bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae)
Authors: Milián-García Yoamel , Hempel Christopher A. , Janke Lauren A. A. , Young Robert G. , Furukawa-Stoffer Tara , Ambagala Aruna , Steinke Dirk , Hanner Robert H. 
Published: August 2022

Abstract
Background
Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides, a globally distributed, megadiverse genus containing 1,347 species.

Aim
Generating novel mitogenomic information from single Culicoides sonorensis and C. biguttatus specimens, comparing available mitogenome mapping and de novo assembly tools, and identifying the best performing strategy and tools for Culicoides species.

Results
We present two novel and fully annotated mitochondrial haplotypes for two Culicoides species, C. sonorensis and C. biguttatus. We also annotated or re-annotated the only available reference mitogenome for C. sonorensis and C. arakawae. All species present a high similarity in mitogenome organization. The general gene arrangement for all Culicoides species was identical to the ancestral insect mitochondrial genome. Only short spacers were found in C. sonorensis (up to 30 bp), contrary to C. biguttatus (up to 114 bp). The mitochondrial genes ATP8, NAD2, NAD6, and LSU rRNA exhibited the highest nucleotide diversity and pairwise interspecific p genetic distance, suggesting that these genes might be suitable and complementary molecular barcodes for Culicoides identification in addition to the commonly utilized COI gene.
We observed performance differences between the compared mitogenome generation strategies. The mapping strategy outperformed the de novo assembly strategy, but mapping results were partially biased in the absence of species-specific reference mitogenome. Among the utilized tools, BWA performed best for C. sonorensis while SPAdes, MEGAHIT, and MitoZ were among the best for C. biguttatus. The best-performing mitogenome annotator was MITOS2. Additionally, we were able to recover exogenous mitochondrial DNA from Bos taurus (biting midges host) from a C. biguttatus blood meal sample.

Conclusions
Two novel annotated mitogenome haplotypes for C. sonorensis and C. biguttatus using High-Throughput Sequencing are presented. Current results are useful as the baseline for mitogenome reconstruction of the remaining Culicoides species from single specimens to HTS and genome annotation. Mapping to a species-specific reference mitogenome generated better results for Culicoides mitochondrial genome reconstruction than de novo assembly, while de novo assembly resulted better in the absence of a closely related reference mitogenome. These results have direct implications for molecular-based identification of these vectors of human and zoonotic diseases, setting the basis for using the whole mitochondrial genome as a marker in Culicoides identification.
Conceptual framework for the insect metamorphosis from larvae to pupae by transcriptomic profiling, a case study of Helicoverpa armigera (Lepidoptera: Noctuidae)
Authors: Gao Xinxin , Zhang Jihong , Wu Peipei , Shu Ruihao , Zhang Huan , Qin Qilian , Meng Qian 
Published: August 2022

Abstract
Background
Insect metamorphosis from larvae to pupae is one of the most important stages of insect life history. Relatively comprehensive information related to gene transcription profiles during lepidopteran metamorphosis is required to understand the molecular mechanism underlying this important stage. We conducted transcriptional profiling of the brain and fat body of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) during its transition from last instar larva into pupa to explore the physiological processes associated with different phases of metamorphosis.

Results
During metamorphosis, the differences in gene expression patterns and the number of differentially expressed genes in the fat body were found to be greater than those in the brain. Each stage had a specific gene expression pattern, which contributed to different physiological changes. A decrease in juvenile hormone levels at the feeding stage is associated with increased expression levels of two genes (juvenile hormone esterase, juvenile hormone epoxide hydrolase). The expression levels of neuropeptides were highly expressed at the feeding stage and the initiation of the wandering stage and less expressed at the prepupal stage and the initiation of the pupal stage. The transcription levels of many hormone (or neuropeptide) receptors were specifically increased at the initiation of the wandering stage in comparison with other stages. The expression levels of many autophagy-related genes in the fat body were found to be gradually upregulated during metamorphosis. The activation of apoptosis was probably related to enhanced expression of many key genes (Apaf1, IAP-binding motif 1 like, cathepsins, caspases). Active proliferation might be associated with enhanced expression levels in several factors (JNK pathway: jun-D; TGF-β pathway: decapentaplegic, glass bottom boat; insulin pathway: insulin-like peptides from the fat body; Wnt pathway: wntless, TCF/Pangolin).

