bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the metabolomic diversity of plant species across spatial (leaf and stem) components and phylogenic groups
Authors: Lee Sunmin , Oh Dong-Gu , Singh Digar , Lee Jong Seok , Lee Sarah , Lee Choong Hwan 
Published: January 2020

Abstract
Background
Plants have been used as an important source of indispensable bioactive compounds in various cosmetics, foods, and medicines. However, the subsequent functional annotation of these compounds seems arduous because of the largely uncharacterized, vast metabolic repertoire of plant species with known biological phenotypes. Hence, a rapid multi-parallel screening and characterization approach is needed for plant functional metabolites.

Results
Fifty-one species representing three plant families, namely Asteraceae, Fabaceae, and Rosaceae, were subjected to metabolite profiling using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and ultrahigh-performance liquid chromatography quadrupole orbitrap ion trap tandem mass spectrometry (UHPLC-Q-orbitrap-MS/MS) as well as multivariate analyses. Partial least squares discriminant analysis (PLS-DA) of the metabolite profiling datasets indicated a distinct clustered pattern for 51 species depending on plant parts (leaves and stems) and relative phylogeny. Examination of their relative metabolite contents showed that the extracts from Fabaceae plants were abundant in amino acids, fatty acids, and genistein compounds. However, the extracts from Rosaceae had higher levels of catechin and ellagic acid derivatives, whereas those from Asteraceae were higher in kaempferol derivatives and organic acids. Regardless of the different families, aromatic amino acids, branch chain amino acids, chlorogenic acid, flavonoids, and phenylpropanoids related to the shikimate pathway were abundant in leaves. Alternatively, certain amino acids (proline, lysine, and arginine) as well as fatty acids levels were higher in stem extracts. Further, we investigated the associated phenotypes, i.e., antioxidant activities, affected by the observed spatial (leaves and stem) and intra-family metabolomic disparity in the plant extracts. Pearson’s correlation analysis indicated that ellagic acid, mannitol, catechin, epicatechin, and quercetin derivatives were positively correlated with antioxidant phenotypes, whereas eriodictyol was positively correlated with tyrosinase inhibition activity.

Conclusions
This work suggests that metabolite profiling, including multi-parallel approaches and integrated bioassays, may help the expeditious characterization of plant-derived metabolites while simultaneously unraveling their chemodiversity.
A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Authors: Cramer Grant R. , Cochetel Noé , Ghan Ryan , Destrac-Irvine Agnès , Delrot Serge 
Published: January 2020

AbstractBackgroundGrape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition.ResultsTo better understand the effect of “place” on transcript abundance during the late stages of berry ripening, Cabernet Sauvignon berries grown in Bordeaux and Reno were compared at similar sugar levels (19 to 26 °Brix (total soluble solids)). Day temperatures were warmer and night temperatures were cooler in Reno. °Brix was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-Seq analysis identified 5528 differentially expressed genes between Bordeaux and Reno grape skins at 22°Brix. Weighted Gene Coexpression Network Analysis for all expressed transcripts for all four °Brix levels measured indicated that the majority (75%) of transcript expression differed significantly between the two locations. Top gene ontology categories for the common transcript sets were translation, photosynthesis, DNA metabolism and catabolism. Top gene ontology categories for the differentially expressed genes at 22°Brix involved response to stimulus, biosynthesis and response to stress. Some differentially expressed genes encoded terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. Bordeaux berries had higher transcript abundance with differentially expressed genes associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with differentially expressed genes involved in water deprivation, cold response, ABA signaling and iron homeostasis.ConclusionsTranscript abundance profiles in the berry skins at maturity were highly dynamic. RNA-Seq analysis identified a smaller (25% of total) common core set of ripening genes that appear not to depend on rootstock, vineyard management, plant age, soil and climatic conditions. Much of the gene expression differed between the two locations and could be associated with multiple differences in environmental conditions that may have affected the berries in the two locations; some of these genes may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result.
Alterations in gut microbiota of abdominal aortic aneurysm mice
Authors: Xie Jiahe , Lu Weiling , Zhong Lintao , Hu Yuhua , Li Qingrui , Ding Rongming , Zhong Zhonggao , Liu Ziyou , Xiao Hai , Xie Dongming , Zheng Guofu , Ye Bo , Zhong Yiming , Liu Zuheng 
Published: January 2020

Abstract
Background
The gut microbiome plays an important role in various cardiovascular diseases, such as atherosclerosis and hypertension, which are associated with abdominal aortic aneurysms (AAAs).

