bluuebunny/crossref_metadata_2025_split huggingface dataset:
Encystation stimuli sensing mediated by adenylate cyclase AC2-dependent cAMP signaling in Giardia
Authors: Paredez Alexander , Shih Han-Wei , Alas Germain 
Published: April 2023

Abstract
Protozoan parasites use cAMP signaling to precisely regulate the place and time of developmental differentiation, yet it is unclear how this signaling is initiated. Encystation of the intestinal parasite Giardia lamblia can be activated by multiple stimuli, which we hypothesize result in a common physiological change. We demonstrate that bile alters plasma membrane fluidity by reducing cholesterol-rich lipid microdomains, while alkaline pH enhances bile function. Through depletion of the cAMP producing enzyme Adenylate Cyclase 2 (AC2) and the use of a newly developed Giardia-specific cAMP sensor, we show that AC2 is necessary for encystation stimuli-induced cAMP upregulation and activation of downstream signaling. Conversely, over expression of AC2 or exogenous cAMP were sufficient to initiate encystation. Our findings indicate that encystation stimuli induce membrane reorganization, trigger AC2-dependent cAMP upregulation, and initiate encystation-specific gene expression, thereby advancing our understanding of a critical stage in the life cycle of a globally important parasite.
Safe Use of Hepatitis B Surface Antigen-Positive Grafts in Liver Transplantation: A Nationwide Study Based on the KOTRY Data
Authors: Gang Sujin , Choi YoungRok , Lee Kwang-Woong , Kim Bong-Wan , Kim Dong-Sik , Nah Yang Won , Kim Jong Man , Lee Jae Geun , Ryu Je Ho , Jeong Jaehong , Hong Geun 
Published: April 2023

Abstract

In the era of nucleoside analogs (NA), we investigated liver transplantation (LT) outcomes using hepatitis B surface antigen (HBsAg)-positive(+) grafts and Korean Organ Transplantation Registry (KOTRY) data. The KOTRY database registered 4,265 LTs between April 2014 and January 2020; 20 (0.5%) using HBsAg(+) grafts were identified. HBsAg(+) liver grafts [S(+)] were compared to HBsAg-negative(−) liver grafts (n = 4,100) for LT outcomes. The S(+) group was compared with LTs using HBsAg(−)/hepatitis B core antibody (HBcAb) (+) [C(+), n = 882] and HBsAg(−)/HBcAb(−) [SC(−), n = 3,132] grafts by propensity score matching (PSM) (1:1). Sixteen of 20 HBsAg(+) graft recipients maintained hepatitis B immunoglobulin. Tenofovir is the most commonly used NA. Compared to the HBsAg(II) group, the S(+) group showed no significant differences in patient (P = 0.332) or graft survival (P = 0.152). Age (hazard ratio [HR] = 1.03, P = 0.016), hepatocellular carcinoma (HCC) (HR = 4.61, P < 0.001), the model for end-stage liver disease (MELD) score (HR = 2.82, P = 0.001), ascites (HR = 2.14, P = 0.002), and encephalopathy (HR = 2.53, P < 0.001) were risk factors for patient survival. The graft survival risk factors were HCC (HR = 4.01, P = 0.001), preoperative treatment for HCC (HR = 0.54, P = 0.006), MELD score (HR = 2.14, P = 0.012), ascites (HR = 2.52, P < 0.001), and encephalopathy (HR = 1.99, P < 0.001). PSM between groups S(+) and C(+) and groups S(+) and SC(−) revealed no significant difference in patient survival (P = 0.863 and P = 0.547, respectively) or graft survival (P = 0.576 and P = 0.327, respectively). In hepatitis B virus (HBV)-endemic areas, HBsAg(+) liver grafts can expand the donor pool without compromising outcomes.
Prediction of Autism spectrum disorder from high dimensional data using Machine Learning Techniques
Authors: Pottem Archana , Sirisha G.N.V.G. , Chaitanya R. Krishna 
Published: April 2023

