bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic content of chemosensory genes correlates with host range in wood-boring beetles (Dendroctonus ponderosae, Agrilus planipennis, and Anoplophora glabripennis)
Authors: Andersson Martin N. , Keeling Christopher I. , Mitchell Robert F. 
Published: October 2019

Abstract
Background
Olfaction and gustation underlie behaviors that are crucial for insect fitness, such as host and mate selection. The detection of semiochemicals is mediated via proteins from large and rapidly evolving chemosensory gene families; however, the links between a species’ ecology and the diversification of these genes remain poorly understood. Hence, we annotated the chemosensory genes from genomes of wood-boring coleopterans, and compared the gene repertoires from stenophagous species with those from polyphagous species.

Results
We annotated 86 odorant receptors (ORs), 60 gustatory receptors (GRs), 57 ionotropic receptors (IRs), 4 sensory neuron membrane proteins (SNMPs), 36 odorant binding proteins (OBPs), and 11 chemosensory proteins (CSPs) in the mountain pine beetle (Dendroctonus ponderosae), and 47 ORs, 30 GRs, 31 IRs, 4 SNMPs, 12 OBPs, and 14 CSPs in the emerald ash borer (Agrilus planipennis). Four SNMPs and 17 CSPs were annotated in the polyphagous wood-borer Anoplophora glabripennis. The gene repertoires in the stenophagous D. ponderosae and A. planipennis are reduced compared with those in the polyphagous A. glabripennis and T. castaneum, which is largely manifested through small gene lineage expansions and entire lineage losses. Alternative splicing of GR genes was limited in D. ponderosae and apparently absent in A. planipennis, which also seems to have lost one carbon dioxide receptor (GR1). A. planipennis has two SNMPs, which are related to SNMP3 in T. castaneum. D. ponderosae has two alternatively spliced OBP genes, a novel OBP “tetramer”, and as many as eleven IR75 members. Simple orthology was generally rare in beetles; however, we found one clade with orthologues of putative bitter-taste GRs (named the "GR215 clade"), and conservation of IR60a from Drosophila melanogaster.

Conclusions
Our genome annotations represent important quantitative and qualitative improvements of the original datasets derived from transcriptomes of D. ponderosae and A. planipennis, facilitating evolutionary analysis of chemosensory genes in the Coleoptera where only a few genomes were previously annotated. Our analysis suggests a correlation between chemosensory gene content and host specificity in beetles. Future studies should include additional species to consolidate this correlation, and functionally characterize identified proteins as an important step towards improved control of these pests.
A Comparison of Ocular Trauma Scores in a Pediatric Population
Authors: Awidi Abdelhalim , Kraus Courtney L 
Published: October 2019

Abstract
Objective: Pediatric ocular trauma represents a major concern for ophthalmologists. Delays in presentation, incomplete exams, inaccurate visual acuity (VA) results, and amblyopia can limit accurately predicting final visual outcomes in pediatric eye trauma. We performed a retrospective clinical study to describe the demographics and causes of eye trauma. We also compared 2 ocular trauma scoring systems, one specifically designed for pediatric trauma, to classify injuries and determine which better predicted VA outcomes. A retrospective chart review of 3 years of pediatric globe trauma was performed. Analysis was focused on mechanisms of injury and VA outcomes. Complex factors that may worsen outcomes were recorded. Ocular Trauma Score (OTS) and Pediatric Ocular Trauma Score (POTS) were used to assign Groups 1-5 to each case. Group 1 was poorest prognosis, Group 5 best. Association between Group and final VA was examined. Accuracy of the two systems was compared. Results: 23 children met eligibility criteria (13 male). Initial VA averaged 20/200 (range no light perception (NLP) – 20/20). Final VA was 20/150 (range NLP - 20/20). Objects of injury were sharp metallic household objects (7), miscellaneous (4), toys (3), BB pellets (2), stick/wood (2), pencil/pen (1).
Tobacco Use and Associated Risk Factors in Burkina Faso: Results from a Population-Based Cross-Sectional Survey.
Authors: Bonnechère Bruno , Kadari Cissé , Tiéba Millogo , Gautier Ouédraogo H. , Franck Garanet , Mariam Ouedraogo A. , Gabriela Boyle , Sékou Samadoulougou , Seni Kouanda , Fati Kirakoya-Samadoulougou 
Published: October 2019

