bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of Biliverdin protected cerebral ischemia–reperfusion injury in rats
Authors: Bai Wenya , Huo Siying , Li Junjie , Yang Yuan , Zhou Guilin , Shao Jianlin 
Published: November 2023

AbstractBiliverdin, a heme metabolite, has been previously reported to alleviate cerebral ischemic reperfusion injury (CIRI). However, the alterations of brain proteome profiles underlying this treatment remain elusive. The objective of this study is to analyze the differential protein expression profile in cerebral cortex of rats involved in anti-CIRI effects of Biliverdin, providing experimental foundation for searching specific marker proteins. Rat model of MCAO/R was established, HE staining, TTC staining, TUNEL staining, and neurological behavioral examination, corner turning test, adhesive removal test, were performed to validate the effects of Biliverdin, and the results indicated that Biliverdin plays a significant role in alleviating CIRI. Furthermore, proteomic analysis of brain tissues of rats subjected to CIRI following Biliverdin treatment was performed using an integrated TMT-based quantitative proteomic approach coupled with LC-MS/MS technology to clarify the comprehensive mechanisms of Biliverdin in CIRI. First, we conducted strict quality control data for TMT experiments. Finally, a total of 7366 proteins were identified, of which 95 proteins were differentially expressed (DEPs) between the CIRI group and the Sham group and 52 between the CIRI and BV groups. In addition, two overlapping proteins among the 147 DEPs, Atg4c and Camlg, were validated by RT-qPCR and western blotting, and their levels were consistent with the results of TMT analysis. Taken together, the current findings firstly mapped comprehensive proteomic changes after CIRI treated with Biliverdin, providing a foundation for developing potentially therapeutic targets of anti-CIRI of Biliverdin and clinically prognostic biomarkers of stroke.
Design of high bulk moduli high entropy alloys using machine learning
Authors: Kandavalli Manjunadh , Agarwal Abhishek , Poonia Ansh , Kishor Modalavalasa , Ayyagari Kameswari Prasada Rao 
Published: November 2023

AbstractIn this work, the authors have demonstrated the use of machine learning (ML) models in the prediction of bulk modulus for High Entropy Alloys (HEA). For the first time, ML has been used for optimizing the composition of HEA to achieve enhanced bulk modulus values. A total of 12 ML algorithms were trained to classify the elemental composition as HEA or non-HEA. Among these models, Gradient Boosting Classifier (GBC) was found to be the most accurate, with a test accuracy of 78%. Further, six regression models were trained to predict the bulk modulus of HEAs, and the best results were obtained by LASSO Regression model with an R-square value of 0.98 and an adjusted R-Square value of 0.97 for the test data set. This work effectively bridges the gap in the discovery and property analysis of HEAs. By accelerating material discovery via providing alternate means for designing virtual alloy compositions having favourable bulk modulus for respective applications, this work opens new avenues of applications of HEAs.
Genetic architecture of individual meiotic crossover rate and distribution in Atlantic Salmon
Authors: Brekke Cathrine , Johnston Susan E. , Knutsen Tim M. , Berg Peer 
Published: November 2023

AbstractMeiotic recombination through chromosomal crossovers ensures proper segregation of homologous chromosomes during meiosis, while also breaking down linkage disequilibrium and shuffling alleles at loci located on the same chromosome. Rates of recombination can vary between species, but also between and within individuals, sex and chromosomes within species. Indeed, the Atlantic salmon genome is known to have clear sex differences in recombination with female biased heterochiasmy and markedly different landscapes of crossovers between males and females. In male meiosis, crossovers occur strictly in the telomeric regions, whereas in female meiosis crossovers tend to occur closer to the centromeres. However, little is known about the genetic control of these patterns and how this differs at the individual level. Here, we investigate genetic variation in individual measures of recombination in > 5000 large full-sib families of a Norwegian Atlantic salmon breeding population with high-density SNP genotypes. We show that females had 1.6 × higher crossover counts (CC) than males, with autosomal linkage maps spanning a total of 2174 cM in females and 1483 cM in males. However, because of the extreme telomeric bias of male crossovers, female recombination is much more important for generation of new haplotypes with 8 × higher intra-chromosomal genetic shuffling than males. CC was heritable in females (h2 = 0.11) and males (h2 = 0.10), and shuffling was also heritable in both sex but with a lower heritability in females (h2 = 0.06) than in males (h2 = 0.11). Inter-sex genetic correlations for both traits were close to zero, suggesting that rates and distribution of crossovers are genetically distinct traits in males and females, and that there is a potential for independent genetic change in both sexes in the Atlantic Salmon. Together, these findings give novel insights into the genetic architecture of recombination in salmonids and contribute to a better understanding of how rates and distribution of recombination may evolve in eukaryotes more broadly.
Small peptide formulas versus standard polymeric formulas in critically ill patients with acute gastrointestinal injury: a systematic review and meta-analysis
Authors: Wang Youquan , Li Yanhua , Li Hongxiang , Li Yuting , Li Xinyu , Zhang Dong 
Published: November 2023

