. Therefore, dietary guidance for elderly individuals should be personalized based on their specific health conditions. Accurate and tailored recommendations are crucial for promoting optimal health outcomes.
Silver nanoclusters as label free non-enzymatic fast glucose assay with the fluorescent enhancement signal
Authors: Moosavi Razieh , Alizadeh Naader 
Published: July 2023

Abstract
A simple and low-cost green preparation method was used for BSA capped silver nanoclusters (BSA-Ag NCs) as turn on fluorescent probe for glucose. Non-enzymatic fast glucose detection assay with a widest concentration range was proposed which requires neither nanoclusters (NCs) modification nor complicated enzyme immobilization. The DLS analysis, HRTEM patterns, fluorescence and UV-visible measurement well supported the synthesis product. The advantages of the fabricated glucose sensor based on fluorescence increasing of probe compared to other established optical techniques was inspected and summarized as well. The glucose sensor exhibited a high sensitivity, fast response time (in seconds), satisfactory selectivity, well stability (at least two months), low detection limit (31 µmol L− 1) and a wide concentration response (three orders of magnitudes) to glucose between 0.1 to 92 mmol L− 1 as calibration plot. The facile preparation and excellent sensing performance of BSA-Ag NCs in the real samples (plasma and juice) make sure that synthesized probe material is a promising candidate for advanced enzyme-free glucose sensing approach.
Effects of gene polymorphisms on delayed MTX clearance, toxicity, and metabolomic changes after HD-MTX treatment in children with acute lymphoblastic leukemia
Authors: Zhou Yao , He Haoping , Ding Luping , Wang Tianjiao , Liu Xiaomeng , Zhang Minghao , Zhang Aijun , Fu Jinqiu 
Published: July 2023

Abstract
Objective
To assess the role of methotrexate-related gene polymorphisms in children with acute lymphoblastic leukemia (ALL) during high-dose methotrexate (HD-MTX) therapy and to explore their effects on serum metabolites before and after HD-MTX treatment.
Methods
The MTHFR 677C > T, MTHFR 1298A > C, ABCB1 3435C > T, and GSTP1 313A > G genotypes of 189 children with ALL who received chemotherapy with the CCCG-ALL-2020 regimen from January 2020 to April 2023 were analyzed, and toxic effects were reported according to the Common Terminology Criteria for Adverse Events (CTCAE, version 5.0). Fasting peripheral blood serum samples were collected from 27 children before and after HD-MTX treatment, and plasma metabolites were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS).
Results
The results of univariate and multivariate analyses showed that MTHFR 677C > T and ABCB1 3435 C༞T gene polymorphisms were associated with the delayed MTX clearance (P < 0.05) and lower platelet count after treatment in children with MTHFR 677 mutation compared with wild-type ones (P < 0.05), and pure mutations in ABCB1 3435 were associated with higher serum creatinine levels (P < 0.05). No significant association was identified between MTHFR 677C > T, MTHFR 1298A > C, ABCB1 3435 C > T, and GSTP1 313A > G genes and hepatotoxicity or nephrotoxicity (P > 0.05). However, the serum metabolomic analysis indicated that the presence of the MTHFR 677C > T gene polymorphism could potentially contribute to delayed MTX clearance by influencing L-phenylalanine metabolism, leading to the occurrence of related toxic side effects.
Conclusion
MTHFR 677C > T and ABCB1 3435 C > T predicted the risk of delayed MTX clearance during HD-MTX treatment in children with ALL. Serum L-phenylalanine levels were significantly elevated after HD-MTX treatment in children with the MTHFR 677C > T mutation gene.