bluuebunny/crossref_metadata_2025_split huggingface dataset:
A versatile 5′ RACE-Seq methodology for the accurate identification of the 5′ termini of mRNAs
Authors: Adamopoulos Panagiotis G. , Tsiakanikas Panagiotis , Stolidi Irene , Scorilas Andreas 
Published: February 2022

Abstract
Background
Technological advancements in the era of massive parallel sequencing have enabled the functional dissection of the human transcriptome. However, 5′ ends of mRNAs are significantly underrepresented in these datasets, hindering the efficient analysis of the complex human transcriptome. The implementation of the template-switching mechanism at the reverse transcription stage along with 5′ rapid amplification of cDNA ends (RACE) constitutes the most prominent and efficient strategy to specify the actual 5′ ends of cDNAs. In the current study, we developed a 5′ RACE-seq method by coupling a custom template-switching and 5′ RACE assay with targeted nanopore sequencing, to accurately unveil 5′ termini of mRNA targets.

Results
The optimization of the described 5′ RACE-seq method was accomplished using the human BCL2L12 as control gene. We unveiled that the selection of hybrid DNA/RNA template-switching oligonucleotides as well as the complete separation of the cDNA extension incubation from the template-switching process, significantly increase the overall efficiency of the downstream 5′ RACE. Collectively, our results support the existence of two distinct 5′ termini for BCL2L12, being in complete accordance with the results derived from both direct RNA and PCR-cDNA sequencing approaches from Oxford Nanopore Technologies. As proof of concept, we implemented the described 5′ RACE-seq methodology to investigate the 5′ UTRs of several kallikrein-related peptidases (KLKs) gene family members. Our results confirmed the existence of multiple annotated 5′ UTRs of the human KLK gene family members, but also identified novel, previously uncharacterized ones.

Conclusions
In this work we present an in-house developed 5′ RACE-seq method, based on the template-switching mechanism and targeted nanopore sequencing. This approach enables the broad and in-depth study of 5′ UTRs of any mRNA of interest, by offering a tremendous sequencing depth, while significantly reducing the cost-per reaction compared to commercially available kits.
Changes in root microbiome during wheat evolution
Authors: Gholizadeh Somayeh , Mohammadi Seyed Abolghasem , Salekdeh Ghasem Hosseini 
Published: February 2022

Abstract
Background
Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.

Results
In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.

Conclusions
This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.
Bacteria associated with acne use glycosaminoglycans as cell adhesion receptors and promote changes in the expression of the genes involved in their biosynthesis
Authors: Martín Carla , Ordiales Helena , Vázquez Francisco , Pevida Marta , Rodríguez David , Merayo Jesús , Vázquez Fernando , García Beatriz , Quirós Luis M. 
Published: February 2022

Abstract
Background
Cell surface glycosaminoglycans (GAGs) participate in many physiological and pathological processes, including infections and inflammatory response. Acne is a common chronic inflammatory skin disorder that affects the pilosebaceous unit and has a multifactorial etiology, including bacterial colonization of the hair follicle. This study aimed to investigate the participation of GAG in the adhesion of Propionibacterium acnes, Staphylococcus aureus and Staphylococcus epidermidis to keratinocytes and fibroblasts of the skin by competition experiments and cell surface removal using specific liases. The alteration in the transcription of the genes responsible for the synthesis of GAG induced by the adhesion of these bacteria was also analyzed by qRT-PCR.

Results
GAGs are involved in bacterial adherence to skin cells, especially fibroblasts, where chondroitin sulfate displayed the higher effect. Bacterial adherence produced different alterations in the transcription of the genes responsible for GAG structures. P. acnes induced mostly changes in keratinocytes, while S. epidermidis was the main cause of alterations in fibroblasts. These variations in gene expression affected all the stages in the biosynthesis of the main species of GAGs, heparan and chondroitin sulphate.