AbstractSmall peptide formulas versus standard polymeric formulas for enteral nutrition in critically ill patients with acute gastrointestinal injury (AGI) have been a topic of debate. A systematic review and meta-analysis were conducted to compare their clinical and nutritional outcomes. Relevant studies from January 1980 to June 2022 were searched in PubMed, Cochrane, and Embase databases. Randomized controlled trials involving AGI grade I-IV patients were included, while children, non-AGI patients, and non-critically ill patients were excluded. Results indicated no significant difference in all-cause mortality. Patients receiving small peptide formulas showed higher daily protein intake, greater albumin growth, and higher prealbumin levels. They also had shorter lengths of stay in the intensive care unit and hospital. Conversely, patients receiving standard polymeric formulas had a higher daily calorie intake. In conclusion, the choice of formula may not affect mortality in critically ill patients with AGI. Small peptide formulas were more conducive to increase daily protein intake, decrease intensive care unit and hospital length of stay. Further large-scale randomized controlled trials evaluating the effects of these two nutritional formulas on clinical and nutritional outcomes in critically ill patients with AGI are needed to confirm these results.
Validation of a modified visual analogue scale to measure user-perceived comfort of a lower-limb exoskeleton
Authors: Mohammed El Husaini Mohammed , Maberry Axl , Martin Anne E. 
Published: November 2023

AbstractUser perceived exoskeleton comfort is likely important for device acceptance, but there is currently no validated instrument to measure it. The Visual Analogue Scale (VAS) is an existing tool to measure subjective human feedback by asking the user to mark a point on a line with each end of the line representing an opposing anchor statement. It can be modified to show the previous response, allowing the subject to directly indicate if the current condition is better or worse than the previous one. The goal of this study was to determine how well the modified VAS could measure user-perceived comfort as the exoskeleton control parameters were varied. To validate the survey, 14 healthy subjects walked in a pair of ankle exoskeletons with approximately ten distinct sets of control parameters tested in a prescribed order. Each set of control parameters was tested twice. After each trial, user-perceived comfort was measured using a two-question VAS survey. The repeatability coefficient was approximately 40 mm, similar to the total range of responses. The results were also inconsistent, with relative rankings between consecutive pairs of conditions matching for approximately 50% of comparisons. Thus, as tested, the VAS was not repeatable or consistent. It is possible that subject adaptation within the trial and over the course of the experiment may have impacted the results. Additional work is needed to develop a repeatable method to measure comfort and to determine how perceived comfort varies as subjects’ gain exoskeleton experience.
Diagnostic implications of lncRNA NORAD in breast cancer
Authors: Zhang Yaping , Fan Xiaowei , Hong Jianfeng , Yang Enyu , Xuan Cheng , Fang Hongming , Ding Xianfeng 
Published: November 2023

AbstractThis study aimed to assess the expression levels of non-coding RNA activated by DNA damage (NORAD) in the cells, tissues, and serum of breast cancer (BRCA) patients and benign breast nodules and investigate its association with clinicopathological characteristics and prognosis in BRCA. NORAD was analyzed using TCGA-BRCA, GSE77308, Cellminer, and Sangerbox databases, revealing its significance in BRCA prognosis, immune microenvironment, and cell function. Serum samples from 38 BRCA patients, 80 patients with benign breast nodules (50 fibroadenoma and 30 breast adenosis cases), and 42 healthy individuals were collected from Zhejiang Xiaoshan Hospital. NORAD expression was quantified using quantitative reverse transcription PCR (RT-qPCR). Differential NORAD expression between benign and malignant breast nodules and its relationship to clinicopathological characteristics were assessed. NORAD demonstrated elevated expression in BRCA patient serum compared to healthy individuals and those with benign breast nodules (P < 0.05). Moreover, its expression correlated with TNM-stage, lymph node metastasis, and luminal classification. These findings highlight the elevated NORAD expression in BRCA patient serum and its correlation with clinicopathological characteristics, providing insights into its potential as a diagnostic biomarker or therapeutic target.
Environmental DNA-based biomonitoring of Cuban Crocodylus and their accompanying vertebrate fauna from Zapata Swamp, Cuba
Authors: Pérez-Fleitas Etiam , Milián-García Yoamel , Sosa-Rodríguez Gustavo , Amato George , Rossi Natalia , Shirley Matthew H. , Hanner Robert H. 
Published: November 2023