Abstract
Background: Tobacco is a leading preventable cause of non-communicable diseases (NCDs). Studies characterizing the prevalence of tobacco use in low-income countries are lacking. This study describes the prevalence of tobacco use in Burkina Faso and its associated factors.
Methods: Data from the 2013 Burkina Faso World Health Organization (WHO) Stepwise approach to Surveillance (STEPS) were analyzed. The prevalence of any tobacco product use, cigarette smoking, and other tobacco use was calculated. Logistic regression analyses identified factors associated with tobacco use. Overall, 4,691 people were included in this analysis.
Results: The prevalence of any tobacco use was 19.8% (95% CI: 18.4–21.2). Tobacco use was higher for men (29.2% [27.0–31.5]) than women (11.8% [10.3–13.4]). The prevalence of smoked tobacco was 11.3% (10.3–12.4), with a significantly higher prevalence among men (24.5% [22.1–27.0]) than women (0.1% [0.01–0.3]). The overall prevalence of other tobacco use was 8.9% (7.4–10.7), with lower values for men (5.6% [4.1–7.2]) compared to women (11.7% [9.4–14.1]). Tobacco smoking among men was significantly associated with an increased age and alcohol consumption. The analysis of risk factors for other tobacco use stratified by gender showed that age, education, residence, and alcohol consumption were significantly associated with consumption for women, and age and alcohol consumption for men.
Conclusion: Tobacco use is common in Burkina Faso. To effectively reduce tobacco use in Burkina Faso, a comprehensive tobacco control program should consider associated factors, such as gender, age, and alcohol consumption.
Patient’s perception of kidney stone prevention within the emergency department and its adherence factors: A single institution study.
Authors: Moussa Mohamad , Chakra Mohamed Abou 
Published: October 2019

Abstract
Background:
No known data in the literature assessing practice of kidney stone prevention in the emergency department (ED) is available.
Objectives:
Assess patient perception and compliance to kidney stone prevention given within the emergency department. It also indirectly detects the attitude and practice patterns of primary care providers in kidney stone prevention.
Materials and Methods
This is a qualitative study done in a single institution from January 2018 to January 2019 that includes 99 patients that were diagnosed with kidney or ureteral stone in ED and were discharged home, all of them where stone formers. They were asked to fill a self- administered questionnaire when they are able to read, or interviewed by the resident within the ED when they are unable to read.
Results
The majority of patients (68%) did not receive any instructions about kidney stones prevention within the ED. Most of patients who follow instructions if it was given were educated (90 %), had an insurance coverage (85%), and had an income higher than $1000 per month (76%), (p<0.05).
Seventy one percents of patients believe in the effectiveness of stone prevention if it was provided and most of them are interested in learning about these preventive strategies (82%).
Reasons for not following the instructions about kidney stones prevention measures were the cost (53.1%) following by the lack of explanation by ED physicians (18.8%).
The majority of patients (62.6%) prefer to receive kidney stones prevention measures from urologists.
Conclusion:
Most of patients in our institute did not receive kidney stones prevention measures in ED despite that they declared their interest in following these measures. Most of the time they did not adhere to those measures due to socioeconomic factors and lack of clarifications. If these instructions were given within the ED, it could lead to an acceptable compliance rate.
Clonal diversity of Haemophilus influenzae carriage isolated from under the age of 6 years children
Authors: Shooraj Fahimeh , Author) Bahman Mirzaei(Former Corresponding , Author) Seyed Fazlollah Mousavi(New Corresponding , Hosseini Farzaneh 
Published: October 2019

Abstract
Objectives: Pharyngeal carriers such as H. influenzae seem to constitute the only reservoir and probably the only transmission vehicle of the invasive disease. The aims of this study were to estimate the prevalence of H. influenzae carriage, to characterize antibiotic susceptibility, and to explore genetic diversity of H. influenzae isolates. Sampling was carried out as nasopharynx swabs among children less than 6 years old volunteers. After traditional biochemical tests, isolates were confirmed by targeting omp6 sequence. Following the susceptibility tests, genomic diversity of strains was analyzed by Pulsed-Field Gel Electrophoresis procedure.
Results: Out of 328 nasopharynx swabs,73 strains were identified as H. influenzae. Among H. influenzae isolates, resistance to chloramphenicol (42%) and ampicillin (43%) was observed. Levofloxacin is the most effective antibiotic and the least effect belonged to tetracycline. By genomic analysis of selected H. influenza, 28 PFGE patterns were achieved among which 11 patterns included at least 2 strains. All strains clustered into 25 different clones. The dendrogram analysis of the isolated H. influenzae strains showed that some of these strains had a clonal relationship and common genetic origin. According to our results, antibiotic resistance didn’t show any significant correlation with the clonality of strains.
Transcriptomic evidence connecting low aggression to disease risk in honey bees
Authors: Rittschof Clare C , Rubin Benjamin E.R. , Palmer Joseph H. 
Published: October 2019