Methods
Here, we used 16S rRNA sequencing to explore gut microbiota in C57BL ApoE−/− mice with AAAs. A mouse model of abdominal aortic aneurysms was induced with angiotensin II (Ang II) (1000 ng/min per kg). On day 28 after the operation, fecal samples were collected and stored at − 80 °C until DNA extraction. We determined the relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding, and sequences were analyzed using a combination of mother software and UPARSE.

Results
We found that the gut microbiome was different between control and AAA mice. The results of correlation analysis between AAA diameter and the gut microbiome as well as LEfSe of the genera Akkermansia, Odoribacter, Helicobacter and Ruminococcus might be important in the progression of AAAs.

Conclusions
AAA mice is subjected to gut microbial dysbiosis, and gut microbiota might be a potential target for further investigation.
Does potentially inappropriate prescribing predict an increased risk of admission to hospital and mortality? A longitudinal study of the ‘oldest old’
Authors: Cardwell Karen , Kerse Ngaire , Hughes Carmel M. , Teh Ruth , Moyes Simon A. , Menzies Oliver , Rolleston Anna , Broad Joanna B. , Ryan Cristín 
Published: January 2020

Abstract
Background
Potentially inappropriate prescribing (PIP) is associated with negative health outcomes, including hospitalisation and mortality. Life and Living in Advanced Age: a Cohort Study in New Zealand (LiLACS NZ) is a longitudinal study of Māori (the indigenous population of New Zealand) and non-Māori octogenarians. Health disparities between indigenous and non-indigenous populations are prevalent internationally and engagement of indigenous populations in health research is necessary to understand and address these disparities. Using LiLACS NZ data, this study reports the association of PIP with hospitalisations and mortality prospectively over 36-months follow-up.

Methods
PIP, from pharmacist applied criteria, was reported as potentially inappropriate medicines (PIMs) and potential prescribing omissions (PPOs). The association between PIP and hospitalisations (all-cause, cardiovascular disease-specific and ambulatory-sensitive) and mortality was determined throughout a series of 12-month follow-ups using binary logistic (hospitalisations) and Cox (mortality) regression analysis, reported as odds ratios (ORs) and hazard ratios (HRs), respectively, and the corresponding confidence intervals (CIs).

Results
Full demographic data were obtained for 267 Māori and 404 non-Māori at baseline, 178 Māori and 332 non-Māori at 12-months, and 122 Māori and 281 non-Māori at 24-months. The prevalence of any PIP (i.e. ≥1 PIM and/or PPO) was 66, 75 and 72% for Māori at baseline, 12-months and 24-months, respectively. In non-Māori, the prevalence of any PIP was 62, 71 and 73% at baseline, 12-months and 24-months, respectively. At each time-point, there were more PPOs than PIMs; at baseline Māori were exposed to a significantly greater proportion of PPOs compared to non-Māori (p = 0.02). In Māori: PPOs were associated with a 1.5-fold increase in hospitalisations and mortality. In non-Māori, PIMs were associated with a double risk of mortality.

Conclusions
PIP was associated with an increased risk of hospitalisation and mortality in this cohort. Omissions appear more important for Māori in predicting hospitalisations, and PIMs were more important in non-Māori in predicting mortality. These results suggest understanding prescribing outcomes across and between population groups is needed and emphasises prescribing quality assessment is useful.
Retrospective analysis of acute HBV infections occurred in 1978–79 and 1994–95 in North-East Italy: increasing prevalence of BCP/pre-core mutants in sub-genotype D3
Authors: Bruni Roberto , Villano Umbertina , Taffon Stefania , Equestre Michele , Madonna Elisabetta , Chionne Paola , Candido Angela , Dettori Stefano , Pisani Giulio , Rapicetta Maria , Bortolotti Flavia , Ciccaglione Anna Rita 
Published: January 2020

Abstract
Background
At the end of the 1970s, in Italy more than 2% of the general population was HBsAg carrier. In the late ‘70s and late ‘80s, two remarkable events might have impacted on HBV strains transmitted in North-East Italy: (a) the increased HBV incidence due to parenteral drugs between 1978 and 1982; (b) the preventive anti-HIV educational campaign, started locally in 1985.

