bluuebunny/crossref_metadata_2025 huggingface dataset:
Insolvency judges meet strategic behaviour: A comparative empirical study
Authors: van Dijck Gijs , Hollemans Ruben , Maśnicka Monika , Frade Catarina , Benedetti Lorenzo , Galanti Lucilla , Fernando Paula , Kruczalak – Jankowska Joanna , Abriani Niccolo , Jesus Ruben , Machnikowska Anna , Pagni Ilaria
Published: March 2020

This article reports the results of a comparative empirical legal study that analyzed (1) strategic behaviour by actors in insolvencies that is salient to insolvency judges and (2) how insolvency judges respond to such behaviour. After examining four different European countries, namely Italy, the Netherlands, Poland, and Portugal, the study reveals how differences regarding case allocation, judge – insolvency practitioner (IP) interaction, and remuneration and case financing can result in strategic behaviour on both the side of the judges and the IPs. From this, it follows that improving the efficiency and effectiveness is not merely a matter of implementing legislation and case law, but that it also requires a look into the dynamics between insolvency judges, IPs, and other actors in the insolvency process.
“Something fruitful for all of us”: Social annotation as a signature pedagogy for literature education
Authors: Clapp Jeffrey , DeCoursey Matthew , Lee Sze Wah Sarah , Li Kris
Published: March 2020

New social annotation practices have the potential to become a “signature pedagogy” for educators in literary studies, because social annotation encapsulates both the expected learning outcomes and the underlying value commitments of literature education. We give an account of a project conducted by colleagues at the Education University of Hong Kong, during which colleagues explored social annotation technologies in literary studies courses. After implementing social annotation in our courses, instructors held roundtable discussions, collected surveys and conducted focus group interviews. Basing our interpretation of these data on Louise Rosenblatt’s transactional theory of reading and writing, we propose that social annotation can help students engage with literary texts more effectively by showing them how to move toward an aesthetic mode of reading. Students participating in social annotation, moreover, understood its application to literary studies in ways that directly reproduced Rosenblatt’s account of literary interpretation.
Prognostic value of non-invasive fibrosis indices post-curative resection in hepatitis-B-associated hepatocellular carcinoma patients
Authors: Zhang Ting-Ting , Ye Si-Si , Liang Jun , Bai Li
Published: March 2020

The occurrence and acuteness of liver cirrhosis were strongly associated with the hepatocarcinogenesis and the prognosis of hepatocellular carcinoma (HCC). This study compared the prognostic significance of non-invasive fibrosis panel containing 15 indices in hepatitis-B-associated HCC patients’ post-curative resection. Four hundred and five consecutive hepatitis-B-related HCC patients who went through curative hepatectomy were investigated retrospectively. The multivariate Cox proportional hazard model was used to evaluate independent prognostic factors for overall survival (OS). The accuracy in diagnosis of each non-invasive fibrosis index in cirrhosis detection was determined by the area under receiver operating characteristic (AUC) curve. Preoperative AST to platelet ratio index (APRI), Goteburg University Cirrhosis Index (GUCI), and King Score all exhibited a superior performance in diagnosis of cirrhosis detection with AUC > 0.7. APRI and Fibro-α Score were the risk factors that behaved independently in predicting the OS of HCC patients, with an hazard ratio (HR) value of 1.550 (P = 0.012) and 1.420 (P = 0.033), respectively. Preoperative APRI was a relatively accurate predictor of cirrhotic status and prognosis in HCC due to hepatitis-B among the 15 non-invasive fibrosis indices.

Impact statement

Non-invasive fibrosis indices, according to regular laboratory and clinical data, could be useful in assessing liver fibrosis in chronic hepatitis patients. However, the role of these biomarkers remains unclear in predicting the outcome of HBV-associated HCC in patients. This study was carried out retrospectively and included a relatively large sample size (n = 405) with a heterogeneous population of HBV infected patients and longer duration of prospective follow-up. Our study suggested that APRI and Fibro-α Scores are inversely correlated with overall survival in HBV-associated HCC patients. Meanwhile, GUCI, King Score, and APRI were highly correlated with cirrhosis status. Also, in subgroups of cirrhosis or non-cirrhosis, Fibro-α Scores could differentiate patients with good prognosis from those with poor outcome. This result would aid clinicians in acquiring preventive and therapeutic methods in patients with high risk.
Blood Gene Expression Profile Study Revealed the Activation of Apoptosis and p53 Signaling Pathway May Be the Potential Molecular Mechanisms of Ionizing Radiation Damage and Radiation-Induced Bystander Effects
Authors: He Guangyao , Tang Anzhou , Xie Mao , Xia Wei , Zhao Pengcheng , Wei Jianglian , Lai Yongjing , Tang Xianglong , Zou Yi Ming , Liu Heng
Published: March 2020