Abstract
Background: Many organisms display a generalized suite of behaviors that indicate infection or predict infection susceptibility. We apply this concept to honey bee aggression, a behavior that has been associated with positive health outcomes in previous studies. We sequenced the transcriptomes of the brain, fat body, and midgut of adult sibling worker bees who developed as pre-adults in relatively high versus low aggression colonies. Previous studies showed that this pre-adult experience impacted both aggressive behavior and resilience to pesticides. We performed enrichment analyses on differentially expressed genes to determine whether variation in aggression resembles the molecular response to infection. We further assessed whether the transcriptomic signature of aggression in the brain overlapped with that observed following acute predator threat, exposure to a high-aggression environment as an adult, or changes associated with adult behavioral maturation.
Results: Across all three tissues assessed, genes that are differentially expressed as a function of aggression significantly overlap with genes whose expression is modulated by a variety of pathogens. In the fat body, and to a lesser degree the midgut, we find evidence of directional concordance consistent with the hypothesis that low aggression resembles a diseased or parasitized state. However, we find little evidence of acute infection in low aggression individuals. Furthermore, we find little evidence that the brain molecular signature of aggression in the current study is enriched for genes modulated by either ephemeral or stable social cues that induce aggression in adults. However, we do find evidence that genes associated with adult behavioral maturation are enriched in our brain samples, with no clear directional bias.
Conclusions: Results support the hypothesis that low aggression resembles a molecular state associated with infection. This pattern is most robust in the peripheral fat body, an immune responsive tissue in the honey bee. Although these results are correlative, we find no evidence of acute infection in low aggression bees, suggesting the physiological state associated with low aggression may predispose bees to negative health outcomes. The similarity of molecular signatures associated with the seemingly disparate traits of aggression and disease suggests that these characteristics may, in fact, be intimately tied.
Different transcriptome profiles between human retinoblastoma Y79 cells and an etoposide-resistant subline reveal a chemoresistance mechanism
Authors: Song Wen-ping , Zheng Si , Yao Hong-juan , Zhou Xiao-fei , Li Rui , Zhang Cheng-yue , Zhao Jun-yang , Wang Lie-wei , Shao Rong-guang , Li Liang 
Published: October 2019

Abstract
Background: Retinoblastoma (RB) is the most frequent pediatric retinal tumor. In the present study, to elucidate chemoresistance mechanisms and identify potential biomarkers in RB, we utilized RNA sequencing (RNAseq) technological platforms to reveal transcriptome profiles and identify any differentially expressed genes (DEGs) between an etoposide drug-resistant subline (Y79/EDR) and parental Y79 cells.
Methods: To test whether Y79/EDR cells showed resistance to antineoplastic agents for RB, we treated the cells with etoposide, carboplatin and vincristine and analyzed them with a Cell Counting Kit-8 (CCK-8). Y79/EDR and parental Y79 cells were used for RNAseq and bioinformatics analysis to enable a genome-wide review of DEGs between the two lines using the DESeq R package (1.10.1). Then, DEG enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was analyzed with KOBAS software. Next, real-time quantitative reverse transcription polymerase chain reaction (real time QRT-PCR) and cytotoxicity assays were performed to experimentally and functionally validate the identified candidate biomarkers.
Results: Y79/EDR cells showed resistance to etoposide, carboplatin and vincristine at different concentrations. In total, 524 transcripts were differentially expressed in Y79/EDR cells based on analysis of fragments per kilobase of transcript per million fragments mapped (FPKM); among these, 57 genes were downregulated and 467 genes were upregulated in Y79/EDR cells compared to parental Y79 cells. We selected candidate DEGs, including ARHGAP9 , HIST1H4H , RELN , DDIT4 , HK2 , STC1 and PFKFB4, for mRNA expression validation with real time QRT-PCR assays and found that the expression levels determined by real time QRT-PCR were consistent with the RNAseq data. Further studies involving downregulation of ARHGAP9 with a specific siRNA showed that ARHGAP9 altered the cellular sensitivity of Y79 cells to etoposide and carboplatin.
Conclusion: Our initial findings provided a genomic view of the transcription profiles of etoposide-induced acquired resistance in RB. Follow-up studies indicated that ARHGAP9 might be a chemoresistance biomarker in RB, providing insight into potential therapeutic targets for overcoming acquired chemoresistance in RB. These findings can aid in understanding and overcoming chemoresistance during treatment of RB in the clinic.
Antimicrobial Resistance in Syria
Authors: Kaddour Samer Haj , Alhamid Ahmad , Homsi Muhannad , Albakkar Abdulmalek , Aldana Fadi , Nahhas Rabea , Alholo Zain Alabedeen , Jabbour Ali , Alghabra Yasser , Mayhoub Marie , Jabas Mustafa , Sahhar Ahmed , Mohammed Sura , Tahan Zaher Samman 
Published: October 2019

