bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoscopic ultrasound-guided trans-duodenal fine-needle biopsy of a small renal mass: case report and review of the literature
Authors: Kwong Justin , May Gary , Ordon Michael 
Published: October 2021

Abstract
Background
The incidental detection of small renal masses (SRMs) is increasing and biopsy to obtain pathological diagnosis is increasingly proposed as a diagnostic tool to guide further management. Renal mass biopsies are traditionally performed via a percutaneous approach. However, this is not always feasible due to anatomical limitations. A rarely reported alternative biopsy approach for SRMs is endoscopic ultrasound (EUS)-guided fine-needle biopsy (FNB). Herein, we describe a case of EUS-guided trans-duodenal FNB for a SRM that was not amenable to standard percutaneous biopsy.

Case presentation
A 48-year-old man was incidentally found to have a right-sided SRM measuring 2.9 × 2.2 × 2.4 cm during evaluation for a hernia. It was anterior, interpolar, completely endophytic and near the renal hilum. The tumor was not amenable to traditional percutaneous biopsy due to its anterior location. However, the renal mass was in close proximity to the descending duodenum and so it was felt that an EUS-guided trans-duodenal FNB would be feasible. The procedure was successful without any complications. The specimen adequacy was satisfactory for evaluation and consistent with renal papillary carcinoma with WHO/ISUP grade 3 nuclear changes.

Conclusion
Our case report demonstrated that EUS-guided trans-duodenal FNB was a safe and feasible approach to obtaining biopsy tissue diagnosis of a SRM that was not amenable to percutaneous biopsy.
Travellers’ preferences towards existing and emerging means of first/last mile transport: a case study for the Almere centrum railway station in the Netherlands
Authors: Stam Bas , van Oort Niels , van Strijp-Harms Hilke J. , van der Spek Stefan C. , Hoogendoorn Serge P. 
Published: October 2021

AbstractFirst/last mile transport is essential for transit but is often found to be the weakest link in a trip. Moreover, as a result of multiple developments (e.g. demographic shifts, urbanization, climate change, technology advancement) first/last mile transport will likely change rapidly. The literature review of this study shows six different categories of factors affecting first/last mile mode choice: (1) traveller, (2) psychological, (3) first/last mile trip, (4) first/last mile modes, (5) built environment, and (6) main stage. We used this framework to understand and predict the complex process of mode choice, specifically given the emerge of new modes. The performed mode choice experiment shows varying results regarding the preferences of travellers for existing and new means of first/last mile transport. Four future scenarios (varying in level of sharing and flexibility of rides) are investigated. Traditional means of transport such as private vehicles and traditional ride services remain preferred over shared vehicles and on-demand ride services. For instance, 21% of the travellers chooses a private but no shared vehicle, and 12% chooses a traditional but no on-demand ride service. On the other hand, 21% of the travellers prefer a shared vehicle and 23% prefer an on-demand ride service whenever these vehicles/services are available. These results illustrate that when mode choice factors are absent and there are no restrictions taken into account (for example the possession of a car and driving license when choosing car), the actual chosen means of transport in the current situation differs from the preferred means of transport in the future. The results also show potential for new, emerging, means of first/last mile transport. According to the ‘preferred situation’ by travellers, transit nodes and first/last mile systems require a different design regarding first/last mile facilities, dependent on the scenario(s) that will develop. The challenge for decision makers and planners is to steer mode choice decisions in the direction according to their policy objectives, where our insights support the corresponding design choices and policy interventions.
Distinct patterns of whole blood transcriptional responses are induced in mice following immunisation with adenoviral and poxviral vector vaccines encoding the same antigen
Authors: Sheerin Dylan , Dold Christina , O’Connor Daniel , Pollard Andrew J. , Rollier Christine S. 
Published: October 2021

Abstract
Background
Viral vectors, including adenovirus (Ad) and modified vaccinia Ankara (MVA), have gained increasing attention as vaccine platforms in recent years due to their capacity to express antigens from a wide array of pathogens, their rapid induction of humoral and cellular protective immune responses, and their relatively low production costs. In particular, the chimpanzee Ad vector, ChAdOx1, has taken centre stage as a leading COVID-19 vaccine candidate. However, despite mounting data, both clinical and pre-clinical, demonstrating effective induction of adaptive immune responses, the innate immune signals that precede the protective responses that make these vectors attractive vaccine platforms remain poorly understood.