Conclusions
GAGs species are involved in the adhesion of acne-related bacteria to skin cells in a differential manner depending on each microorganism and cellular type, although other receptors seem to exist. Bacterial adherence led to variations on gene expression in skin cells affecting GAG chains structure what, consequently, should alter their interactions with different ligands, affecting the development of acne disease.
Genomic prediction models for traits differing in heritability for soybean, rice, and maize
Authors: Kaler Avjinder S. , Purcell Larry C. , Beissinger Timothy , Gillman Jason D. 
Published: February 2022

Abstract
Background
Genomic selection is a powerful tool in plant breeding. By building a prediction model using a training set with markers and phenotypes, genomic estimated breeding values (GEBVs) can be used as predictions of breeding values in a target set with only genotype data. There is, however, limited information on how prediction accuracy of genomic prediction can be optimized. The objective of this study was to evaluate the performance of 11 genomic prediction models across species in terms of prediction accuracy for two traits with different heritabilities using several subsets of markers and training population proportions. Species studied were maize (Zea mays, L.), soybean (Glycine max, L.), and rice (Oryza sativa, L.), which vary in linkage disequilibrium (LD) decay rates and have contrasting genetic architectures.

Results
Correlations between observed and predicted GEBVs were determined via cross validation for three training-to-testing proportions (90:10, 70:30, and 50:50). Maize, which has the shortest extent of LD, showed the highest prediction accuracy. Amongst all the models tested, Bayes B performed better than or equal to all other models for each trait in all the three crops. Traits with higher broad-sense and narrow-sense heritabilities were associated with higher prediction accuracy. When subsets of markers were selected based on LD, the accuracy was similar to that observed from the complete set of markers. However, prediction accuracies were significantly improved when using a subset of total markers that were significant at P ≤ 0.05 or P ≤ 0.10. As expected, exclusion of QTL-associated markers in the model reduced prediction accuracy. Prediction accuracy varied among different training population proportions.

Conclusions
We conclude that prediction accuracy for genomic selection can be improved by using the Bayes B model with a subset of significant markers and by selecting the training population based on narrow sense heritability.
Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution
Authors: Amenu Sara Getachew , Wei Neng , Wu Lei , Oyebanji Oyetola , Hu Guangwan , Zhou Yadong , Wang Qingfeng 
Published: February 2022

Abstract
Background
The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices.

Results
All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance.

Conclusions
Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.
Analgesic effects of different concentrations of ropivacaine in transversalis fascia plane block during laparotomy
Authors: Tian Ye , Zhan Yong , Liu Ke , Bu Shaojin , Tian Yalin , Xiong Chunyan , Shen Jintao 
Published: February 2022

Abstract
Objective
To explore the analgesic effects of different concentrations of ropivacaine in transversalis fascia plane (TFP) block during laparotomy.

Methods
Ninety patients who underwent laparotomy admitted to our hospital from March 2019 to March 2020 were selected as the study subjects and were divided equally into a low concentration group, a medium concentration group, and a high concentration group according to the randomized grouping method. The low concentration group adopted 0.4% ropivacaine 40 ml, the medium concentration group was given 0.5% ropivacaine 40 ml, and the high concentration group was given 0.6% ropivacaine 40 ml. The hemodynamic indexes and the incidence of adverse reactions in the two groups were compared. The Numerical Rating Scale (NRS) was used to assess the postoperative pain in the three groups, the Bruggrmann comfort scale (BCS) was used to assess the comfort level in the three groups, and the Mini-mental State Examination (MMSE) was used to evaluate the postoperative cognitive function of the three groups of patients.

Results
The mean artery pressure (MAP) and heart rate (HR) levels at T1 and T2 were significantly lower in the medium concentration group than in the other two groups (P < 0.05). The low concentration group had a significantly higher NRS score at T2 than the medium concentration group and the high concentration group (P < 0.05). A significantly higher BCS score was observed in the high concentration group than the other two groups (P < 0.05). There were significantly higher Ramsay scores and MMSE scores in the medium concentration group than in the low concentration and high concentration groups (P < 0.05). The overall incidence of adverse reactions of the high concentration group was significantly higher than that of the low concentration group (P < 0.05), but showed similar results with the medium concentration group.

Conclusion
The medium concentration group exhibits a better analgesic effect than the low concentration group and higher safety than the high concentration group. Therefore, the use of medium concentration ropivacaine in TFP block may provide a referential basis for clinical treatment.
Regional variation in coronary angiography rates: the association with supply factors and the role of indication: a spatial analysis
Authors: Frank-Tewaag Julia , Bleek Julian , Günster Christian , Schneider Udo , Horenkamp-Sonntag Dirk , Marschall Ursula , Franke Sebastian , Schlößler Kathrin , Donner-Banzhoff Norbert , Sundmacher Leonie 
Published: February 2022

Abstract
Background
Coronary angiographies (CAs) are among the most common diagnostic procedures carried out in German hospitals, and substantial regional differences in their frequency of use have been documented. Given the heterogeneity with regard to the expected benefits and the varying scope for discretion depending on the indication for the procedure, we hypothesized that the observed variation and the association of need and supply factors differs by indication for CA.