Conclusions
This study revealed several vital physiological processes and molecular events of metamorphosis and provided valuable information for illustrating the process of insect metamorphosis from larvae to pupae.
Transcriptome analysis of different life-history stages and screening of male-biased genes in Daphnia sinensis
Authors: Wang Ziyan , Zhang Feiyun , Jin Qide , Wang Yeping , Wang Wenping , Deng Daogui 
Published: August 2022

Abstract
Background
In the life history of Daphnia, the reproductive mode of parthenogenesis and sexual reproduction alternate in aquatic ecosystem, which are often affected by environmental and genetic factors. Recently, the sex-biased genes are of great significance for clarifying the origin and evolution of reproductive transformation and the molecular regulation mechanism of sex determination in Daphnia. Although some genes on reproductive transition of Daphnia had been researched, molecular mechanism on the maintenance of sexually dimorphic phenotypes of Daphnia are still not well known, including differentially expressed genes in different life-history stages.

Results
In this study, four life-history stages of Daphnia sinensis, juvenile female (JF), parthenogenetic female (PF), sexual female (SF) and male (M), were performed for transcriptome, and male-biased genes were screened. A total of 110437 transcripts were obtained and assembled into 22996 unigenes. In the four life-history stages (JF, PF, SF and M), the number of unique unigenes is respectively 2863, 445, 437 and 586, and the number of common unigenes is 9708. The differentially expressed genes (DEGs) between male and other three female stages (M vs JF, M vs PF and M vs SF) were 4570, 4358 and 2855, respectively. GO gene enrichment analysis showed that the up-regulated genes in male were mainly enriched in hydrolase activity and peptidase activity. Thirty-six genes in male were significantly higher expression than in the three female stages, including one Doublesex (Dsx) gene, one laminin gene, five trypsin genes and one serine protease genes, and one chitin synthase gene and two chitinase genes.

Conclusions
Our results showed that thirty-six candidate genes may be as the male-biased genes involving in the maintenance of sexually dimorphic phenotypes. This work will provide a reference for further exploring the functional genes related to sex differentiation in Daphnia species. Moreover, according to previous investigations, we thought that the expression level of functional genes may be related to the life-history stages of organisms, and may be also affected by different Daphnia species.
Identification and validation of stable reference genes for quantitative real time PCR in different minipig tissues at developmental stages
Authors: Song Jeongah , Cho Jeonghee , Park Jeongsik , Hwang Jeong Ho 
Published: August 2022

Abstract
Background
Quantitative real time PCR (qPCR) is a powerful tool to evaluate mRNA expression level. However, reliable qPCR results require normalization with validated reference gene(s). In this study, we investigated stable reference genes in seven tissues according to four developmental stages in minipigs. Six candidate reference genes and one target gene (ACE2) were selected and qPCR was performed. BestKeeper, geNorm, NormFinder, and delta Ct method through the RefFinder web-based tool were used to evaluate the stability of candidate reference genes. To verify the selected stable genes, relative expression of ACE2 was calculated and compared with each other.

Results
As a result, HPRT1 and 18S genes had lower SD value, while HMBS and GAPDH genes had higher SD value in all samples. Using statistical algorithms, HPRT1 was the most stable gene, followed by 18S, β-actin, B2M, GAPDH, and HMBS. In intestine, all candidate reference genes exhibited similar patterns of ACE2 gene expression over time, whereas in liver, lung, and kidney, gene expression pattern normalized with stable reference genes differed from those normalized with less stable genes. When normalized with the most stable genes, the expression levels of ACE2 in minipigs highly increased in intestine and kidney at PND28, which is consistent with the ACE2 expression pattern in humans.