Results
In this study, a mouse immunisation model was used to evaluate whole blood gene expression changes 24 h after either a single dose or heterologous prime-boost regimen of an Ad and/or MVA vaccine. We demonstrate through comparative analysis of Ad vectors encoding different antigens that a transgene product-specific gene signature can be discerned from the vector-induced transcriptional response. Expression of genes involved in TLR2 stimulation and γδ T cell and natural killer cell activation were induced after a single dose of Ad, while MVA led to greater expression of type I interferon genes. The order of prime-boost combinations was found to influence the magnitude of the gene expression changes, with MVA/Ad eliciting greater transcriptional perturbation than Ad/MVA. Contrasting the two regimens revealed significant enrichment of epigenetic regulation pathways and augmented expression of MHC class I and II molecules associated with MVA/Ad.

Conclusion
These data demonstrate that the order in which vaccines from heterologous prime-boost regimens are administered leads to distinct transcriptional responses and may shape the immune response induced by such combinations. The characterisation of early vaccine-induce responses strengthens our understanding of viral vector vaccine mechanisms of action ahead of their characterisation in human clinical trials and are a valuable resource to inform the pre-clinical design of appropriate vaccine constructs for emerging infectious diseases.
Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle
Authors: Liu Lihe , Amorín Rocío , Moriel Philipe , DiLorenzo Nicolás , Lancaster Phillip A. , Peñagaricano Francisco 
Published: October 2021

Abstract
Background
The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively.

Results
Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons.

Conclusions
Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.
Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina
Authors: Chen Gang , Qian Hong-Mei , Chen Jing , Wang Jie , Guan Ji-Tian , Chi Zai-Long 
Published: October 2021

Abstract
Background
The molecular complexity of neural retina development remains poorly studied. Knowledge of retinal neurogenesis regulation sheds light on retinal degeneration therapy exploration. Therefore, we integrated the time-series circRNA, lncRNA, miRNA, and mRNA expression profiles of the developing retina through whole-transcriptome sequencing. The key functional ncRNAs and the ceRNA network regulating retinal neurogenesis were identified.

Results
Transcriptomic analysis identified circRNA as the most variable ncRNA subtype. We screened a series of neurogenesis-related circRNAs, lncRNAs, and miRNAs using different strategies based on their diversified molecular functions. The expression of circCDYL, circATXN1, circDYM, circPRGRIP, lncRNA Meg3, and lncRNA Vax2os was validated by quantitative real-time PCR. These circRNAs and lncRNAs participate in neurotransmitter transport and multicellular organism growth through the intricate circRNA/lncRNA-miRNA-mRNA network.

Conclusion
Whole-transcriptome sequencing and bioinformatics analysis systematically screened key ncRNAs in retinal neurogenesis. The validated ncRNAs and their circRNA/lncRNA-miRNA-mRNA network involve neurotransmitter transport and multicellular organism growth during retinal development.
Seed priming with proline improved photosystem II efficiency and growth of wheat (Triticum aestivum L.)
Authors: Ambreen Sarah , Athar Habib-ur-Rehman , Khan Ameer , Zafar Zafar Ullah , Ayyaz Ahsan , Kalaji Hazem M. 
Published: October 2021

Abstract
Background
Proline can promote growth of plants by increasing photosynthetic activity under both non-stress and abiotic stress conditions. However, its role in non-stressed conditions is least studied. An experiment was conducted to assess as to whether increase in growth of wheat due to seed priming with proline under non-stress condition was associated with proline-induced changes in photosystem II (PSII) activity. Seeds of four wheat varieties (S-24, Sehar-06, Galaxy-13, and Pasban-90) were primed with different concentrations of proline (0, 5, 15 and 25 mM) for 12 h and allowed to grow under normal conditions. Biomass accumulation and photosynthetic performance, being two most sensitive features/indicators of plant growth, were selected to monitor proline modulated changes.