Radiotherapy is an effective treatment for local solid tumors, but the mechanism of damage to human body caused by radiation therapy needs further study. In this study, gene expression profiles of human peripheral blood samples exposed to different doses and rates of ionizing radiation (IR) were used for bioinformatics analysis to investigate the mechanism of IR damage and radiation-induced bystander effect (RIBE). Differentially expressed genes analysis, weighted gene correlation network analysis, functional enrichment analysis, hypergeometric test, gene set enrichment analysis, and gene set variation analysis were applied to analyze the data. Moreover, receiver operating characteristic curve analysis was performed to identify core genes of IR damage. Weighted gene correlation network analysis identified 3 modules associated with IR damage, 2 were positively correlated and 1 was negatively correlated. The analysis showed that the positively correlated modules were significantly involved in apoptosis and p53 signaling pathway, and ESR1, ATM, and MYC were potential transcription factors regulating these modules. Thus, the study suggested that apoptosis and p53 signaling pathway may be the potential molecular mechanisms of IR damage and RIBE, which could be driven by ESR1, ATM, and MYC.
Comparative effectiveness of oral prostacyclin pathway drugs on hospitalization in patients with pulmonary hypertension in the United States: a retrospective database analysis
Authors: McConnell John W. , Tsang Yuen , Pruett Janis , III William Drake
Published: March 2020

Two oral medications targeting the prostacyclin pathway are available to treat pulmonary arterial hypertension in the United States: oral treprostinil and selexipag. We compared real‐world hospitalization in patients receiving these medications. A retrospective administrative claims study was conducted using the Optum® Clinformatics® Data Mart database. Patients with pulmonary hypertension were identified using diagnostic codes. Cohort inclusion required age ≥ 18 years, first oral treprostinil or selexipag prescription between 1 January 2015 and 30 September 2017 (index date), and continuous enrollment in the prior ≥6 months. Patients who switched index drug were excluded. Follow‐up was from index date until the first of end of index drug exposure, end of continuous enrollment, death, or 31 December 2017. Multivariable Cox proportional hazard and Poisson regression were used to compare risk and rate, respectively, of hospitalization associated with oral treprostinil vs. selexipag, adjusting for potential confounders. The study cohort included 99 patients receiving oral treprostinil and 123 receiving selexipag. Mean age was 61 years, and most patients were females (71%). Compared with oral treprostinil, selexipag was associated with a 46% lower risk of all‐cause hospitalization (hazard ratio 0.54, 95% confidence interval 0.31, 0.92; P = 0.02), a 47% lower risk of pulmonary hypertension‐related hospitalization (hazard ratio 0.53, 95% confidence interval 0.31, 0.93; P = 0.03), a 42% lower all‐cause hospitalization rate (rate ratio 0.58, 95% confidence interval 0.39, 0.87; P = 0.01), and a 46% lower pulmonary hypertension‐related hospitalization rate (rate ratio 0.54, 95% confidence interval 0.35, 0.82; P = 0.004). This study suggests that selexipag is associated with lower hospitalization risk and rate than oral treprostinil.
Surgical Outcomes In The Frequency, Etiology, Direction, Severity (feds) Classification System For Shoulder Instability
Authors: Magnuson Justin A. , Wolf Brian R. , Cronin Kevin J. , Jacobs Cale A. , Ortiz Shannon , Kuhn John E. , Group MOON Shoulder , Hettrich Carolyn M.
Published: March 2020

Objectives:

The Frequency, Etiology, Direction, Severity (FEDS) system is a reliable and reproducible classification of glenohumeral instability. Frequency is defined as Solitary (1), Occasional (2-5), or Frequent (>5) episodes per year; etiology as Traumatic or Atraumatic; direction as Anterior, Posterior, or Inferior; and severity as a Subluxation or Dislocation. 36 total combinations are possible, named by the first letter of each variable in order. The purpose of this descriptive study was to investigate epidemiology, surgical outcomes, and failure using FEDS in patients undergoing surgery in a large multicenter cohort of prospectively enrolled patients.

Methods:

1204 patients undergoing surgery were assigned to FEDS categories. Two-year follow-up at time of analysis was available for 629 patients (85.7% of those eligible based on date of surgery). Those categories consisting of at least 5% of patients were further analyzed by patient reported outcomes (PROs) and failure rates for a total of 466 patients. PROs included American Shoulder and Elbow Surgeons score (ASES), Western Ontario Shoulder Instability index (WOSI), and Single Assessment Numeric Evaluation (SANE). Failure benchmarks included rates of recurrent subluxation, dislocation, and revision surgery.