Conclusions
We suggest that HPRT1 and 18S are good choices for analyzing all these samples across the seven tissues and four developmental stages. However, this study can be a reference literature for gene expression experiments using minipig because reference gene should be validated and chosen according to experimental conditions.
Antibiotic resistance patterns of Helicobacter pylori strains isolated from the Tibet Autonomous Region, China
Authors: Tang Xiaoqiong , Wang Zhonghua , Shen Yalin , Song Xiaona , Benghezal Mohammed , Marshall Barry J. , Tang Hong , Li Hong 
Published: August 2022

Abstract
Background
The prevalence of Helicobacter pylori antibiotic susceptibility in the Tibet Autonomous Region, China is not determined. This study aimed to evaluate the antibiotic resistance patterns of H. pylori isolates there.

Results
A total of 153 (38.5%) H. pylori strains were successfully isolated from 397 patients in People's Hospital of Tibet Autonomous Region, China. The overall resistance rates were as follows: clarithromycin (27.4%), levofloxacin (31.3%), metronidazole (86.2%), amoxicillin (15.6%), tetracycline (0%), furazolidone (0.6%), and rifampicin (73.2%). Only 2.0% of H. pylori isolates were susceptible to all tested antimicrobials, with mono resistance, dual resistance, triple resistance, quadruple resistance, and quintuple resistance being 18.3%, 44.4%, 18.3%, 12.4%, and 4.6%, respectively. The resistance rates to levofloxacin (40.5%) and amoxicillin (21.5%) in strains isolated from female patients were significantly higher than those from male patients (21.6% and 9.5%, respectively).

Conclusions
This study demonstrates high H. pylori resistance rates to clarithromycin, levofloxacin, metronidazole, and rifampicin, whereas moderate resistance to amoxicillin, and negligible resistant to tetracycline, and furazolidone in Tibet Autonomous Region, China. The high resistance to rifampicin warns further investigation of its derivative, rifabutin.
Full-length transcriptome analysis of maize root tips reveals the molecular mechanism of cold stress during the seedling stage
Authors: Xuhui Li , Weiwei Chen , Siqi Lu , Junteng Fang , Hang Zhu , Xiangbo Zhang , Yongwen Qi 
Published: August 2022

Abstract
Background
As maize originated in tropical or subtropical zones, most maize germplasm is extremely sensitive to low temperatures during the seedling stage. Clarifying the molecular mechanism of cold acclimation would facilitate the breeding of cold tolerant maize varieties, which is one of the major sustainability factors for crop production. To meet this goal, we investigated two maize inbred lines with contrasting levels of cold tolerance at the seedling stage (IL85, a cold tolerant line; B73, a cold sensitive line), and performed full-length transcriptome sequencing on the root tips of seedlings before and after 24 h of cold treatment.

Results
We identified 152,263 transcripts, including 20,993 novel transcripts, and determined per-transcript expression levels. A total of 1,475 transcripts were specifically up-regulated in the cold tolerant line IL85 under cold stress. GO enrichment analysis revealed that 25 transcripts were involved in reactive oxygen species (ROS) metabolic processes and 15 transcripts were related to the response to heat. Eight genes showed specific differential alternative splicing (DAS) in IL85 under cold stress, and were mainly involved in amine metabolism. A total of 1,111 lncRNAs were further identified, 62 of which were up-regulated in IL85 or B73 under cold stress, and their corresponding target genes were enriched in protein phosphorylation.

Conclusions
These results provide new insights into the molecular mechanism of cold acclimation during the seedling stage in maize, and will facilitate the development of cultivars with improved cold stress tolerance.
Genome-wide screening of lectin putative genes from Sorghum bicolor L., distribution in QTLs and a probable implications of lectins in abiotic stress tolerance
Authors: Osman Makarim El-fadil M. , Dirar Amina Ibrahim , Konozy Emadeldin Hassan E. 
Published: August 2022

Abstract
Background
Sorghum bicolor is one of the most important crops worldwide with the potential to provide resilience when other economic staples might fail against the continuous environmental changes. Many physiological, developmental and tolerance traits in plants are either controlled or influenced by lectins; carbohydrate binding proteins. Hence, we aimed at providing a comprehensive in silico account on sorghum’s lectins and study their possible implication on various desired agronomical traits.