Results
Seed priming with proline increased the fresh and dry weights of shoots and roots, and plant height of all four wheat varieties. Maximum increase in growth attributes was observed in all four wheat varieties at 15 mM proline. Maximum growth improvement due to proline was found in var. Galaxy-13, whereas the reverse was true for S-24. Moreover, proline treatment changed the Fo, Fm, Fv/Fo, PIABS, PITot in wheat varieties indicating changes in PSII activity. Proline induced changes in energy fluxes for absorption, trapping, electron transport and heat dissipation per reaction center indicated that var. Galaxy-13 had better ability to process absorbed light energy through photosynthetic machinery. Moreover, lesser PSII efficiency in var. S-24 was due to lower energy flux for electron transport and greater energy flux for heat dissipation. This was further supported by the fact that var. S-24 had disturbance at acceptor side of PSI as reflected by reduction in ΔVIP, probability and energy flux for electron transport at the PSI end electron acceptors.

Conclusion
Seed priming with proline improved the growth of wheat varieties, which depends on type of variety and concentration of proline applied. Seed priming with proline significantly changed the PSII activity in wheat varieties, however, its translation in growth improvement depends on potential of processing of absorbed light energy by electron acceptors of electron transport chain, particularly those present at PSI end.
Genome-wide identification of the tobacco GDSL family and apical meristem-specific expression conferred by the GDSL promoter
Authors: Lv Jing , Dai Chang-Bo , Wang Wei-Feng , Sun Yu-He 
Published: October 2021

Abstract
Background
GDSL esterases/lipases are a large protein subfamily defined by the distinct GDSL motif, and play important roles in plant development and stress responses. However, few studies have reported on the role of GDSLs in the growth and development of axillary buds. This work aims to identify the GDSL family members in tobacco and explore whether the NtGDSL gene contributes to development of the axillary bud in tobacco.

Results
One hundred fifty-nine GDSL esterase/lipase genes from cultivated tobacco (Nicotiana tabacum) were identified, and the dynamic changes in the expression levels of 93 of these genes in response to topping, as assessed using transcriptome data of topping-induced axillary shoots, were analysed. In total, 13 GDSL esterase/lipase genes responded with changes in expression level. To identify genes and promoters that drive the tissue-specific expression in tobacco apical and axillary buds, the expression patterns of these 13 genes were verified using qRT-PCR. GUS activity and a lethal gene expression pattern driven by the NtGDSL127 promoter in transgenic tobacco demonstrated that NtGDSL127 is specifically expressed in apical buds, axillary buds, and flowers. Three separate deletions in the NtGDSL127 promoter demonstrated that a minimum upstream segment of 235 bp from the translation start site can drive the tissue-specific expression in the apical meristem. Additionally, NtGDSL127 responded to phytohormones, providing strategies for improving tobacco breeding and growth.

Conclusion
We propose that in tobacco, the NtGDSL127 promoter directs expression specifically in the apical meristem and that expression is closely correlated with axillary bud development.
“The PLCP gene family of grapevine (Vitis vinifera L.): characterization and differential expression in response to Plasmopara Viticola”
Authors: Kang Jun , Gong Peijie , Ge Mengqing , Sadeghnezhad Ehsan , Liu Zhongjie , Zhang Mengwei , Shangguan Lingfei , Fang Jinggui 
Published: October 2021