Results:

Sixteen categories represented at least one percent of patients. Occasional Traumatic Anterior Dislocation (OTAD) was the most common category with 16.4% of patients. Five other anterior categories (STAS, OTAS, FTAS, STAD, FTAD) and one posterior category (STPS) represented at least 5%. PROs and failure rates for anterior categories are summarized in Figure 1. PROs improved significantly for each category. A downward trend in WOSI and ASES was noted in particular with increasing frequency of the dislocation groups. The highest rates of each type of failure occurred in the occasional and frequent groups for both dislocation and subluxation. Low rates of failure occurred in STPS, with 17.9% reporting subluxation, 3.6% dislocation, and no revisions.

Conclusion:

While overall success was good, different FEDS categories showed varying degrees of improvement and failure rates, indicating that the system can be used to provide prognostic insight for presurgical education. Overall, outcomes for traumatic anterior instability decreased with higher initial frequency, showing worse PROs and higher failure. Frequency appeared to have the greatest effect on outcomes. Early surgical intervention may be beneficial in preventing progression to more severe FEDS categories, with higher frequency having previously been associated with both higher rates of bone loss and greater time between initial event and surgical stabilization.
Does Intra-operative PRP Improve Patient Function & Complication Rates Following ACL Reconstruction With Meniscus Repair?
Authors: Weldon Matthew , Lowe Walter R. , Lauck Kyle , Kleihege Jacquelyn , Warth Ryan J. , Syed Mohammad , Pontes Ana C. , Hayes Matthew , Bailey Lane B.
Published: March 2020

Objectives:

The frequent injury and compromised healing of intra-articular structures (i.e. cruciate ligaments and menisci) has led to an intense interest among surgeons and scientists for discovering new methods of enhancing the biological healing response of these tissues. Platelet-rich-plasma (PRP) contains various growth factors that positively effect biological healing, unfortunately few existing clinical studies are available to determine the risks and benefits of these therapies. Therefore, the purpose of this study was to determine the influence of intraoperative PRP on postoperative knee function and complications out to 2-years following ACL reconstruction with meniscus repair.

Methods:

A matched case-control study was conducted using a single surgeon database of 673 patients undergoing ACL reconstruction with concomitant meniscus repair (Figure 1) resulting in 324 patients [PRP (n = 162) vs matched-control (n = 162)] who met the study criteria. Patients were matched on age, gender, graft type, and meniscus tear size and location. The single assessment numeric evaluation (SANE) was administered at 2-years and served as the primary outcome measure. Secondary outcomes included the time to return-to-activity (mo), self-reported knee function [International Knee Disability Committee (IKDC)], objective functional testing (knee ROM, single-leg balance, single leg-hopping, agility testing), and postoperative complications (graft failure, infection, loss of motion, venous thrombosis, etc). Univariate models were used for between groups comparisons and alpha was set at .05 for all analyses.

Results:

There were no differences in SANE knee function scores between the PRP and matched-control groups at 2-years, respectively (91.6 ±11.2 vs 92.4 ±10.6, P = .599). Additionally, no differences were observed between groups for self-reported function (IKDC score; 87.6 ±13.3 vs 88.1 ±12.6, P = .952), objective functional testing (P > .05), and timing of return-to-activity (7.8 ±1.9 vs 8.0 ±1.9, P = .765). The PRP group demonstrated a higher rate of postoperative knee motion loss complications when compared to the control group (13.5% vs 4.9%, P < .001). No other differences were observed in postoperative complications (P > .05).

Conclusion:

The added use of intraoperative PRP did not improve self-reported knee function, objective functional testing, and timing of return-to-activity for patients undergoing ACL reconstruction with concomitant meniscus repair. Furthermore, the use of PRP may have negative consequences for regaining knee ROM after surgery. Based on these data, surgeons should cautiously consider the application of PRP when surgical planning for intra-articular injuries of the knee.
The Effect Of Playing Surface On Anterior Cruciate Ligament Injury In NCAA Soccer
Authors: Howard Mark , Kang Hyunwoo Paco , Solaru Samantha , Weber Alexander E. , Rick C Mark F.
Published: March 2020

Objectives:

Previous orthopaedic literature has examined the effect of synthetic playing surfaces on the risk of anterior cruciate ligament (ACL) injury in athletes and produced varying and inconclusive results. The objective of this study was to examine the role of playing surface on the incidence and risk of ACL injury in collegiate soccer athletes.

Methods:

The NCAA Injury Surveillance Program (ISP) database was queried for ACL injuries for male and female soccer players from the 2004-05 through the 2013-14 seasons at all levels of competition. The number of athlete exposures (AEs), defined as 1 athlete participating in 1 practice or competition in which they were exposed to the possibility of athletic injury, were recorded for grass and synthetic playing surfaces. Both the reported injuries and exposures provided were weighted in order to represent the entire NCAA collegiate soccer population. Normalized ACL incidence rates were calculated as well as 95% confidence intervals (95%CI). Rate ratios comparing competition type amongst both competition and practice were calculated.