AbstractCrocodylians globally face considerable challenges, including population decline and extensive habitat modification. Close monitoring of crocodylian populations and their habitats is imperative for the timely detection of population trends, especially in response to management interventions. Here we use eDNA metabarcoding to identify the Critically EndangeredCrocodylus rhombiferand the VulnerableC. acutus, as well as vertebrate community diversity, in Cuba’s Zapata Swamp. We tested four different primer sets, including those used previously inCrocodyluspopulation genetic and phylogenetic research, for their efficiency at detecting crocodylian eDNA. We detectedC. rhombifereDNA in 11 out of 15 sampled locations within its historical geographic distribution. We found that data analyses using the VertCOI primers and the mBRAVE bioinformatics pipeline were the most effective molecular marker and pipeline combination for identifying this species from environmental samples. We also identified 55 vertebrate species in environmental samples across the four bioinformatics pipelines— ~ 85% known to be present in the Zapata ecosystem. Among them were eight species previously undetected in the area and eight alien species, including known predators of hatchling crocodiles (e.g.,Clariassp.) and egg predators (e.g.,Mus musculus). This study highlights eDNA metabarcoding as a powerful tool for crocodylian biomonitoring within fragile and diverse ecosystems, particularly where fast, non-invasive methods permit detection in economically important areas and will lead to a better understanding of complex human-crocodile interactions and evaluate habitat suitability for potential reintroductions or recovery programs for threatened crocodylian species.
PBK correlates with prognosis, immune escape and drug response in LUAD
Authors: Ma Hongyu , Zhang Jing , Shi Yan , Wang Ziqiang , Nie Wenhu , Cai Jingjing , Huang Yinglong , Liu Bin , Wang Xiaojing , Lian Chaoqun 
Published: November 2023

AbstractPBK (PDZ-binding kinase) is a protein-coding gene that encodes a serine/threonine protein kinase associated with the dual-specific mitogen-activated protein kinase (MAPKK) family. Overexpression of this gene is closely linked to tumor development. In this study, we aimed to investigate the role of PBK in lung adenocarcinoma (LUAD) progression, prognosis, and immune evasion. We conducted a pan-cancer analysis of PBK to examine its expression and prognostic value. In the LUAD cohort, we analyzed PBK expression, prognosis, mutational features, and immune infiltration in groups with different PBK expression levels. We constructed a PBK-associated genomic model, integrated it into a nomogram, and compared high and low-risk subgroups. In our pan-cancer analysis, PBK was significantly upregulated, particularly in LUAD patients, and displayed poor prognosis. The high PBK expression group had many deletion mutations but still showed gene upregulation. Immune infiltration analysis indicated that PBK-triggered immune escape in the high expression group might relate to antigen presentation, dendritic cell, and CD8+ T cell infiltration. We constructed a 5-gene prognostic model and a nomogram to quantify individual survival probabilities. The PBK-associated gene prognostic model reliably predicted patient prognosis and drug response. Our findings offer new insights into PBK-induced immune escape and targeted therapy during LUAD development, providing valuable suggestions for clinical treatment approaches.
NPLOC4 is a potential target and a poor prognostic signature in lung squamous cell carcinoma
Authors: Wang Naixue , Zhu Dantong , Liu Yao , Wu Jingran , Wang Meiling , Jin Shanxiu , Fu Fangwei , Li Baolei , Ji Hongjuan , Du Cheng , Zheng Zhendong 
Published: November 2023