Abstract
Over the past few years due to the changes in the environmental and human lifestyle, several neurodevelopmental disorders are shooting their existence. Autism prevalence percentage is significant when compared to other neurodevelopmental disorders. To diagnose autism spectrum disorder medical experts, need big medical data and lot of time. Early detection of autism at an early age helps in curing the disorder. Machine Learning models are developed to predict Autism in high dimensional datasets. Dimensionality reduction is applied to identify features that effect Autism. Feature subsets are extracted using chi-square test, mutual information and lightgbm. Later the performances of the machine learning algorithms are analysed to find out suitable classifier that predicts the autism spectrum disorder. Using feature selection, the performance of Naïve Bayesian, K Nearest Neighbour has improved. Decision trees classifier performed the best with a performance score of 97.47%.
Comprehensive Analysis of the Expression of the IGF2BPs gene family in Head and Neck Squamous Cell Carcinoma: Association with Prognostic Value and Tumor Immunity
Authors: Tang Hai , Liu Jingpeng , Zhao Jianjiang 
Published: April 2023

Abstract
Background:
Head and neck squamous cell carcinoma (HNSCC) represents a predominant type of malignant cancer found in the head and neck region, characterized by a high incidence and unfavorable prognosis. The IGF2BPs gene family, which belongs to the RNA-binding protein class, has been critically implicated in several cancers, and its involvement in HNSCC necessitates further exploration.
Objective:
To explore the clinical significance and potential biological functions of the IGF2BPs gene family in HNSCC.
Methods:
A bioinformatic methodology was employed to examine the expression profile, diagnostic and prognostic significance, and biological mechanisms of the IGF2BPs gene family in HNSCC, with a particular emphasis on its involvement in the immune function of HNSCC. This was followed by in vitro investigations to unravel the biological roles of the IGF2BPs gene family in HNSCC.
Results:
This investigation has demonstrated that, in contrast with normal control tissue, HNSCC has a substantial elevation in the expression level of the IGF2BPs gene family. Patients with a high level of IGF2BPs gene family expression demonstrated higher prediction accuracy for HNSCC. Furthermore, patients with HNSCC and elevated IGF2BPs gene family expression levels exhibited poor survival outcomes. The IGF2BPs gene family displayed a significant association with a variety of immune infiltrating cells and immune genes in HNSCC. Studies conducted in vitro have confirmed that IGF2BP2 silencing suppressed the migration, proliferation, and invasion of HNSCC cells.
Conclusions:
It has been determined that the IGF2BPs gene family plays a crucial part in the onset and progression of HNSCC, and its association with tumor immunity has been established. The IGF2BPs gene family holds promising potential as a diagnostic and prognostic biomarker for HNSCC.
Robertsonian fusion triggers recombination suppression on sex chromosomes in Coleonyx geckos
Authors: Lisachov Artem , Tishakova Katerina , Romanenko Svetlana , Lisachova Lada , Davletshina Guzel , Prokopov Dmitry , Kratochvíl Lukáš , O`Brien Patricia , Ferguson-Smith Malcolm , Borodin Pavel , Trifonov Vladimir 
Published: April 2023