Results:

ACL injuries were more common on grass surfaces (1.16 per 10,000 AEs, 95%CI 1.12-1.20) than artificial turf (0.92 per 10,000 AEs, 95%CI 0.84-1.04). This difference was statistically significant (IRR 1.26, p<0.0001), and driven primarily by the difference in injury incidence during practice. The injury incidence during practice on natural grass (1.18 per 10,000 AEs, 95% CI 1.11-1.26) was significantly greater than the injury incidence rate during practice on artificial turf (0.067 per 10,000 AEs, 95%CI 0.043-0.096). Players were 17.7 times more likely (95%CI 10.6678-27.2187, p<0.0001) to sustain an ACL injury during practice on natural grass when compared to practice on artificial turf. However, there was no significant difference in injury incidence during matches (IRR 0.96, p=0.44), with matches on natural grass (3.35 per 10,000 AEs, 95% CI 3.21-3.51) equivalent to matches on artificial surfaces (3.49 per 10,000 AEs, 95%CI 3.18-3.81). When comparing exposure type, the injury rate was significantly greater during matches (3.38 per 10,000 AEs, 95% CI 3.25-3.52) compared to practices (0.82 per 10,000 AEs, 95%CI 0.77-0.88), with a 4.10-fold increase in ACL injury incidence during matches compared to practice (p<0.0001).

Conclusion:

Between 2004 and 2014, NCAA soccer players experienced a greater number of ACL injuries on natural grass playing surfaces compared with artificial turf playing surfaces. This difference is driven by injuries during practice, where athletes were nearly 18 times more likely to suffer an ACL injury on grass versus artificial turf. While ACL injuries were more likely during matches compared to practices, no difference in incidence was noted between playing surfaces. Additional study is warranted investigating potential causes for this observed increased risk with soccer practice on grass fields.
Knee Scooter–Related Injuries: A Survey of Foot and Ankle Orthopedic Surgeons
Authors: Rahman Rafa , Shannon Brett A. , Ficke James R.
Published: March 2020

Background:

Knee scooters (“scooters”) are a commonly used device to facilitate postoperative adherence to weightbearing restrictions. Although high rates of falls have been reported, little is known about injuries related to scooter use.

Methods:

We analyzed survey responses from 316 of 2046 members (15%) of the American Orthopaedic Foot & Ankle Society in May-June 2019 describing (1) frequency of scooter recommendation; (2) indications for which they recommended scooters; (3) characteristics of patients for whom they recommended scooters; (4) prevalence, anatomic locations, mechanisms, and sequelae of scooter-related injuries; and (5) characteristics of patients with scooter-related injuries. Descriptive statistics and χ2 goodness-of-fit tests were performed (alpha = .05).

Results:

Mean frequency with which respondents recommended scooters in particular was 69%. Respondents most often recommended scooters after hindfoot arthrodesis (97% [305/316]), ankle arthrodesis (96% [302/316]), and for total nonweightbearing (64% [202/316]) and to patients who were overweight (vs obese) or aged 45-75 years. Mean prevalence of scooter-related injuries was 2.5%. The most common injury mechanism was making a sharp turn (reported by 62% [103/166]). Thirty-four percent (56/166) of respondents with injured patients said patients underwent surgery to treat scooter-related injuries. Patients with scooter-related injuries were more often women, >44 years old, obese, and sedentary.

Conclusion:

Scooters were commonly recommended postoperatively, most often for total nonweightbearing after hindfoot or ankle arthrodesis, and most often in overweight adults or those aged 45-75 years. Mean reported prevalence of scooter-related injuries was 2.5%. Female sex, older age, obesity, and sedentary lifestyle were associated with scooter-related injury.

Level of Evidence:

Level IV, retrospective case series.
Phase dependent hypothalamic activation following trigeminal input in cluster headache
Authors: Schulte Laura H. , Haji Ame Abdu , May Arne
Published: March 2020

Background

Task-free imaging approaches using PET have shown the posterior hypothalamus to be specifically activated during but not outside cluster headache attacks. Evidence from task related functional imaging approaches however is scarce.

Methods

Twenty-one inactive cluster headache patients (episodic cluster headache out of bout), 16 active cluster headache patients (10 episodic cluster headache in bout, 6 chronic cluster headache) and 18 control participants underwent high resolution brainstem functional magnetic resonance imaging of trigeminal nociception using gaseous ammonia as a painful stimulus.

Results

Following trigeminonociceptive stimulation with ammonia there was a significantly stronger activation within the posterior hypothalamus in episodic cluster headache patients out of bout when compared to controls. When contrasting estimates of the pain contrast, active cluster headache patients where in between the two other groups but did not differ significantly from either.

