bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system
Authors: Overholt Will A. , Hölzer Martin , Geesink Patricia , Diezel Celia , Marz Manja , Küsel Kirsten 
Published: August 2020

SummaryAssembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure–function relationships in complex environments. To compare the recovery of genomes from microorganisms and their viruses from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore Technologies (ONT) sequencing platform. Assembly and metagenome‐assembled genome (MAG) metrics for both microbes and viruses were determined from an Illumina‐only assembly, ONT‐only assembly, and a hybrid assembly approach. The hybrid approach recovered 2× more mid to high‐quality MAGs compared to the Illumina‐only approach and 4× more than the ONT‐only approach. A similar number of viral genomes were reconstructed using the hybrid and ONT methods, and both recovered nearly fourfold more viral genomes than the Illumina‐only approach. While yielding fewer MAGs, the ONT‐only approach generated MAGs with a high probability of containing rRNA genes, 3× higher than either of the other methods. Of the shared MAGs recovered from each method, the ONT‐only approach generated the longest and least fragmented MAGs, while the hybrid approach yielded the most complete. This work provides quantitative data to inform a cost–benefit analysis of the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups.
Expression and functional characterization of odorant‐binding protein genes in the endoparasitic wasp Cotesia vestalis
Authors: Zhou Yue‐Nan , Xie Shuang , Chen Jia‐Ni , Wang Ze‐Hua , Yang Pei , Zhou Si‐Cong , Pang Lan , Li Fei , Shi Min , Huang Jian‐Hua , Chen Xue‐Xin 
Published: August 2020

AbstractOdorant‐binding proteins (OBPs) are crucial in insect's olfactory perception, which participate in the initial step of odorant molecules transporting from the external environment to olfactory receptor neurons. To better understand the roles for OBPs in olfactory perception in Cotesia vestalis, a solitary larval endoparasitoid of diamondback moth, Plutella xylostella, we have comprehensively screened the genome of C. vestalis, and obtained 20 CvesOBPs, including 18 classic OBPs and two minus‐C OBPs. Motif‐pattern analysis indicates that the motifs of C. vestalis OBPs are highly conserved in Hymenoptera. The results of tissue expression analysis show that five OBPs (CvesOBP1/11/12/14/16) are highly expressed in male antennae, whereas six other OBP genes (CvesOBP7/8/13/17/18/19) are significantly transcriptionally enriched in female antennae. The results of RNA interference experiments for three most highly expressed OBP genes (CvesOBP17/18/19) in female antennae demonstrate that they are likely involved in parasitic processes of female wasps, as the wasps take a longer time to target the hosts when they are knocked down.
Relationship between serrated polyps and synchronous and metachronous advanced neoplasia: A retrospective study
Authors: Tao En‐Wei , Wang Yong Feng , Zou Tian Hui , Cui Yun , Chen Ying Xuan , Gao Qin Yan 
Published: August 2020

ObjectiveSerrated polyps (SP) are regarded as precursor lesions of colorectal cancer (CRC). We conducted this single‐center study aiming to investigate the relationship between SP and synchronous and metachronous advanced neoplasia in the Chinese population.MethodsThe data for this retrospective study were collected from the Endoscopy Center and Department of Gastroenterology of Renji Hospital, School of Medicine, Shanghai Jiao Tong University between May 2012 and May 2019. Altogether 2205 patients were pathologically confirmed with colorectal SP.ResultsThe detection rate of SP among all polyps has gradually increased since 2014 and reached 8.74% by 2019. Among all the SP cases, 1540 (69.84%) were confirmed as having hyperplasic polyps (HP), 486 (22.04%) were having sessile serrated lesions (SSL), and 171 (7.76%) had traditional serrated adenomas (TSA). Compared with HP (2.14%), SSL and TSA were larger and more likely to be accompanied by synchronous and metachronous advanced neoplasia (6.79% and 6.08%). We next found that large SP (diameter ≥10 mm) (odds ratio [OR] 2.52, 95% confidence interval [CI] 1.40‐4.55, P = 0.002) and SSL with high‐grade intraepithelial neoplasia (OR 13.85, 95% CI 3.28‐58.56, P < 0.001) were associated with an increased risk of synchronous advanced neoplasia. However, we failed to find a relationship between SP and metachronous advanced neoplasia because few patients had developed metachronous advanced neoplasia.ConclusionLarge SP and SSL with high‐grade intraepithelial neoplasia are associated with synchronous advanced neoplasia and require timely surveillance.
Unraveling the role of cigarette use in neural cannabis cue reactivity in heavy cannabis users
Authors: Kuhns Lauren , Kroon Emese , Filbey Francesca , Cousijn Janna 
Published: August 2020