Methods
To address if those events impacted on circulating HBV variants, acute cases occurred in North-East Italy in 1978–79 (n = 50) and 1994–95 (n = 30) were retrospectively analysed. HBV sequences obtained from serum samples were subjected to phylogenetic analysis and search for BCP/pre-core and S mutations.

Results
HBV-D was the most prevalent genotype in both 1978–79 (43/50, 86%) and 1994–95 (24/30, 80.0%), with HBV-A in all but one remaining cases. Among HBV-D cases, sub-genotype HBV-D3 was the most prevalent (25/29, 86.2% in 1978–79; 13/16, 81.2% in 1994–95), with HBV-D1 and HBV-D2 in the remaining cases. All HBV-A cases were sub-genotype A2.
Single and multiple BCP/pre-core mutations, responsible for HBeAg(−) hepatitis, were detected in 6/50 (12%) cases in 1978/79 vs. 12/30 (40.0%) in 1994/95 (p = 0.006). They were found exclusively in HBV-D; in the most abundant sub-genotype, HBV-D3, they were detected in 2/25 (8%) cases in 1978–79 vs. 6/13 (46%) in 1994–95 (p = 0.011). No vaccine escape S mutations were observed. The IDU risk factor was significantly more frequent in 1994–95 (8/30, 26.7%) than in 1978–79 (4/50, 8%) (p = 0.048).

Conclusions
The above mentioned epidemiological and public health events did not affect the proportion of genotypes and sub-genotypes that remained unchanged over 16 years. In contrast, the proportion of BCP/pre-core mutants increased more than three-fold, mostly in HBV-D3, a sub-genotype highly circulating in IDUs; drug abuse likely contributed to the spread of these mutants.
The findings contribute to explain a previously described major change in HBV epidemiology in Italy: the proportion of HBeAg(−) cases in the carrier cohort changed from low in late 1970s, to high at the beginning of the 2000s. In addition to other recognized factors, the increased circulation of BCP/pre-core mutants likely represents a further factor that contributed to this change.
Use of a rapid recombinase-aided amplification assay for Mycoplasma pneumoniae detection
Authors: Xue Guanhua , Li Shaoli , Zhao Hanqing , Yan Chao , Feng Yanling , Cui Jinghua , Jiang Tingting , Yuan Jing 
Published: January 2020

Abstract
Background
Mycoplasma pneumoniae is one of the most common causative pathogens of community-acquired pneumonia (CAP), accounting for as many as 30–50% of CAP during peak years. An early and rapid diagnostic method is key for guiding clinicians in their choice of antibiotics.

Methods
The recombinase-aided amplification (RAA) assay is a recently developed, rapid detection method that has been used for the detection of several pathogens. The assays were performed in a one-step single tube reaction at 39° Celsius within 15–30 min. In this study, we established an RAA assay for M. pneumoniae using clinical specimens for validation and commercial real-time PCR as the reference method.

Results
The analytical sensitivity of the RAA assay was 2.23 copies per reaction, and no cross-reactions with any of the other 15 related respiratory bacterial pathogens were observed. Compared with the commercial real-time PCR assay used when testing 311 respiratory specimens, the RAA assay obtained 100% sensitivity and 100% specificity with a kappa value of 1.

Conclusions
These results demonstrate that the proposed RAA assay will be of benefit as a faster, sensitive, and specific alternative tool for the detection of M. pneumoniae.
Exoskeleton for post-stroke recovery of ambulation (ExStRA): study protocol for a mixed-methods study investigating the efficacy and acceptance of an exoskeleton-based physical therapy program during stroke inpatient rehabilitation
Authors: Louie Dennis R. , Mortenson William B. , Durocher Melanie , Teasell Robert , Yao Jennifer , Eng Janice J. 
Published: January 2020

Abstract
Background
The ability to walk is commonly reported as a top rehabilitation priority for individuals after a stroke. However, not all individuals with stroke are able to practice walking, especially those who require more assistance from their therapist to do so. Powered robotic exoskeletons are a new generation of robotic-assisted gait training devices, designed to assist lower extremity movement to allow repetitious overground walking practice. To date, minimal research has been conducted on the use of an exoskeleton for gait rehabilitation after stroke. The following research protocol aims to evaluate the efficacy and acceptability, and thus adoptability, of an exoskeleton-based gait rehabilitation program for individuals with stroke.