Abstract
The classical hypothesis proposes that the lack of recombination on sex chromosomes arises due to selection for linkage between a sex-determining locus and sexually antagonistic loci, primarily facilitated by inversions. However, cessation of recombination on sex chromosomes could be attributed also to neutral processes, connected with other chromosome rearrangements or can reflect sex-specific recombination patterns existing already before sex chromosome differentiation. Three Coleonyx gecko species share complex X1X1X2X2/X1X2Y system of sex chromosomes evolved via a fusion of the Y chromosome with an autosome. We analyzed synaptonemal complexes and sequenced the flow-sorted sex chromosomes to investigate the effect of the chromosomal rearrangement on recombination and differentiation of these sex chromosomes. The gecko sex chromosomes evolved from syntenic regions that were also co-opted for sex chromosomes in other reptiles. We showed that male recombination is more prevalent in the proximal regions of gecko chromosomes and is even further drastically reduced around the centromere of the neo-Y chromosome. We highlight that pre-existing recombination patterns and Robertsonian fusions can be responsible for the cessation of recombination on sex chromosomes and that such processes can be largely neutral.
Comparison of widefield swept-source optical coherence tomographic angiography and fluorescein fundus angiography for detection of retinal neovascularization with diabetic retinopathy
Authors: Yang Yanyan , li Fengjiao , Liu Tingting , jiao wanzhen , Zhao Bojun 
Published: April 2023

Abstract
Background: To compare vitreous angiomosaic images (VAMIs), obtained by
widefield swept-source optical coherence tomographic angiography (wfSS-OCTA) and the image of fluorescein fundus angiography (FFA) in the identification of retinal neovascularization (NV) in patients with diabetic retinopathy (DR).
Methods: In this prospective observational study, severe non-proliferative diabetic retinopathy (NPDR) or proliferative DR (PDR) patients were included. All patients underwent FFA and wfSS-OCTA. The number of NVs identified by wfSS-OCTA VAMIs using five fixations 12×12 mm montage scans and the resembling FFA images were compared.
Results: Fifty-three eyes of 29 patients were enrolled. NVs were detected in 25 eyes by using FFA, including 9 NVs of the disc (NVDs) and 72 NVs elsewhere (NVEs), and in 29 eyes by OCTA, including 11 NVDs and 90 NVEs. The detection rate of NV and NVD of OCTA was comparable to that of FFA (p > 0.05), and the level of agreement was excellent (κ = 0.850, κ = 0.754). Using FFA as the gold standard, the sensitivity for detection of NV by OCTA was 100.0%, specificity was 85.7%, the positive-predictive value was 86.2%, and the negative-predictive value was 100.0%. Compared with FFA, OCTA was superior in terms of the number of NVEs identified (p = 0.024). When we excluded images of patients treated with anti-vascular endothelial growth factor (VEGF) intravitreal therapy for < 3 months, OCTA was comparable to FFA in terms of the number of NVEs discovered (p = 0.203), with excellent agreement (intraclass correlation coefficient = 0.941).
Conclusions: WfSS-OCTA is an independent non-invasive alternative to FFA for NV discovery, NVD detection, and individual NVE identification, particularly in patients with PDR who have a history of prior treatment with anti-VEGF.
Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection
Authors: Xiao Jun , Lin Xuelei , Xu Yongxin , Wang Dongzhi , Yang Yiman , Zhang Xiaoyu , Bie Xiao Min , Wang Hongzhe , Jiang Jiafu , Chen Zhongxu , Gui Lixuan , Ding Yiliang , Che Yuqing , Li Aili , Zhang Xueyong , Lu Fei , Zhao Xiang Yu , Zhang Xian Sheng , Fu Xiangdong 
Published: April 2023