AbstractBackgroundPapain-like cysteine proteases (PLCPs), a large group of cysteine proteases, are structurally related to papain. The members belonging to PLCPs family contribute to plant immunity, senescence, and defense responses in plants. ThePLCPgene family has been identified in Arabidopsis, rice, soybean, and cotton. However, no systematic analysis ofPLCPgenes has been undertaken in grapevine. SincePlasmopara viticolaas a destructive pathogen could affect immunity of grapes in the field, we considered that the members belonged to PLCPs family could play a crucial role in defensive mechanisms or programmed cell death. We aimed to evaluate the role ofPLCPsin 2 different varieties of grapevines and compared the changes of their expressions with the transcriptional data in response toP. viticola.ResultsIn this study, 23 grapevinePLCP(VvPLCP) genes were identified by comprehensive bioinformatics analysis. Subsequently, the chromosomal localizations, gene structure, conserved domains, phylogenetic relationship, gene duplication, and cis-acting elements were analyzed. Numerous cis-acting elements related to plant development, hormone, and stress responses were identified in the promoter of theVvPLCPgenes. Phylogenetic analysis grouped theVvPLCPgenes into nine subgroups. The transcription ofVvPLCPin different inoculation time points and varieties indicated thatVvPLCPmay have vital functions in grapevine defense againstPlasmopara viticola. According to transcriptome data and qPCR analysis, we observed the increasing expression levels ofVvRD21–1at 72 h after inoculation in resistant variety, inferring that it was related to grape downy mildew resistance. Meanwhile, 3 genes includingVvXBCP1,VvSAG12–1,andVvALP1showed higher expression at 24 h after pathogen inoculation in the susceptible variety and might be related to the downy mildew phenotype. We nominated these four genes to function during hypersensitive response (HR) process, inferring that these genes could be associated with downy mildew resistance in grapes.ConclusionsOur results provide the reference for functional studies ofPLCPgene family, and highlight its functions in grapevine defense againstP. viticola. The results help us to better understand the complexity of thePLCPgene family in plant immunity and provide valuable information for future functional characterization of specific genes in grapevine.
Predictors of treatment failure among patients with gunshot wounds and post-traumatic stress disorder
Authors: Kuchyn Iurii Leonidovych , Horoshko Vasyl’ Romanovych 
Published: October 2021

Abstract
Background
The 82.1% treatment failure of post-traumatic stress disorder (PTSD), associated with gunshot wounds, is related to high incidence of chronic pain syndrome as well as resistance to the PTSD treatment. Defining treatment failure predictors among the PTSD patients with gunshot extremity wounds and the following therapy would improve treatment outcomes.

Methods
A total of 218 patients completed the study. The Mississippi Scale for Combat-Related PTSD (M-PTSD) was used for assessment of the treatment outcome rate. The risk relation between treatment failure and factors was assessed by a univariate or multivariate logistic regression method, with the model accuracy measured by the AUC – Area under the ROC curve. The odds ratio (OR) was considered for the qualitative factor assessment.

Results
The predictors of the PTSD treatment failure among the patients with gunshot wounds to the extremities are: 1) anesthesia type: the risk of failure is higher with the general anesthesia compared to the regional (p = 0.002), OR = 0.30 (95% CI 0.13-0.69) and the regional one with sedation (p = 0.004), OR = 0.30 (95% CI 0,14-0.65); 2) severe postoperative pain: the risk of treatment failure rises with increased pain intensity assessed by the visual analogue scale (p = 0.02), OR = 3.2 (95% CI 1.2-8.3).

Conclusions
The analysis showed that administration of general anesthesia compared to the regional one (regardless of the sedation) and high postoperative pain intensity are associated with higher risk of the PTSD treatment failure among patients with gunshot wounds to the extremities. The preference of regional anesthesia and postoperative pain control may potentially improve the treatment outcomes.