Methods
We investigated the correlation between supply factors and the regional rates of CAs in Germany while controlling for need using spatial‐autoregressive error models (SARE) and spatial cross-regressive models with autoregressive errors (SCRARE). The overall rates of CAs and the rates in specific patient subgroups, namely, patients with and without myocardial infarction (MI), were calculated based on a comprehensive set of nationwide routine data from three statutory health insurances at the district level.

Results
Although little variation was found in cases with MI, considerable variation was seen in the overall cases and cases without MI. The SARE models revealed a positive association between the number of hospitals with a cardiac catheterization laboratory per 10,000 population and the rates of overall cases and cases without MI, whereas no such relationship existed in cases with MI. Additionally, an association between regional deprivation and the rates of CAs was found in cases with MI, but no such association was seen in cases without MI.

Conclusions
The results supported the hypothesis that the relative association of need and supply factors differed by the indication for CA. Although the regional differences in the frequency of use of CAs can only be explained in part by the factors examined in our study, it offers insight into patient access to and the provision of CA services and can provide a platform for further local research.
Prevalence and impact of migraine among university students in Bangladesh: findings from a cross-sectional survey
Authors: Rafi Abdur , Islam Saiful , Hasan M. Tasdik , Hossain Golam 
Published: February 2022

Abstract
Background
Migraine is one of the main causes of long-term morbidity, and it is one of the major contributors of all types of headaches in worldwide. Despite its disruptive effect, it is frequently underdiagnosed and undertreated in Bangladesh. The aim of the present study was to determine the prevalence of migraines and its impact on daily life of university students in Bangladesh.

Methods
This cross-sectional study was conducted among 2,352 students of Rajshahi University and Jahangirnagar University during March 2020 through a self-administered online survey. ID Migraine™ scale and HIT-6 scale were used to screen migraine and its impact respectively. Frequency distribution, Chi-square test and t-test along with multiple logistic regressions model were used to determine the prevalence and associated factors of migraine respectively.

Results
The overall prevalence of migraine among the participants was 21.4%. The prevalence was higher among females (29%) than males (12%). A multivariable logistic regression model provided the following eight risk factors of migraine: (i) gender (p < 0.01), (ii) family income (p < 0.01), (iii) marital status (p < 0.01), (iv) infrequent exercise (p < 0.01), (v) family history of headache (p < 0.01), (vi) high screen time (p < 0.05), (vii) depressive symptoms (p < 0.05) and (viii) anxiety disorder (p < 0.01). More than two-thirds of the people with migraines reported more than five attacks during the past month with moderate to severe intense headache. Stress was the most reported trigger of migraine among university students (71%) followed by irregular sleep (47%), academic pressure (33%), and external noise (28%). Almost 37% of the participants who had migraines reported that headache caused severe impact in their day to day life.

Conclusions
The prevalence of migraine among university students of Bangladesh is alarmingly high. Frequent migraine attacks and severe intensity of headache cause a substantial level of impact among the sufferers. Cautious avoidance of the triggering factors through appropriate interventions and prophylactic medication can mitigate the negative impact of migraine as well as improve the quality of life.
Norepinephrine promotes glioma cell migration through up-regulating the expression of Twist1
Authors: Wang Xue , Wang Ying , Xie Fang , Song Zi-Tian , Zhang Zi-Qian , Zhao Yun , Wang Shi-Da , Hu Hui , Zhang Yan-Shu , Qian Ling-Jia 
Published: February 2022

Abstract
Background
Glioma cells are characterized by high migration ability, resulting in aggressive growth of the tumors and poor prognosis of patients. It has been reported that the stress-induced hormone norepinephrine (NE) contributes to tumor progression through mediating a number of important biological processes in various cancers. However, the role of NE in the regulation of glioma migration is still unclear. Epithelial-to-mesenchymal transition (EMT) is one of the most important steps for tumor migration and metastasis. Twist1, as a key regulator of EMT, has been found to be elevated during glioma migration. But it is still unknown whether Twist1 is involved in the effect of NE on the migration of glioma cells.