Conclusion

The posterior hypothalamus might thus be hyperexcitable in cluster headache patients outside the bout while excitability to external nociceptive stimuli decreases during in bout periods, probably due to frequent hypothalamic activation and possible neurotransmitter exhaustion during cluster attacks.
Reducing the effective dose of cisplatin using gold nanoparticles as carriers
Authors: González-López M. A. , Gutiérrez-Cárdenas E. M. , Sánchez-Cruz C. , Hernández-Paz J. F. , Pérez I. , Olivares-Trejo J. J. , Hernández-González O.
Published: March 2020

Nanotechnology is a frequent treatment for cancer. Nanomaterials are the vehicles which deliver drugs in smaller but equally effective quantities. The aim of this investigation is to synthesize gold nanoparticles, functionalize them for the transportation of cisplatin and release them to the cancer-affected area. They have the same cytotoxicity as conventional treatments but with the smallest effective quantity of cisplatin. We synthesized spherical gold nanoparticles using the Turkevich method. We functionalized them with polyethylene glycol and cisplatin, adapting the method used by Sun. Using electronic transmission microscopy, Dynamic Light Scattering and potential Z, we analyzed the size, hydrodynamic size, shape and stability of the synthesized nanoparticles. We analyzed their composition using images from scanning electronic microscopy to carry out energy dispersive spectroscopy measurements, ultraviolet/visible light spectroscopy and Fourier transform infrared spectroscopy. We used MTT tests to find cell viability and obtained the IC50 of the different cancer cell lines. The synthesized nanoparticles were spherical in shape and, after functionalization, were of the core–shell type. They contain approximately 7% cisplatin. The IC50 obtained diminished approximately 7 times (compared to the IC50 of cisplatin used alone) when using the gold nanoparticles. Therefore, this study opens up the possibility of an alternative way of transporting the cisplatin anticancer drug, using gold nanoparticles. It decreases the dose and has the same effect as the cisplatin, so that the undesired side effects decrease.
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly
Authors: Wcisel Dustin J. , Howard J. Thomas , Yoder Jeffrey A. , Dornburg Alex
Published: March 2020

Background

Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.

Results

We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.

Conclusions

TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference.

Software, a detailed manual, and example data files are available through github carolinafishes.github.io
A large-scale comparative study of isoform expressions measured on four platforms
Authors: Zhang Wei , Petegrosso Raphael , Chang Jae-Woong , Sun Jiao , Yong Jeongsik , Chien Jeremy , Kuang Rui
Published: March 2020

Background

Most eukaryotic genes produce different transcripts of multiple isoforms by inclusion or exclusion of particular exons. The isoforms of a gene often play diverse functional roles, and thus it is necessary to accurately measure isoform expressions as well as gene expressions. While previous studies have demonstrated the strong agreement between mRNA sequencing (RNA-seq) and array-based gene and/or isoform quantification platforms (Microarray gene expression and Exon-array), the more recently developed NanoString platform has not been systematically evaluated and compared, especially in large-scale studies across different cancer domains.

Results

In this paper, we present a large-scale comparative study among RNA-seq, NanoString, array-based, and RT-qPCR platforms using 46 cancer cell lines across different cancer types. The goal is to understand and evaluate the calibers of the platforms for measuring gene and isoform expressions in cancer studies. We first performed NanoString experiments on 59 cancer cell lines with 404 custom-designed probes for measuring the expressions of 478 isoforms in 155 genes, and additional RT-qPCR experiments for a subset of the measured isoforms in 13 cell lines. We then combined the data with the matched RNA-seq, Exon-array, and Microarray data of 46 of the 59 cell lines for the comparative analysis.

Conclusion

In the comparisons of the platforms for measuring the expressions at both isoform and gene levels, we found that (1) the agreement on isoform expressions is lower than the agreement on gene expressions across the four platforms; (2) NanoString and Exon-array are not consistent on isoform quantification even though both techniques are based on hybridization reactions; (3) RT-qPCR experiments are more consistent with RNA-seq and Exon-array than NanoString in isoform quantification; (4) different RNA-seq isoform quantification methods show varying estimation results, and among the methods, Net-RSTQ and eXpress are more consistent across the platforms; and (5) RNA-seq has the best overall consistency with the other platforms on gene expression quantification.
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Authors: Takahashi Hiro , Hayashi Noriya , Hiragori Yuta , Sasaki Shun , Motomura Taichiro , Yamashita Yui , Naito Satoshi , Takahashi Anna , Fuse Kazuyuki , Satou Kenji , Endo Toshinori , Kojima Shoko , Onouchi Hitoshi
Published: March 2020

Background

Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST betweenArabidopsisand any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.