Trial registration
ClinicalTrials.gov: Retrospectively registered on December 30, 2020, NCT04689022.
Comparison of the hemodynamic response of dexmedetomidine versus additional intravenous lidocaine with propofol during tracheal intubation: a randomized controlled study
Authors: Seangrung Rattaphol , Pasutharnchat Koravee , Injampa Subundit , Kumdang Sirima , Komonhirun Rojnarin 
Published: October 2021

AbstractBackgroundLaryngoscopy and tracheal intubation are strong stimuli that cause a reflex increase in blood pressure (BP), heart rate (HR), and serum catecholamine level. These can lead to myocardial infarction or cerebrovascular accidents. The purpose of this study is to compare the efficacy of dexmedetomidine and lidocaine combined with propofol in attenuating the hemodynamic response following laryngoscopy and endotracheal intubation.MethodsThis study was a randomized controlled study and adhered to the CONSORT guidelines. One-hundred and six patients undergoing elective general anesthesia with endotracheal intubation were divided randomly into two groups. Group D received dexmedetomidine (1 μg kg− 1) before induction. Group LP received lidocaine (1.5 mg kg− 1) before induction with additional propofol (0.5 mg kg− 1) before laryngoscopy. The primary endpoint was hemodynamic including systolic (S) BP, diastolic (D) BP, mean arterial blood pressure (MAP) and HR measured before and after induction and ≤ 10 min after intubation. Secondary outcome was complications/adverse effects.ResultsAfter induction, the mean SBP, DBP, MAP and HR decreased significantly from baseline in both groups except for mean HR in group LP at 1 min. Differences in mean values of SBP, DBP, and MAP were significantly lower in group D after intubation at 4–10 min (P <  0.05). Group LP had a non-inferior effect in blunting BP at all time points except 1 and 2 min after induction, and 2 min after intubation. The mean difference in HR in group D was significantly lower than that in group LP at all time points (P <  0.001). Group D had significantly more episodes of bradycardia (18.87% vs. 0%,P = 0.001) and hypotension (52.83% vs. 15.09%,P < 0.001) than did group LP.ConclusionLidocaine (1.5 mg kg− 1) with additional propofol (0.5 mg kg− 1) had a non-inferior effect compared with dexmedetomidine (1 μg kg− 1) in attenuating the hemodynamic response following laryngoscopy and endotracheal intubation, and had fewer adverse effects.Trial registrationThai Clinical Trial Registry, (TRTC20190206002). Retrospectively registered 4 February 2019.
Using the South African Triage Scale for prehospital triage: a qualitative study
Authors: Dixon Julia , Burkholder Taylor , Pigoga Jennifer , Lee Michael , Moodley Kubendhren , de Vries Shaheem , Wallis Lee , Mould-Millman Nee-Kofi 
Published: October 2021

Abstract
Background
Triage is a critical component of prehospital emergency care. Effective triage of patients allows them to receive appropriate care and to judiciously use personnel and hospital resources. In many low-resource settings prehospital triage serves an additional role of determining the level of destination facility. In South Africa, the Western Cape Government innovatively implemented the South African Triage Scale (SATS) in the public Emergency Medical Services (EMS) service in 2012. The prehospital provider perspectives and experiences of using SATS in the field have not been previously studied.

Methods
In this qualitative study, focus group discussions with cohorts of basic, intermediate and advanced life support prehospital providers were conducted and transcribed. A content analysis using an inductive approach was used to code transcripts and identify themes.

Results
15 EMS providers participated in three focus group discussions. Data saturation was reached and four major themes emerged from the qualitative analysis: Implementation and use of SATS; Effectiveness of SATS; Limitations of the discriminator; and Special EMS considerations. Participants overall felt that SATS was easy to use and allowed improved communication with hospital providers during patient handover. Participants, however, described many clinical cases when their clinical gestalt triaged the patient to a different clinical acuity than generated by SATS. Additionally, they stated many clinical discriminators were too subjective to effectively apply or covered too broad a range of clinical severity (e.g., ingestions). Participants provided examples of how the prehospital environment presents additional challenges to using SATS such as changing patient clinical conditions, transport times and social needs of patients.

Conclusions
Overall, participants felt that SATS was an effective tool in prehospital emergency care. However, they described many clinical scenarios where SATS was in conflict with their own assessment, the clinical care needs of the patient or the available prehospital and hospital resources. Many of the identified challenges to using SATS in the prehospital environment could be improved with small changes to SATS and provider re-training.