Methods
This research protocol describes a prospective, multi-center, mixed-methods study comprised of a randomized controlled trial and a nested qualitative study. Forty adults with subacute stroke will be recruited from three inpatient rehabilitation hospitals and randomized to receive either the exoskeleton-based gait rehabilitation program or usual physical therapy care. The primary outcome measure is the Functional Ambulation Category at post-intervention, and secondary outcomes include motor recovery, functional mobility, cognitive, and quality-of-life measures. Outcome data will be collected at baseline, post-intervention, and at 6 months. The qualitative component will explore the experience and acceptability of using a powered robotic exoskeleton for stroke rehabilitation from the point of view of individuals with stroke and physical therapists. Semi-structured interviews will be conducted with participants who receive the exoskeleton intervention, and with the therapists who provide the intervention. Qualitative data will be analyzed using interpretive description.

Discussion
This study will be the first mixed-methods study examining the adoptability of exoskeleton-based rehabilitation for individuals with stroke. It will provide valuable information regarding the efficacy of exoskeleton-based training for walking recovery and will shed light on how physical therapists and patients with stroke perceive the device. The findings will help guide the integration of robotic exoskeletons into clinical practice.

Trial registration
NCT02995265 (clinicaltrials.gov), Registered 16 December 2016.
High-risk behaviors and their association with awareness of HIV status among participants of a large-scale prevention intervention in Athens, Greece
Authors: Pavlopoulou Ioanna D. , Dikalioti Stavroula K. , Gountas Ilias , Sypsa Vana , Malliori Meni , Pantavou Katerina , Jarlais Don Des , Nikolopoulos Georgios K. , Hatzakis Angelos 
Published: January 2020

AbstractBackgroundAristotle was a seek-test-treat intervention during an outbreak of human immunodeficiency virus (HIV) infection among people who inject drugs (PWID) in Athens, Greece that started in 2011. The aims of this analysis were: (1) to study changes of drug injection-related and sexual behaviors over the course of Aristotle; and (2) to compare the likelihood of risky behaviors among PWID who were aware and unaware of their HIV status.MethodsAristotle (2012–2013) involved five successive respondent-driven sampling rounds of approximately 1400 PWID each; eligible PWID could participate in multiple rounds. Participants were interviewed using a questionnaire, were tested for HIV, and were classified as HIV-positive aware of their status (AHS), HIV-positive unaware of their status (UHS), and HIV-negative. Piecewise linear generalized estimating equation models were used to regress repeatedly measured binary outcomes (high-risk behaviors) against covariates.ResultsAristotle recruited 3320 PWID (84.5% males, median age 34.2 years). Overall, 7110 interviews and blood samples were collected. The proportion of HIV-positive first-time participants who were aware of their HIV infection increased from 21.8% in round A to 36.4% in the last round. The odds of dividing drugs at least half of the time in the past 12 months with a syringe someone else had already used fell from round A to B by 90% [Odds Ratio (OR) (95% Confidence Interval-CI): 0.10 (0.04, 0.23)] among AHS and by 63% among UHS [OR (95% CI): 0.37 (0.19, 0.72)]. This drop was significantly larger (p = 0.02) among AHS. There were also decreases in frequency of injection and in receptive syringe sharing in the past 12 months but they were not significantly different between AHS (66 and 47%, respectively) and UHS (63 and 33%, respectively). Condom use increased only among male AHS from round B to the last round [OR (95% CI): 1.24 (1.01, 1.52)].ConclusionsThe prevalence of risky behaviors related to drug injection decreased in the context of Aristotle. Knowledge of HIV infection was associated with safer drug injection-related behaviors among PWID. This highlights the need for comprehensive interventions that scale-up HIV testing and help PWID become aware of their HIV status.
Generation of recombinant baculovirus expressing atoxic C-terminal CPA toxin of Clostridium perfringens and production of specific antibodies
Authors: Forti Katia , Cagiola Monica , Pellegrini Martina , Anzalone Lucia , Di Paolo Antonella , Corneli Sara , Severi Giulio , De Giuseppe Antonio 
Published: January 2020