AbstractCue reactivity is an important biomarker of cannabis use disorder (CUD). Despite high rates of cigarette and cannabis co‐use, its role in cannabis cue reactivity remains unclear. Using a visual functional magnetic resonance imaging cue reactivity paradigm, we investigated interactive effects of cannabis and cigarette use on cannabis cue relative to cigarette and neutral cue reactivity in a priori regions of interest—the amygdala, striatum, anterior cingulate cortex (ACC), ventral tegmental area (VTA), and orbitofrontal cortex—and a whole‐brain analysis. In our sample of cannabis users and controls closely matched on cigarette use, significant interactions between cannabis and cigarette use status emerged in the amygdala, striatum, ACC, frontal pole, and inferior frontal gyrus. Cannabis‐only users showed heightened cue reactivity in the amygdala compared with nonusing controls. Co‐users did not show heightened cue reactivity compared with cigarette smoking controls, although cue‐induced VTA activity was positively correlated with grams per week of cannabis. Cigarette smoking controls showed unexpectedly heightened cue reactivity compared to co‐users and nonsmoking controls. These findings and the high prevalence of cannabis and cigarette co‐use underscore the importance of considering cigarette smoking status when investigating the role of cue reactivity in heavy cannabis use.
Susceptibility of the bird cherry‐oat aphid, Rhopalosiphum padi (Hemiptera: Aphididae), to four insecticides
Authors: Umina Paul A , Reidy‐Crofts Jenny , Babineau Marielle , Maino James L , Edwards Owain R 
Published: August 2020

AbstractThe bird‐cherry oat aphid (Rhopalosiphum padi) is a global pest, attacking most cereal crops including barley, wheat, oats and triticale. The aphids cause yield losses through direct feeding damage and the transmission of plant viruses. In Australia, feeding injury can reduce cereal yields by 6%, with the damage caused by aphid‐vectored viruses reducing the yield of cereal crops by up to 30%. Aphid control in these crops is achieved almost exclusively with insecticides, and there is growing concern surrounding insecticide resistance evolution in multiple aphid species. In this study, nine field populations of R. padi were collected from localities representing the major grain growing regions of Australia. Toxicity data against four insecticides (dimethoate, alpha‐cypermethrin, pirimicarb and imidacloprid) was generated for each aphid population. This revealed little differences in population responses for three of these insecticides. For alpha‐cypermethrin, a widely used insecticide in Australia, there were significant differences between several populations. These data will be important for future monitoring of insecticide responses of R. padi and highlight the impending pest management challenges growers could encounter in Australia.
Genomics to accelerate genetic improvement in tilapia
Authors: Yáñez J. M. , Joshi R. , Yoshida G. M. 
Published: August 2020

SummarySelective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth‐, quality‐ and robustness‐related traits. Novel phenotyping technologies (i.e. phenomics), lower‐cost whole‐genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.
A three‐dimensional pelvimetric assessment on pelvic cavity of gazelle (Gazella subgutturosa) by computed tomography
Authors: Demircioglu Ismail , Yilmaz Bestami , Gündemir Ozan , Dayan Mustafa Orhun 
Published: August 2020