Abstract
Spike architecture largely affects grain number embraced, which is an important trait to optimize during wheat breeding process. In this study, we incorporated multi-omic data and investigated the genetic regulation of wheat spike development. We generated transcriptome and epigenome profiles of shoot apex at eight developmental stages and observed that chromatin accessibility and H3K27me3 abundance coordinated with transcriptome alteration for flowering transition. A core transcriptional regulatory network (TRN) that drove the formation of the wheat spike was constructed. Integration of the TRN and genome-wide association analysis (GWAS) led to the identification of 227 transcription factors (TFs) with both known (42) and unknown (185) functions. Multi-layer regulatory module among TaSPL6, TaMADS34 and TaMADS15 identified by TRN was validated experimentally. Of the 85 novel TFs with homozygous mutant lines in TILLING library, 38 showed altered spike architecture or flowering time, including bHLH, MYB, and WRKY. Furthermore, we demonstrated that TaMYB4-A regulates fertile spikelet number likely via regulating hormones homeostasis and signaling, and is downstream of, and repressed by WFZP. The elite allele of TaMYB4-A, with a C-SNP at the WFZP binding site, was selected for balancing spikelet number and fertility during breeding process in China. Collectively, our findings provide high-confidence novel regulators and an efficient strategy for studying the genetic basis of wheat spike development for practical breeding applications.
A Novel CT-Based Radiomics Model for Predicting Response and Prognosis of Chemoradiotherapy in Esophageal Squamous Cell Carcinoma
Authors: Kasai Akinari , Miyoshi Jinsei , Sato Yasushi , Okamoto Koichi , Miyamoto Hiroshi , Kawanaka Takashi , Harada Masafumi , Goto Masakazu , Yoshida Takahiro , Haga Akihiro , Takayama Tetsuji 
Published: April 2023

Abstract
No clinically relevant biomarker has been identified for predicting the response of esophageal squamous cell carcinoma (ESCC) to chemoradiotherapy (CRT). Herein, we established a CT-based radiomics model with artificial intelligence (AI) to predict the response and prognosis of CRT in ESCC. A total of 44 ESCC patients (stage I-IV) were enrolled in this study; training (n = 27) and validation (n = 17) cohorts. First, we extracted a total of 476 radiomics features from three-dimensional CT images of cancer lesions in training cohort, selected 110 features associated with the CRT response by ROC analysis (AUC ≥ 0.7) and identified 12 independent features, excluding correlated features by Pearson’s correlation analysis (r ≥ 0.7). Based on the 12 features, we constructed 5 prediction models of different machine learning algorithms (Random Forest (RF), Ridge Regression, Naive Bayes, Support Vector Machine, and Artificial Neural Network models). Among those, the RF model showed the highest AUC in the training cohort (0.99, p < 0.001) as well as in the validation cohort (0.92, p < 0.001) to predict the CRT response. Additionally, Kaplan-Meyer analysis of the validation cohort and all the patient data revealed that the PFS and OS in the high-prediction score group were significantly longer than those in the low-prediction score group. Univariate and multivariate analyses revealed that the radiomics prediction score could be an independent prognostic biomarker, and moreover significantly superior to serum SCC-Ag, the conventional tumor marker of ESCC. In conclusion, we have developed a novel and robust CT-based radiomics model using AI, which successfully predicts the CRT response as well as the prognosis for ESCC patients with high accuracy, non-invasiveness, and cost-effectiveness.
The Use of Broad-Spectrum Antibiotics Plus Metronidazole in Newborns with Gastric Perforation: Impact on Short-term Outcomes
Authors: Wei Huan , Liu Yu , Liu Wei , Zhu Ting , Tang Shuo , Cui Mengying , Wang Zheng-Li , Shi Yuan 
Published: April 2023