AbstractBackgroundClostridium perfringensis the causative agent of several diseases and enteric infections in animals and humans. The virulence ofC. perfringensis largely attributable to the production of numerous toxins; of these, the alpha toxin (CPA) plays a crucial role in histotoxic infections (gas gangrene). CPA toxin consists of two domains, i.e., the phospholipase C active site, which lies in the N-terminal domain amino acid (aa residues 1–250), and the C-terminal region (aa residues 251–370), which is responsible for the interaction of the toxin with membrane phospholipids in the presence of calcium ions. All currently produced clostridial vaccines contain toxoids derived from culture supernatants that are inactivated, mostly using formalin. The CPA is an immunogenic antigen; recently, it has been shown that mice that were immunized with the C-terminal domain of the toxin produced inE. coliwere protected againstC. perfringensinfections and the anti-sera produced were able to inhibit the CPA activity. Monoclonal and polyclonal antibodies were produced only against full-length CPA and not against the truncated forms.ResultsIn the present study, we have reported for the first time; about the generation of a recombinant baculovirus capable of producing a deleted rCPA toxin (rBacCPA250–363H6) lacking the N-terminal domain and the 28 amino acids (aa) of the putative signal sequence. The insertion of theL21consensus sequence upstream of the translational start codon ATG, drastically increases the yield of recombinant protein in the baculovirus-based expression system. The protein was purified by Ni-NTA affinity chromatography and the lack of toxicity in vitro was confirmed in CaCo-2 cells. Polyclonal antibodies and eight hybridoma-secreting Monoclonal antibodies were generated and tested to assess specificity and reactivity. The anti-sera obtained against the fragment rBacCPA250–363H6 neutralized the phospholipase C activity of full-length PLC.ConclusionsTheL21leader sequence enhanced the expression of atoxic C-terminal recombinant CPA protein produced in insect cells. The monoclonal and polyclonal antibodies obtained were specific and highly reactive. The availability of these biologicals could contribute to the development of diagnostic assays and/or new recombinant protein vaccines.
Usage of cloud storage facilities by medical students in a low-middle income country, Sri Lanka: a cross sectional study
Authors: Hettige Samankumara , Dasanayaka Eshani , Ediriweera Dileepa Senajith 
Published: January 2020

Abstract
Background
Cloud storage facilities (CSF) has become popular among the internet users. There is limited data on CSF usage among university students in low middle-income countries including Sri Lanka. In this study we present the CSF usage among medical students at the Faculty of Medicine, University of Kelaniya.

Methods
We undertook a cross sectional study at the Faculty of Medicine, University of Kelaniya, Sri Lanka. Stratified random sampling was used to recruit students representing all the batches. A self-administrated questionnaire was given.

Results
Of 261 (90.9%) respondents, 181 (69.3%) were females. CSF awareness was 56.5% (95%CI: 50.3–62.6%) and CSF usage was 50.8% (95%CI: 44.4–57.2%). Awareness was higher in males (P = 0.003) and was low in senior students. Of CSF aware students, 85% knew about Google Drive and 70.6% used it. 73.6 and 42.1% knew about Dropbox and OneDrive. 50.0 and 22.0% used them respectively. There was no association between CSF awareness and pre-university entrance or undergraduate examination performance. Inadequate knowledge, time, accessibility, security and privacy concerns limited CSF usage. 69.8% indicated that they would like to undergo training on CSF as an effective tool for education.

Conclusion
CSF awareness and usage among the students were 56.5 and 50.8%. Google drive is the most popular CSF. Lack of knowledge, accessibility, concerns on security and privacy limited CSF usage among students. Majority were interested to undergo training on CSF and undergraduate Information Communication Technology (ICT) curricula should introduce CSF as effective educational tools.