AbstractThe gazelles (Gazella subgutturosa), which are at the risk of extinction and are legally protected, have a cultural and aesthetic value in Turkey. It becomes incredibly important to increase their numbers in order to ensure their survival. In this context, it is required to examine thoroughly the pelvic cavity which contains reproductive organs and is used as the birth canal, as well. This study was conducted to determine the pelvimetric data of the gazelles by scanning their pelvic cavity via a multidetector computed tomography (MDCT) and preparing three‐dimensional models of the pelvic cavity. Twelve adult (6 females, 6 males) gazelle carcasses were used in the study. After the pelvic cavity was scanned using the MDCT device with 64 detectors at 80 kV, 200 mA, 639 mGY and 0.625 mm cross‐section thickness, the MDCT images were obtained. The three‐dimensional models of the images obtained using MIMICS 20.1 (The Materialise Group, Leuven, Belgium) program were prepared. Pelvimetric measurements of the pelvic cavity were taken using these models. It was determined based on the pelvimetric examinations that there was a significant difference between the female and male gazelles in terms of conjugate diameter, vertical diameter, intermediate traversal diameter, and cranial and medial transverse diameter data at p < .05. Also, there was a significant difference in their data related to caudal transverse diameter and ischial arch at p < .01. Consequently, it is thought that the use of pelvimetric values belonging to the pelvic cavity of gazelles would reveal the sexual dimorphism of the species and its differences with other species and would contribute to clinical sciences.
Specific inflammatory profile in each pregnancy complication: A comparative study
Authors: Brien Marie‐Eve , Boufaied Ines , Bernard Nathalie , Forest Jean‐Claude , Giguere Yves , Girard Sylvie 
Published: August 2020

ProblemPre‐eclampsia (PE), preterm birth (PTB) and intra‐uterine growth restriction (IUGR) affect 5%‐12% of pregnancies. They have been associated with placental inflammation, although the detection of inflammatory mediators in the maternal circulation is still controversial. Our goal was to determine the inflammatory changes occurring in the second part of pregnancy to identify profiles distinguishing pathological pregnancies from each other.Method of StudyWe performed a nested case‐control study of 200 women randomly selected from a cohort recruited at the CHU de Quebec‐Universite Laval, Quebec, Canada. Women with uncomplicated term pregnancy (CTRL); PE (severe or not); PTB or IUGR (N = 50/each) were included. Plasma samples, obtained from the late second trimester and at delivery, were analysed for over 30 selected mediators (including cytokines/alarmins), by multiplex, ELISA or specific assays. Demographic and obstetrical information were obtained for classification.ResultsIn CTRL, we observed significant differences between 2nd trimester and delivery, with increased levels of inflammatory mediators (ex. MCP‐1, IL‐6), supporting an inflammatory profile towards term. Increased levels of IL‐6, CXCL10 and CRP were observed in PE as compared to CTRL. In PTB, we observed increased CXCL9 in 2nd trimester and decreased progesterone at delivery. In IUGR, increased HMGB1 and IL‐1α were observed only in the 2nd trimester.ConclusionsOur work showed significant inflammatory changes in uncomplicated pregnancies towards delivery, supporting that normal delivery is pro‐inflammatory, although not to the same extent as in pathological pregnancies. Inflammatory profiles are specific to each pregnancy complication which may help to understand the contribution of inflammation to the clinical presentation of these conditions.
Diagnostic workup including CD203c‐based basophil activation test in immediate hypersensitivity due to metronidazole and ornidazole and evaluation of cross‐reactivity in between
Authors: Beyaz Şengül , Akdeniz Nilgün , Yılmaz Abdullah , Demir Semra , Öztop Nida , Çolakoğlu Bahauddin , Büyüköztürk Suna , Deniz Günnur , Gelincik Aslı 
Published: August 2020