Results

To efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.

Conclusions

This study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.
Transcriptome profiling of non-climacteric ‘yellow’ melon during ripening: insights on sugar metabolism
Authors: Schemberger Michelle Orane , Stroka Marília Aparecida , Reis Letícia , de Souza Los Kamila Karoline , de Araujo Gillize Aparecida Telles , Sfeir Michelle Zibetti Tadra , Galvão Carolina Weigert , Etto Rafael Mazer , Baptistão Amanda Regina Godoy , Ayub Ricardo Antonio
Published: March 2020

Background

The non-climacteric ‘Yellow’ melon (Cucumis melo, inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related pathways can contribute to the development of new field management and post-harvest practices, making it possible to deliver better quality fruits to consumers.

Results

The RNA-seq associated with RT-qPCR analyses of four maturation stages were performed to identify important enzymes and pathways that are involved in the ripening profile of non-climacteric ‘Yellow’ melon fruit focusing on sugar metabolism. We identified 895 genes 10 days after pollination (DAP)-biased and 909 genes 40 DAP-biased. The KEGG pathway enrichment analysis of these differentially expressed (DE) genes revealed that ‘hormone signal transduction’, ‘carbon metabolism’, ‘sucrose metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘spliceosome’ were the most differentially regulated processes occurring during melon development. In the sucrose metabolism, five DE genes are up-regulated and 12 are down-regulated during fruit ripening.

Conclusions

The results demonstrated important enzymes in the sugar pathway that are responsible for the sucrose content and maturation profile in non-climacteric ‘Yellow’ melon. New DE genes were first detected for melon in this study such as invertase inhibitor LIKE 3 (CmINH3), trehalose phosphate phosphatase (CmTPP1) and trehalose phosphate synthases (CmTPS5, CmTPS7, CmTPS9). Furthermore, the results of the protein-protein network interaction demonstrated general characteristics of the transcriptome of young and full-ripe melon and provide new perspectives for the understanding of ripening.
Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase
Authors: Zou Xian , Lu Tingting , Zhao Zhifeng , Liu Guangbin , Lian Zhiquan , Guo Yongqing , Sun Baoli , Liu Dewu , Li Yaokun
Published: March 2020

Background

Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play critical roles in ovarian biological processes, the interaction between mRNAs and miRNAs in follicular development is not yet completely understood. In addition, less attention has been given to the study of single follicle (dominant or atretic follicle) in goats. This study aimed to identify mRNAs, miRNAs, and signaling pathways as well as their interaction networks in the ovarian follicles (large follicles and small follicles) of uniparous and multiple Chuanzhong black goats at estrus phase using RNA-sequencing (RNA-seq) technique.

Results

The results showed that there was a significant difference in the number of large follicles between uniparous and multiple goats (P < 0.05), but no difference in the number of small follicles was observed (P > 0.05). For the small follicles of uniparous and multiple goats at estrus phase, 289 differentially expressed mRNAs (DEmRNAs) and 16 DEmiRNAs were identified; and for the large follicles, 195 DEmRNAs and 7 DEmiRNAs were identified. The functional enrichment analysis showed that DE genes in small follicles were significantly enriched in ovarian steroidogenesis and steroid hormone biosynthesis, while in large follicles were significantly enriched in ABC transporters and steroid hormone biosynthesis. The results of quantitative real-time polymerase chain reaction were consistent with those of RNA-seq. Analysis of the mRNA-miRNA interaction network suggested that CD36 (miR-122, miR-200a, miR-141), TNFAIP6 (miR-141, miR-200a, miR-182), CYP11A1 (miR-122), SERPINA5 (miR-1, miR-206, miR-133a-3p, miR-133b), and PTGFR (miR-182, miR-122) might be related to fertility, but requires further research on follicular somatic cells.

Conclusions

This study was used for the first time to reveal the DEmRNAs and DEmiRNAs as well as their interaction in the follicles of uniparous and multiple goats at estrus phase using RNA-seq technology. Our findings provide new clues to uncover the molecular mechanisms and signaling networks of goat reproduction that could be potentially used to increase ovulation rate and kidding rate in goat.
De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly
Authors: Bayega Anthony , Djambazian Haig , Tsoumani Konstantina T. , Gregoriou Maria-Eleni , Sagri Efthimia , Drosopoulou Eleni , Mavragani-Tsipidou Penelope , Giorda Kristina , Tsiamis George , Bourtzis Kostas , Oikonomopoulos Spyridon , Dewar Ken , Church Deanna M. , Papanicolaou Alexie , Mathiopoulos Kostas D. , Ragoussis Jiannis
Published: March 2020

Background

The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly’s biology and proposing alternative control methods to pesticide use.

Results

Genomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gap-closing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR.