Abstract
Objective
The objective of this retrospective study was to investigate whether the use of broad-spectrum antibiotics plus metronidazole improves short-term outcomes in neonates with gastric perforation.
Methods
Medical records of neonatal gastric perforation were reviewed from January 2016 to December 2021 at Children’s Hospital of Chongqing Medical University. A total of 86 neonates were identified, of which 23 were excluded (12 abandoned before surgery, 11 abandoned after surgery within 1 week). Of the remaining 63 neonates, 15 were treated with metronidazole (group M), while 48 were not (group N). Group M was further matched with group N1 (n = 15, without metronidazole) based on birth weight (< 250 g), gestational age (< 1 week), and age at onset (< 1 day). The data from groups M, N, and N1 were compared and analyzed.
Results
There were no significant differences in baseline characteristics, clinical manifestations, treatments, postoperative outcome indicators, hospital stay, comorbidities, and laboratory results between group M and group N (or N1). However, the age at admission was significantly higher in group M than in group N (P = 0.006) and group N1 (P = 0.005). Group M had significantly higher rate of feeding after birth (P = 0.04) and lower rate of prenatal hormone exposure (P = 0.004) compared to group N. Procalcitonin and blood sodium levels were significantly higher in group M than in group N (P = 0.014 and P = 0.004) and group N1 (P = 0.005 and P = 0.036). Elevated C-reactive protein was significantly different in group M and group N1 (P = 0.020). The incidence rate of surgical site infection (SSI) in group M was higher than in group N (P = 0.046), while there was no significant difference in the incidence rate between group M and group N1 (P > 0.05).
Conclusions
Our study suggests that the use of broad-spectrum antibiotics plus metronidazole may not improve short-term outcomes after surgery in newborns with gastric perforation. Future prospective randomized controlled studies with larger sample sizes are warranted to further investigate the optimal antibiotic regimen for the treatment of neonatal gastric perforation.
Potential protective effects of sodium butyrate on glycinin-induced oxidative stress, inflammatory response and growth inhibition in Cyprinus carpio
Authors: Li Deng-Lai , Zhu Rui , Yang Zhi-Yong , Li Liang , Qu Zi-Hui , Quan Ya-Nan , Wei Xiao-Fang , Shang Guo-Jun , Wang Hao-Tong , Wu Li-Fang 
Published: April 2023

Abstract
Investigated mitigating effects of sodium butyrate (SB) on the inflammatory response, oxidative stress and growth inhibition of common carp (2.94 ± 0.2 g) caused by dietary glycinin. The control group (without glycinin and SB), Gly group (contain glycinin), and the remaining 4 groups were added SB (0.75, 1.50, 2.25, 3.00 g/kg,) respectively based on the Gly group. 6 groups of diets were isonitrogenous and isoenergetic, and fish were fed with these 6 diets for eight weeks. The reduction of FBW, FER, SGR, WGR and PER of common carp caused by dietary glycinin could be significantly improved by supplementing 1.50–2.25 g/kg SB in the diet, but FBW, WGR and SGR did not reach the level of the control group. Hepatopancreas and intestinal protease activities and the content of muscle crude protein were significantly decreased by dietary glycinin, but supplement 1.50–2.25 g/kg SB partially reversed this result. Supplementation with 1.50–2.25 g/kg SB not only raised AST and ALT activities in hepatopancreas but also decreased AST and ALT activities in serum. Glycinin significantly reduced immune and antioxidant enzyme activities, in contrast, supplementation of 1.50–2.25 g/kg SB reversed these adverse effects. Furthermore, compared with the Gly group, supplement 1.50–2.25 g/kg SB eminently up-regulated the TGF-β and IL-10 mRNA, and down-regulated the IL-1β, TNF-α, and NF-κB mRNA in hepatopancreas, mid intestine (MI) and distal intestine (DI). Meanwhile, supplement 1.50–2.25 g/kg SB activated the Keap1-Nrf2-ARE signalling pathway, and upregulate CAT, SOD and HO-1 mRNA expression in hepatopancreas, MI and DI. Summarily, glycinin significantly decreased the digestive function and induced inflammatory response, and oxidative stress of common carp ultimately inducing growth inhibition. However, SB partially mitigated these adverse effects by activating the Keap1-Nrf2-ARE signalling pathway and inhibiting the NF-κB signalling pathway.
Ascorbate oxidation stimulates rice root growth via effects on auxin and abscisic acid levels
Authors: Singh Richard Raj , Demeestere Kristof , Kyndt Tina 
Published: April 2023