Methods
Wound healing assay and transwell assay were conducted to evaluate the migration of glioma cells upon different treatments. The mesenchymal-like phenotype and the expression of Twist1 after NE treatment were assessed by cell diameters, real-time PCR, western blot and immunofluorescence staining. The gain-and loss-of-function experiments were carried out to investigate the biological function of Twist1 in the migration induced by NE. Finally, the clinical significance of Twist1 was explored among three public glioma datasets.

Results
In this study, our finding revealed a facilitative effect of NE on glioma cell migration in a β-adrenergic receptor (ADRB)-dependent way. Mechanistically, NE induced mesenchymal-like phenotype and the expression of Twist1. Twist1 overexpression promoted glioma cells migration, while knockdown of Twist1 abolished the discrepancy in the migration ability between NE treated glioma cells and control cells. In addition, the clinical analysis demonstrated that Twist1 was up-regulated in malignant gliomas and recurrent gliomas, and predicted a poor prognosis of glioma patients.

Conclusions
NE enhanced the migration ability of glioma cells through elevating the expression of Twist1. Our finding may provide potential therapeutic target for protecting patients with glioma from the detrimental effects of stress biology on the tumor progression.
What is the effect of independent medical evaluation on days on sickness benefits for long-term sick listed employees in Norway? A pragmatic randomised controlled trial, the NIME-trial
Authors: Mæland Silje , Holmås Tor Helge , Øyeflaten Irene , Husabø Elisabeth , Werner Erik L. , Monstad Karin 
Published: February 2022

AbstractBackgroundIndependent medical evaluations are used to evaluate degree and reason for work disability, uncertainty around the functional status, and/or the employee’s rehabilitation potential in several jurisdictions, but not in Norway. The main aim of this trial was to test the return to work effect of independent medical evaluation (IME) (summoning and consultation) compared to treatment as usual (TAU) in Norway, for workers who have been on continuous sick leave for 6 months.MethodsThis was a pragmatic randomised controlled trial including all employees aged 18–65 years, sick-listed by their general practitioner and on full or partial sick leave for the past 26 weeks in Hordaland County, Norway in 2015/16. Trial candidates were drawn from a central register at the Norwegian Labour and Welfare Administration at 22 weeks of sick leave. Pregnant women, individuals with cancer or dementia diagnoses, those with secret address, employed by NAV or sick listed by the specialist health services were excluded. Separate regression analyses were conducted to investigate the “intention-to-treat” and “treatment on the treated” effects, using the ordinary least squares and instrumental variable methods, respectively.ResultsAfter exemption based on predefined exclusion criteria, 5888 individuals were randomised to either IME (n = 2616) or TAU (n = 2599). The final intervention group constitutes 1698 individuals, of which 937 attended the IME consultation. No baseline differences were found between the IME and TAU group regarding gender, age, and previous sick leave. Individuals attending the IME were older than those who cancelled the appointment ((47/45),p = 0.006) and those who did not show up without cancelling ((47/42),p < 0.001). Mainly the IME physician agreed with the regular GP upon level of sick leave. In cases with different assessments, the difference tended to be towards a lower sick leave level. There were no intention to treat or treatment on the treated effect on days of sick leave after randomisation during follow up.ConclusionsOverall, the analyses showed no effect of IME on changes in sick leave for sick listed employees. This result was consistent for those who were offered an IME consultation (intention to treat) and those who undertook an IME consultation (treatment on the treated).Trial registrationClinicalTirals.gov trial numberNCT02524392first registration 14.08.2015.
In situ reconstruction of ruptured mycotic iliac artery aneurysm with autologous fascial-peritoneal tissue: a case report and literature review
Authors: Sang GuiFeng , Guo XiaoYan , Liu GuoLong , Che HaiJie 
Published: February 2022

Abstract
Background
Infectious aneurysms are rare in clinic with poor therapeutic outcomes. When artery rupture occurs, the disease tends to progress resulting in a high mortality, and there remains no ideal treatment.

Case presentation
We report a case of rupture of infectious iliac artery pseudoaneurysm, who was assigned to receive artery reconstruction with autologous fascial-peritoneal tissue and obtained satisfied short-term outcome. The follow-up of 6 months after operation was good and long-term follow-up is continuing.

Conclusion
The posterior rectus fascia-peritoneal layer seems to be a feasible autologous biomaterial for vascular substitution in urgent setting when no other autologous material was available.