Results
We have searched sorghum’s genome from grain and sweet types for lectins putative genes that encode proteins with domains capable of differentially binding carbohydrate moieties and trigger various physiological responses. Of the 12 known plant lectin families, 8 were identified regarding their domain architectures, evolutionary relationships, physiochemical characteristics, and gene expansion mechanisms, and they were thoroughly addressed. Variations between grain and sweet sorghum lectin homologs in term of the presence/absence of certain other joint domains like dirigent and nucleotide-binding adaptor shared by APAF-1, R-proteins, and CED-4 (NB-ARC) indicate a possible neofunctionalization. Lectin sequences were found to be preferentially overrepresented in certain quantitative trait loci (QTLs) related to various traits under several subcategories such as cold, drought, salinity, panicle/grain composition, and leaf morphology. The co-localization and distribution of lectins among multiple QTLs provide insights into the pleiotropic effects that could be played by one lectin gene in numerous traits.

Conclusion
Our study offers a first-time inclusive details on sorghum lectins and their possible role in conferring tolerance against abiotic stresses and other economically important traits that can be informative for future functional analysis and breeding studies.
The association between DNA methylation of 6p21.33 and AHRR in blood and coronary heart disease in Chinese population
Authors: Zhu Liya , Zhu Chao , Wang Jinxin , Yang Rongxi , Zhao Xiaojing 
Published: August 2022

Abstract
Background
Early detection could significantly improve the prognosis of coronary heart disease (CHD). In-invitro diagnostic technique may provide a solution when sufficient biomarkers could be identified. Pertinent associations between blood-based aberrant DNA methylation and smoking, the pathogenesis of atherosclerosis, and CHD have been robustly demonstrated and replicated, but that studies in Chinese populations are rare. The blood-based methylation of aryl-hydrocarbon receptor repressor (AHRR) cg05575921 and 6p21.33 cg06126421 has been associated with cardiovascular mortality in Caucasians. Here, we aim to investigate whether the AHRR and 6p21.33 methylation in the blood is associated with CHD in the Chinese population.

Methods
In this case–control study, 180 CHD patients recruited at their first registration in our study center, and 184 controls randomly selected from the people who participated in the annual health examination were enrolled. Methylation intensities of 19 CpG sites, including AHRR cg05575921, 6p21.33 cg06126421, and their flanking CpG sites, were quantified by mass spectrometry. The association between methylation intensities and CHD was estimated by logistic regression analyses adjusted for covariant.

Results
Compared to the controls, lower methylation of 6p21.33_CpG_4.5/cg06126421 was independently associated with increased odds of being a CHD patient (OR per − 10% methylation = 1.42 after adjustment for age, gender, and batch effect; p = 0.032 by multiple testing corrections). No association between blood-based AHRR methylation and CHD was found.

Conclusions
6p21.33 methylation exhibits a significant association with CHD. The combination of 6p21.33 methylation and conventional risk factors might be an intermediate step towards the early detection of CHD.
Estimating causal effects in the presence of competing events using regression standardisation with the Stata command standsurv
Authors: Syriopoulou Elisavet , Mozumder Sarwar I. , Rutherford Mark J. , Lambert Paul C. 
Published: August 2022

Abstract
Background
When interested in a time-to-event outcome, competing events that prevent the occurrence of the event of interest may be present. In the presence of competing events, various estimands have been suggested for defining the causal effect of treatment on the event of interest. Depending on the estimand, the competing events are either accommodated or eliminated, resulting in causal effects with different interpretations. The former approach captures the total effect of treatment on the event of interest while the latter approach captures the direct effect of treatment on the event of interest that is not mediated by the competing event. Separable effects have also been defined for settings where the treatment can be partitioned into two components that affect the event of interest and the competing event through different causal pathways.