AbstractBackgroundLittle is known about the diagnostic approaches for immediate hypersensitivity reactions (IHRs) due to 5‐nitroimidazole antibiotics. The aim was to evaluate the usefulness of in vivo tests and basophil activation test (BAT) for the diagnosis of IHRs due to metronidazole and ornidazole and to determine possible cross‐reactivity in between.MethodsForty‐nine patients with a clear history of IHRs due to these drugs and 20 healthy subjects who were known to tolerate these drugs were included. Skin tests (STs) and single‐blind placebo‐controlled drug provocation tests (SBPCDPTs) were performed with both drugs whereas BAT was applied only with the culprit drug.ResultsThe most and least common reaction types were urticaria/angioedema (34.7%) and anaphylaxis (14.3%), respectively. SBPCDPTs were positive in 15 out of 47 patients, and only 7 had positive STs. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of STs for metronidazole/ornidazole were 33.3%/16.6%, 94.2%/97.3%, 60%/50%, and 84.6%/88.1%, respectively. BAT was positive in 12 out of 15 patients and negative in 10 control subjects, giving a sensitivity rate of 71.4% (CI, 29.0%‐96.3%) for metronidazole and 83.3% (CI, 35.8%‐99.5%) for ornidazole. The optimal concentration of both drugs for BAT was determined as 5 mg/mL. No cross‐reactivity among two drugs was observed according to in vivo tests.ConclusionsOur study showed that SBPCDPT and BAT are both useful diagnostic tools for IHRs due to 5‐nitroimidazole antibiotics and can be used as supplementary to each other. No cross‐reactivity between metronidazole and ornidazole in IHRs exists.
The effect of trimodal prehabilitation on the physical and psychological health of patients undergoing colorectal surgery: a randomised clinical trial
Authors: Fulop A. , Lakatos L. , Susztak N. , Szijarto A. , Banky B. 
Published: August 2020

SummaryPrehabilitation aims to increase the endurance capacity of patients who are awaiting major surgery. However, there are no studies investigating the implementation of this demanding and expensive intervention in low‐income countries. This study aimed to assess the impact of a 4‐week trimodal prehabilitation program on the physical and psychological health of patients waiting for colorectal surgery compared with a control group managed according to enhanced recovery after surgery principles supplemented by nutritional care. This study was a single‐centre, randomised controlled trial. The primary outcome measures for the physical aspects were 6‐minute walking distance (6MWD) and incentive spirometry, whereas the psychological elements were measured using the 36‐item short form survey questionnaire and the hospital anxiety and depression score. In total, data from 149 patients were analysed (77 in the prehabilitation group and 72 in the control group). At the time of surgery, patients in the prehabilitation group had improved 6MWD and incentive spirometry compared with the control group (median (IQR [range]) percentage improvement 131% (112–173 [68–376]) vs. 107% (99–120 [63–163]); p < 0.001 and 113% (100–125 [75–200]) vs. 100% (100–112 [86–167]); p < 0.001 respectively). Patients in the prehabilitation group also had reduced anxiety scores compared with the control group (mean (SD) anxiety score (4 (3) vs. 5 (3) respectively; p = 0.032). However, these effects did not translate into improvements in postoperative mortality and morbidity, or a reduction in duration of hospital stay. Trimodal (physical, emotional and nutritional) prehabilitation is able to improve functional status as well as some parameters of emotional and physical well‐being of patients waiting for colorectal surgery.
Inadequate left ventricular unloading during ramp is associated with hospitalization or death during left ventricular assist device support
Authors: Rosenbaum Andrew N. , Stulak John M. , Clavell Alfredo L. , Behfar Atta 
Published: August 2020