AbstractFew prognostic biomarkers exist for lung squamous cell carcinoma (LUSC), which has a poor five-year survival rate. Using bioinformatics, this study evaluated NPLOC4 as a prognostic marker for patients with lung squamous cell carcinoma. Shorter survival periods and tumor growth were linked to high NPLOC4 expression.Disulfiram (DSF) combined with copper (Cu) targets NPLOC4 to achieve antitumor effects in lung squamous cell carcinoma. Thus, we investigated the effects of DSF with Cu in LUSC. Gene-set enrichment analysis identified ubiquitin-mediated proteolysis as the NPLOC4-associated mechanism influencing LUSC prognosis. In SK-MES-1 cell lines, DSF + Cu increased K48-linked ubiquitinated protein expression and apoptosis. This study identified NPLOC4 as a prognostic biomarker and a potential therapeutic target for LUSC.
Shape configuration of mental targets representation as a holistic measure in a 3D real world pointing test for spatial orientation
Authors: Gerb J. , Brandt T. , Dieterich M. 
Published: November 2023

AbstractDeficits in spatial memory are often early signs of neurological disorders. Here, we analyzed the geometrical shape configuration of 2D-projections of pointing performances to a memorized array of spatially distributed targets in order to assess the feasibility of this new holistic analysis method. The influence of gender differences and cognitive impairment was taken into account in this methodological study. 56 right-handed healthy participants (28 female, mean age 48.89 ± 19.35 years) and 22 right-handed patients with heterogeneous cognitive impairment (12 female, mean age 71.73 ± 7.41 years) underwent a previously validated 3D-real-world pointing test (3D-RWPT). Participants were shown a 9-dot target matrix and afterwards asked to point towards each target in randomized order with closed eyes in different body positions relative to the matrix. Two-dimensional projections of these pointing vectors (i.e., the shapes resulting from the individual dots) were then quantified using morphological analyses. Shape configurations in healthy volunteers largely reflected the real-world target pattern with gender-dependent differences (ANCOVA area males vs. females F(1,73) = 9.00, p 3.69 × 10−3, partial η2 = 0.10, post-hoc difference = 38,350.43, pbonf=3.69 × 10−3**, Cohen’s d 0.76, t 3.00). Patients with cognitive impairment showed distorted rectangularity with more large-scale errors, resulting in decreased overall average diameters and solidity (ANCOVA diameter normal cognition/cognitive impairment F(1,71) = 9.30, p 3.22 × 10−3, partial η2 = 0.09, post-hoc difference = 31.22, pbonf=3.19 × 10−3**, Cohen’s d 0.92, t 3.05; solidity normal cognition/cognitive impairment F(1,71) = 7.79, p 6.75 × 10−3, partial η2 = 0.08, post-hoc difference = 0.07, pbonf=6.76 × 10−3** Cohen’s d 0.84, t 2.79). Shape configuration analysis of the 3D-RWPT target array appears to be a suitable holistic measure of spatial performance in a pointing task. The results of this methodological investigation support further testing in a clinical study for differential diagnosis of disorders with spatial memory deficits.
Unravelling the genome of the brackish water malaria vector Anopheles aquasalis
Authors: Alencar Rodrigo Maciel , Sepulveda Cesar Camilo Prado , Martinez-Villegas Luis , Bahia Ana Cristina , Santana Rosa Amélia , de Souza Igor Belém , D’Elia Gigliola Mayara Ayres , Duarte Ana Paula Marques , de Lacerda Marcus Vinicius Guimarães , Monteiro Wuelton Marcelo , Secundino Nágila Francinete Costa , Pimenta Paulo Filemon Paolucci , Koerich Leonardo Barbosa 
Published: November 2023