Methods
We outline various causal effects that may be of interest in the presence of competing events, including total, direct and separable effects, and describe how to obtain estimates using regression standardisation with the Stata command . Regression standardisation is applied by obtaining the average of individual estimates across all individuals in a study population after fitting a survival model.

Results
With several contrasts of interest can be calculated including differences, ratios and other user-defined functions. Confidence intervals can also be obtained using the delta method. Throughout we use an example analysing a publicly available dataset on prostate cancer to allow the reader to replicate the analysis and further explore the different effects of interest.

Conclusions
Several causal effects can be defined in the presence of competing events and, under assumptions, estimates of those can be obtained using regression standardisation with the Stata command . The choice of which causal effect to define should be given careful consideration based on the research question and the audience to which the findings will be communicated.
TOMM40 genetic variants associated with healthy aging and longevity: a systematic review
Authors: Chen Sunny , Sarasua Sara M. , Davis Nicole J. , DeLuca Jane M. , Boccuto Luigi , Thielke Stephen M. , Yu Chang-En 
Published: August 2022

Abstract
Introduction
Healthy aging relies on mitochondrial functioning because this organelle provides energy and diminishes oxidative stress. Single nucleotide polymorphisms (SNPs) in TOMM40, a critical gene that produces the outer membrane protein TOM40 of mitochondria, have been associated with mitochondrial dysfunction and neurodegenerative processes. Yet it is not clear whether or how the mitochondria may impact human longevity. We conducted this review to ascertain which SNPs have been associated with markers of healthy aging.

Methods
Using the PRISMA methodology, we conducted a systematic review on PubMed and Embase databases to identify associations between TOMM40 SNPs and measures of longevity and healthy aging.

Results
Twenty-four articles were selected. The TOMM40 SNPs rs2075650 and rs10524523 were the two most commonly identified and studied SNPs associated with longevity. The outcomes associated with the TOMM40 SNPs were changes in BMI, brain integrity, cognitive functions, altered inflammatory network, vulnerability to vascular risk factors, and longevity.

Discussions
Our systematic review identified multiple TOMM40 SNPs potentially associated with healthy aging. Additional research can help to understand mechanisms in aging, including resilience, prevention of disease, and adaptation to the environment.
Determining the existence of the foramen of Huschke in patients with temporomandibular joint disorders using cone beam computed tomography: retrospective cohort study
Authors: Hasani Mahvash , Haghnegahdar Abdolaziz , Khojastepour Leila , Golbahar Haghighi Mohammad Javad 
Published: August 2022

Abstract
Background
Foramen of Huschke has been presented as an unusual developmental defect in anteroinferior aspect of external auditory canal. It can be associated with significant otologic complications. The purpose of this study was to determine the association between existence of foramen of Huschke and temporomandibular joint disorders in Cone Beam Computed Tomography (CBCT) images.

Methods
Of an initial sample of 465 patients, we retrospectively evaluated the CBCT images of 118 individuals with clinical signs and symptoms of temporomandibular joint disorders as case group and 256 individuals as control group. The presence, size and localization of foramen of Huschke were assessed in the axial and corrected sagittal images. The sex and age distribution were determined. Fisher’s exact test, T-test and Pearson’s Chi-square were applied to assess the relationship between foramen of Huschke and temporomandibular joint disorders in the case and control groups considering age and sex.

Results
The foramen of Huschke prevalence was slightly higher in patients with temporomandibular joint disorders (3.4%) than patients without temporomandibular joint disorders (0.8%). However, the difference was not statistically significant (P = 0.082). foramen of Huschke was found in five females and one male. There was no significant difference between case and control groups considering the age of patients with foramen of Huschke (P = 0.683). There was no significant difference between the case and control groups, considering the right and left ears in distribution of foramen of Huschke (P = 0.099) (P = 0.183).

Conclusions
Higher prevalence of foramen of Huschke in patients with temporomandibular joint disorders may suggest possible mechanism for temporomandibular joint disorders development that can be affected by presence of foramen of Huschke.