Conclusions

The high-quality genome generated represents a critical tool in olive fruit fly research. We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly. In addition, elucidation of Y-chromosome sequences will advance our understanding of the Y-chromosome’s organization, function and evolution and is poised to provide avenues for sterile insect technique approaches.
iMarmot: an integrative platform for comparative and functional genomics of marmots
Authors: Liu Baoning , Bai Liang , Yu Qingqing , Hu Fang , Wu Jing , Zhao Sihai , Wang Rong , Wang Weirong , Tao Yuanqing , Fan Jianglin , Liu Enqi
Published: March 2020

Background

Marmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields. Due to the rapid accumulation of the genetic data in marmots, a highly integrative database is urgent needed.

Description

iMarmot is freely available on the web at http://www.marmotdb.org/ and currently contains the biological information of 14 marmots, genomic sequence of 6 marmots, syntenic relationship and orthologs among 3 marmots, and expression profiles of several hibernators and plague hosts. To assist with the genomic and transcriptomic analysis, we also integrated a set of analysis and visualization tools, such as KEGG or GO enrichment analysis, PCA, Blast, Muscle, GeneWise, Lastz, and JBrowse. Particularly, one DEGs (differentially expressed genes) module has been implemented in this database to visualize the gene expression changes in hibernators and plague hosts.

Conclusion

This database will provide comprehensive information and analysis platform for researchers interested in understanding the biological features of marmots.
Functional comparison of PBMCs isolated by Cell Preparation Tubes (CPT) vs. Lymphoprep Tubes
Authors: Chen Han , Schürch Christian M. , Noble Kevin , Kim Kenneth , Krutzik Peter O. , O’Donnell Erika , Vander Tuig Jason , Nolan Garry P. , McIlwain David R.
Published: March 2020

Background

Cryopreserved human peripheral blood mononuclear cells (PBMCs) are a commonly used sample type for a variety of immunological assays. Many factors can affect the quality of PBMCs, and careful consideration and validation of an appropriate PBMC isolation and cryopreservation method is important for well-designed clinical studies. A major point of divergence in PBMC isolation protocols is the collection of blood, either directly into vacutainers pre-filled with density gradient medium or the use of conical tubes containing a porous barrier to separate the density gradient medium from blood. To address potential differences in sample outcome, we isolated, cryopreserved, and compared PBMCs using parallel protocols differing only in the use of one of two common tube types for isolation.

Methods

Whole blood was processed in parallel using both Cell Preparation Tubes™ (CPT, BD Biosciences) and Lymphoprep™ Tubes (Axis-Shield) and assessed for yield and viability prior to cryopreservation. After thawing, samples were further examined by flow cytometry for cell yield, cell viability, frequency of 10 cell subsets, and capacity for stimulation-dependent CD4+ and CD8+ T cell intracellular cytokine production.

Results

No significant differences in cell recovery, viability, frequency of immune cell subsets, or T cell functionality between PBMC samples isolated using CPT or Lymphoprep tubes were identified.

Conclusion

CPT and Lymphoprep tubes are effective and comparable methods for PBMC isolation for immunological studies.
Evolutionary analysis of gyrA gene from Neisseria meningitidis bacterial strains of clonal complex 4821 collected in China between 1978 and 2016
Authors: Zhao Pan , Xu Li , Zhang Aiyu , Zhu Bingqing , Shao Zhujun
Published: March 2020

Background

Neisseria meningitidis (N.meningitidis) bacteria belonging to clonal complex 4821 (CC4821) have been mainly reported in China and have been characterized by a high resistance rate to ciprofloxacin (CIP). The aim of this study was to assess the evolution of the DNA gyrase A (gyrA) gene from N.meningitidis CC4821 strains collected in China between 1978 and 2016. The complete sequence of gyrA gene from 77 strains are reported in this study and analyzed in the context of publicly available sequences from N. meningitidis of other CCs as well as other Neisseria species.

Results

The phylogenetic analysis of CC4821 gyrA gene reveals at least 5 distinct genetic clusters. These clusters are not CC4821-specific showing that gyrA evolution is independent of CC4821 evolution. Some clusters contain sequences from other Neisseria species. Recombination within N.meningitidis strains and between Neisseria species was identified in SimPlot analysis. Finally, amino acid substitutions within GyrA protein were analyzed. Only one position, 91 (83 in E.coli gyrA gene), was linked to CIP resistance. Thirty-one additional putative resistance markers were identified, as amino acid substitutions were only found in resistant strains.