AbstractMalaria is a severe public health problem in several developing tropical and subtropical countries. Anopheles aquasalis is the primary coastal malaria vector in Central and South America and the Caribbean Islands, and it has the peculiar feature of living in water with large changes in salinity. Recent research has recognised An. aquasalis as an important model for studying the interactions of murine and human Plasmodium parasites. This study presents the complete genome of An. aquasalis and offers insights into its evolution and physiology. The genome is similar in size and gene content to other Neotropical anophelines, with 162 Mb and 12,446 protein-coding genes. There are 1387 single-copy orthologs at the Diptera level (eg. An. gambiae, An. darlingi and Drosophila melanogaster). An. aquasalis diverged from An. darlingi, the primary malaria vector in inland South America, nearly 20 million years ago. Proteins related to ion transport and metabolism belong to the most abundant gene families with 660 genes. We identified gene families relevant to osmosis control (e.g., aquaporins, vacuolar-ATPases, Na+/K+-ATPases, and carbonic anhydrases). Evolutionary analysis suggests that all osmotic regulation genes are under strong purifying selection. We also observed low copy number variation in insecticide resistance and immunity-related genes for all known classical pathways. The data provided by this study offers candidate genes for further studies of parasite-vector interactions and for studies on how anophelines of brackish water deal with the high fluctuation in water salinity. We also established data and insights supporting An. aquasalis as an emerging Neotropical malaria vector model for genetic and molecular studies.
Reappraisal of clinical trauma trials: the critical impact of anthropometric parameters on fracture gap micro-mechanics—observations from a simulation-based study
Authors: Roland Michael , Diebels Stefan , Orth Marcel , Pohlemann Tim , Bouillon Bertil , Tjardes Thorsten 
Published: November 2023

AbstractThe evidence base of surgical fracture care is extremely sparse with only few sound RCTs available. It is hypothesized that anthropometric factors relevantly influence mechanical conditions in the fracture gap, thereby interfering with the mechanoinduction of fracture healing. Development of a finite element model of a tibia fracture, which is the basis of an in silico population (n = 300) by systematic variation of anthropometric parameters. Simulations of the stance phase and correlation between anthropometric parameters and the mechanical stimulus in the fracture gap. Analysis of the influence of anthropometric parameters on statistical dispersion between in silico trial cohorts with respect to the probability to generate two, with respect to anthropometric parameters statistically different trial cohorts, given the same power assumptions. The mechanical impact in the fracture gap correlates with anthropometric parameters; confirming the hypothesis that anthropometric factors are a relevant entity. On a cohort level simulation of a fracture trial showed that given an adequate power the principle of randomization successfully levels out the impact of anthropometric factors. From a clinical perspective these group sizes are difficult to achieve, especially when considering that the trials takes advantage of a „laboratory approach “, i.e. the fracture type has not been varied, such that in real world trials the cohort size have to be even larger to level out the different configurations of fractures gaps. Anthropometric parameters have a significant impact on the fracture gap mechanics. The cohort sizes necessary to level out this effect are difficult or unrealistic to achieve in RCTs, which is the reason for sparse evidence in orthotrauma. New approaches to clinical trials taking advantage of modelling and simulation techniques need to be developed and explored.
Eco-friendly cellulose hydrogels as controlled release fertilizer for enhanced growth and yield of upland rice
Authors: Abg Ahmad Dayang Fazirah Binti , Wasli Mohd Effendi , Tan Cindy Soo Yun , Musa Zaki , Chin Suk-Fun 
Published: November 2023

AbstractThe effect of urea-loaded cellulose hydrogel, a controlled-release fertilizer (CRF) on growth and yield of upland rice were investigated in upland rice. As with the initial research, nitrogen (N) treatments were applied as CRF treatments; T2H (30 kg N ha−1), T3H (60 kg N ha−1), T4H (90 kg N ha−1), T5H (120 kg N ha−1) and recommended dose of fertilizer (RDF) at 120 kg N ha−1 RDF (T6U) in split application and T1 (0 N) as control. Results from this study indicated that applying CRF at the optimum N rate, T4H resulted in maximum grain yield, increasing by 71%. The analysis of yield components revealed that higher grain yield in T4H CRF was associated with an increase in panicle number and number of grains per panicle. Maximum grain N uptake of 0.25 g kg−1 was also observed in T4H CRF. In addition, T4H CRF recorded the highest harvest index (HI) and N harvest index (NHI) of 45.5% and 67.9%, respectively. Application of T4H CRF also recorded the highest N use efficiency (NUE) and N agronomic efficiency (NAE), 52.6% and 12.8 kg kg−1, respectively. Observations show that CRF with only 75% N applied (T4H) in soil improved grain yield when compared to CRF with 100% N and 100% RDF in farmers’ conventional split application. This suggested that CRF with a moderate N application might produce the highest potential yield and improved N efficiencies while enhancing crop production and further increase in N supply did not increase yield and N efficiencies. The results suggest that the application of T4H CRF for upland rice would enhance HI, N efficiencies and improve the yield of upland rice. Also, all growth parameters and yield were positively influenced by the application of CRF as a basal dose compared to split application of conventional urea fertilizers.