Abstract
Ascorbic acid (AA) and AA oxidation play a vital role in plant growth and development. In this research we investigated their role in rice (Oryza sativa) root growth. Monitoring of germinating and early vegetative seedlings of the AA biosynthesis mutant vtc1 and its corresponding wild type (WT, ‘Nipponbare’) showed vtc1 mutant with a defect in radicle and early vegetative root growth. AA measurement displayed significantly lower levels of total AA, and mainly lower dehydroascorbic acid (DHA) in the roots of the vtc1 mutant. Phytohormone analysis show roots of the vtc1 mutant with lower levels of Indole-3-acetic acid (IAA) and abscisic acid (ABA). The vtc1 radicle and very early vegetative root phenotype could be complemented by exogenous ABA or auxin (1- naphthalene acetic acid (NAA)) application, but not by AA application. However, at the later vegetative root growth phase only NAA could complement this growth phenotype. Our data revealed that, vtc1 germinating seedling and early vegetative root growth can be complemented by DHA and ascorbate oxidase (AO), the enzyme that oxidizes AA to DHA treatments. Also, these treatments promoted radicle and early vegetative root growth similarly in WT as in the vtc1-mutant, implicating that these hormones act downstream of AA biosynthesis. Our data show significantly higher concentration of IAA and ABA upon AO treatment in WT seedlings, implicating that AO-induced rice root growth is regulated via auxin and ABA levels. Taken together, these results imply that ascorbate oxidation stimulates rice root growth via positive effects on auxin and ABA levels.
First records about oxygen consumption by Chironomus sancticaroli (Diptera: Chironomidae): an analysis using microsensors
Authors: Corbi Juliano , Issa Carina , Lamon Antônio 
Published: April 2023

Abstract
The Chironomidae family is one of the most abundant insect groups in freshwater environments. This group is one of the main organisms of benthic fauna due to sediment and vegetation colonization, with high morphological and physiological adaptations. The importance of chironomid responses to changes in the aquatic environment could allow them to be used to monitor streams, lakes, and ponds. Despite the great ecological importance of this aquatic fauna and the countless number of studies in the literature, little is known about oxygen consumption by larvae in aquatic systems. This fact may be related to the difficulty of measuring these limnological variables in small organisms, such as Chironomidae larvae, and the need for refined equipment. A microsensor is a small electrochemical electrode used in laboratories for chemical species detection. Its small dimension offers advantages, such as the slight sample volume required. In this study, we evaluated for the first time, the dissolved oxygen consumption in the Chironomus sancticaroli (Strixino and Strixino 1981) species larvae using microsensors. The results of the experiments showed that there was a high oxygen consumption by C. sancticarolilarvae, under laboratory conditions. The technology of microsensors applied to the study of the aquatic invertebrates seems to have been important for obtaining detailed information on the biology of these organisms.
The Lone Star Tick, Amblyomma americanum, salivary factors exacerbate the clinical outcome of Heartland virus disease in a small animal model
Authors: Reynolds Erin S. , Wooldridge Jacob T. , Stevenson Heather , Thangamani Saravanan 
Published: April 2023

Abstract
Heartland virus was first isolated in 2009 from two patients in Missouri and is transmitted by the lone star tick, Amblyomma americanum. To understand disease transmission and pathogenesis, it is necessary to develop an animal model that utilizes the natural transmission route and manifests in a manner similar to documented human cases. Herein we describe our investigations on identifying A129 mice as the most appropriate small animal model for HRTV pathogenesis that mimics human clinical outcomes. We further investigated the impact of tick saliva in enhancing pathogen transmission and clinical outcomes. Our investigations revealed an increase in viral load in the groups of mice that received both virus and tick salivary gland extract (SGE). Spleens of all infected mice showed extramedullary hematopoiesis (EH), depleted white pulp, and absence of germinal centers. This observation mimics the splenomegaly observed in natural human cases. In the group that received both HRTV and tick SGE, the clinical outcome of HRTV infection was exacerbated compared to HRTV-only infection. EH scores and viral antigens in the spleen were higher in mice that received both HRTV and tick SGE. In conclusion, we have developed a small animal model that mimics natural human infection and also demonstrated the impact to tick salivary factors in exacerbating the HRTV infection.