AbstractA combined right and left‐sided heart catheterization (RHC/LHC) protocol was recently reported to optimize patients supported by left ventricular assist device (LVAD). Using this platform, we sought to evaluate the prognostic significance of several hemodynamic indices, including left ventricular end‐diastolic pressure (LVEDP) and transaortic gradient (peak aortic pressure ‐ peak left ventricular pressure in systole, TAG). We evaluated all patients undergoing RHC/LHC at our institution from 2015 through 2018, and comprehensive clinical data were obtained. Primary end points were (1) a composite outcome that included hospitalization or death and (2) 1‐year overall survival after catheterization. Forty‐two patients were included in the analysis. Optimization resulted in normalization of hemodynamic parameters; all variables were significantly improved from baseline (P ≤ .05). On univariate modeling, final LVEDP was associated with the primary end point (hazard ratio [HR], 1.2 per 1‐mm Hg increase; 95% CI, 1.1‐1.3; P = .002). After adjusting for LVAD speed, TAG, and cardiac index in a multivariate model, the association between LVEDP and the composite end point remained significant (HR, 1.2 per 1‐mm Hg increase; 95% CI, 1.1‐1.4; P = .001). In the setting of LVAD support, inadequate LV unloading was a significant marker of poor outcomes with time, suggesting that LVEDP is a central prognostic marker in this population.
Novel peptides with HIV‐1 reverse transcriptase inhibitory activity derived from the fruits of Quercus infectoria
Authors: Seetaha Supaphorn , Hannongbua Supa , Rattanasrisomporn Jatuporn , Choowongkomon Kiattawee 
Published: August 2020

AbstractThe HIV‐1 reverse transcriptase (HIV‐1 RT), which is responsible for transcription of viral RNA genomes into DNA genomes, has become an important target for the treatment of patients with HIV infection. Hydrolyzed peptides from plants are considered a new source of potential drugs. In order to develop new effective inhibitors, peptides extracted from 111 Asian medicinal plants were screened against the HIV‐1 RT. The crude hydrolyzed peptides from the fruit peel of Quercus infectoria were selected for purification and peptide sequence determination by HPLC and LC‐MS. Two peptides of interest were synthesized, and an IC50 test was performed to determine their ability to inhibit the HIV‐1 RT. The IC50 values of the peptides AIHIILI and LIAVSTNIIFIVV were determined to be 274 ± 5.10 nm and 236.4 ± 7.07 nm, respectively. This indicated that these peptides could be further developed as potential HIV‐1 RT inhibitors.
APPEAL‐2: A pan‐European qualitative study to explore the burden of peanut‐allergic children, teenagers and their caregivers
Authors: DunnGalvin Audrey , Gallop Katy , Acaster Sarah , Timmermans Frans , Regent Lynne , Schnadt Sabine , Podestà Marcia , Sánchez Angel , Ryan Robert , Couratier Pascale , Feeney Mary , Hjorth Betina , Fisher Helen R. , Blumchen Katharina , Vereda Andrea , Fernández‐Rivas Montserrat 
Published: August 2020

AbstractBackgroundAllergy to Peanuts ImPacting Emotions And Life (APPEAL‐1) was a recent European multi‐country questionnaire survey that highlighted the negative impacts of peanut allergy (PA) on quality of life. A follow‐on qualitative study, APPEAL‐2, further assessed the burden of PA and associated coping strategies through semi‐structured interviews.ObjectiveTo gain qualitative insight on the strategies used to cope with and manage PA and the impact of these strategies on the quality of life of children, teenagers and caregivers.MethodsThis cross‐sectional qualitative study was conducted in eight European countries: the United Kingdom, France, Germany, Ireland, Spain, Italy, Denmark and the Netherlands. Semi‐structured interviews were conducted with children (aged 8‐12 years) and teenagers (aged 13‐17 years) with self‐/proxy‐reported moderate or severe PA and with parents/caregivers of children or teenagers (aged 4‐17 years) with moderate or severe PA. Data were analysed using thematic analysis; data saturation was assessed. Two conceptual models were developed to illustrate the impacts of PA and coping strategies used to manage them for (a) individuals with PA and (b) parents/caregivers of children with PA.Results107 participants were interviewed: 24 children, 39 teenagers and 44 caregivers. The conceptual models illustrated themes related to coping and control, driven by the fear of PA reactions, and the associated emotional, social, relationship and work impacts. Factors moderating these impacts included social attitudes and support, child‐caregiver relationship and coping strategies used.Conclusions and Clinical RelevanceThe APPEAL‐2 results substantiate the findings of APPEAL‐1; the results also suggest that the severity of experience with PA may not correlate with perception of its overall burden and show variable impacts by country.