Conclusions

The evolution of gyrA gene of CC4821 N.meningitidis strains is not dependent on CC4821 evolution or on CIP resistance phenotype. Only amino acid 91 is linked to CIP resistance phenotype. Finally, recombination inter- and intra-species is likely to result in the acquisition of various resistance markers, 31 of them being putatively mapped in the present study. Analyzing the evolution of gyrA gene within CC4821 strains is critical to monitor the CIP resistance phenotype and the acquisition of new resistance markers. Such studies are necessary for the control of the meningococcal disease and the development of new drugs targeting DNA gyrase.
Vibiro vulnificus hemolysin associates with gangliosides
Authors: Kashimoto Takashige , Sugiyama Hiroyuki , Kawamidori Keigo , Yamazaki Kohei , Kado Takehiro , Matsuda Kaho , Kodama Toshio , Mukai Takao , Ueno Shunji
Published: March 2020

Background

Vibrio vulnificus hemolysin (VVH) is a pore-forming toxin secreted by Vibrio vulnificus. Cellular cholesterol was believed to be the receptor for VVH, because cholesterol could bind to VVH and preincubation with cholesterol inhibited cytotoxicity. It has been reported that specific glycans such as N-acetyl-D-galactosamine and N-acetyl-D-lactosamine bind to VVH, however, it has not been known whether these glycans could inhibit the cytotoxicity of VVH without oligomer formation. Thus, to date, binding mechanisms of VVH to cellular membrane, including specific receptors have not been elucidated.

Results

We show here that VVH associates with ganglioside GM1a, Fucosyl-GM1, GD1a, GT1c, and GD1b by glycan array. Among them, GM1a could pulldown VVH. Moreover, the GD1a inhibited the cytotoxicity of VVH without the formation of oligomers.

Conclusion

This is the first report of a molecule able to inhibit the binding of VVH to target cells without oligomerization of VVH.
First evidence showing that Pepper vein yellows virus P4 protein is a movement protein
Authors: Li Sangsang , Su Xianyan , Luo Xiangwen , Zhang Yu , Zhang Deyong , Du Jiao , Zhang Zhanhong , OuYang Xian , Zhang Songbai , Liu Yong
Published: March 2020

Background

Plant viruses move through plasmodesmata (PD) to infect new cells. To overcome the PD barrier, plant viruses have developed specific protein(s) to guide their genomic RNAs or DNAs to path through the PD.

Results

In the present study, we analyzed the function of Pepper vein yellows virus P4 protein. Our bioinformatic analysis using five commonly used algorithms showed that the P4 protein contains an transmembrane domain, encompassing the amino acid residue 117–138. The subcellular localization of P4 protein was found to target PD and form small punctates near walls. The P4 deletion mutant or the substitution mutant constructed by overlap PCR lost their function to produce punctates near the walls inside the fluorescent loci. The P4-YFP fusion was found to move from cell to cell in infiltrated leaves, and P4 could complement Cucumber mosaic virus movement protein deficiency mutant to move between cells.

Conclusion

Taking together, we consider that the P4 protein is a movement protein of Pepper vein yellows virus.
Intravenous methylprednisolone or immunoglobulin for anti-glutamic acid decarboxylase 65 antibody autoimmune encephalitis: which is better?
Authors: Li Tao-Ran , Zhang Yu-Di , Wang Qun , Shao Xiao-Qiu , Li Zhi-Mei , Lv Rui-Juan
Published: March 2020

Background

Patients positive for anti-glutamic acid decarboxylase 65 (GAD65) antibodies have attracted increasing attention. Their clinical manifestations are highly heterogeneous and can be comorbid with tumors. Currently, there is no consensus on the therapeutic regimen for anti-GAD65-associated neurological diseases due to the clinical complexity, rarity and sporadic distribution. We reported six anti-GAD65 autoimmune encephalitis (AE) patients who received intravenous methylprednisolone (IVMP) or immunoglobulin (IVIG) or both. Then, we evaluated the therapeutic effect of both by summarizing results in previous anti-GAD65 AE patients from 70 published references.

Results

Our six patients all achieved clinical improvements in the short term. Unfortunately, there was no significant difference between IVMP and IVIG in terms of therapeutic response according to the previous references, and the effectiveness of IVMP and IVIG was 45.56% and 36.71%, respectively. We further divided the patients into different subgroups according to their prominent clinical manifestations. The response rates of IVMP and IVIG were 42.65% and 32.69%, respectively, in epilepsy patients; 60.00% and 77.78%, respectively, in patients with stiff-person syndrome; and 28.57% and 55.56%, respectively, in cerebellar ataxia patients. Among 29 anti-GAD65 AE patients with tumors, the response rates of IVMP and IVIG were 29.41% and 42.11%, respectively. There was no significant difference in effectiveness between the two regimens among the different subgroups.

Conclusion

Except for stiff-person syndrome, we found that this kind of AE generally has a poor response to IVMP or IVIG. Larger prospective studies enrolling large numbers of patients are required to identify the optimal therapeutic strategy in the future.