Abstract
Background Antimicrobial resistance is one of the important and serious public health problems worldwide. Syria has a severe lack of data regarding this problem, especially after war. We aimed from this study to provide a unique snapshot on antimicrobial resistance in Syria.Methods This is a multi-centric cross-sectional in-vitro study. The results of routine antimicrobial susceptibility tests were collected and analyzes from five major hospitals during the period from 1st March 2018 through 31th October 2018.Results Final analysis included 2861 isolates. We noticed extremely high rates of antimicrobial resistance among all the species studied. Gram negatives have high resistance rates for cephalosporins. 77% of E.coli, 73% of Klebsiella and 82% of pseudomonas are resistant for ceftriaxone. We also noticed minimal effect of macrolides on gram negatives. 25% of Salmonella typhi strains were resistant to ciprofloxacin. High resistance rates to nitrofurantoin is seen among uropathogenic bacteria. Most gram positive bacteria still have a low resistance rate to vancomycin and linezolid. 54% of staphylococcus aureus and 38% of streptococcus pyogens are resistant to amoxicillin-clavulanate. Resistance rates to Colistin are minimal. The comparison with resistance rates before war reveals the great impact of war on antimicrobial resistance problem.Conclusion Antimicrobial resistance rates in Syria are worrying. We recommend that the Syrian health authorities apply a policy to restrict the irrational use of antibiotics, and to increase awareness toward antimicrobials use.
Randomised controlled trial of the short-term effects of OROS-methylphenidate on ADHD symptoms and behavioural outcomes in young male prisoners with attention-deficit/hyperactivity disorder (CIAO-II)
Authors: Asherson Philip , Johansson Lena , Holland Rachel , Fahy Thomas , Forester Andrew , Howitt Sheila , Lawrie Stephen , Strang John , Young Susan , Landau Sabine , Thomson Lindsay 
Published: October 2019

Abstract
Background: Attention-deficit/hyperactivity disorder (ADHD) is a highly prevalence disorder, seen in 20-30% of young adult prisoners. Pharmacoepidemiological studies, a small randomised controlled, and open trial data suggest clinically significant reductions in ADHD symptoms, emotional dysregulation, disruptive behaviour and engagement with educational activities. Yet, routine treatment of ADHD in offenders with ADHD is not yet established clinical practice. There is continued uncertainty about the clinical response to methylphenidate, a first line treatment for ADHD, in offenders who often present with an array of complex mental health problems that may better explain states of inattentive, overactive restless and impulsive behaviours. To address this problem we conduct an efficacy trial to establish the short term effects of OROS-methylphenidate (Concerta XL), an extended release formulation of MPH, on ADHD symptoms, emotional dysregulation and behaviour. Methods: Parallel arm randomised placebo-controlled trial of OROS-MPH on ADHD symptoms, behaviour and functional outcomes in young male prisoners aged 16-25, meeting DSM-5 criteria for ADHD. Participants are randomised to 8-weeks treatment with OROS-MPH or placebo, titrated over 5 weeks to balance ADHD symptom improvement against side effects. 200 participants will be recruited with 1:1 ratio of drug to placebo. The primary outcome is change in level of ADHD symptoms after 8-weeks of trial medication. Discussion: Potential benefits include improvement in ADHD symptoms, emotional dysregulation, attitudes towards violence, critical incidents and engagement with educational and rehabilitation programs. Demonstrating efficacy and safety of MPH on ADHD symptoms and associated impairments may provide the data needed to develop effective healthcare pathways for a significant group of young offenders. Establishing efficacy of MPH in this population will provide the foundation needed to establish long term effectiveness studies with the potential for demonstrating significant reductions in criminal behaviour and improved health-economic outcomes. Trial Registration: ISRCTN16827947l; EudraCT Number: 2015-004271-78. Protocol version: v2.0 30.08.2018
Social work support and unmet social needs in life after stroke: a cross-sectional exploratory study
Authors: Lehnerer Sophie Mirabell , Hotter Benjamin , Padberg Inken , Knispel Petra , Remstedt Dike , Liebenau Andrea , Grittner Ulrike , Wellwood Ian , Meisel Andreas 
Published: October 2019

Abstract
Background: Stroke patients are often affected by long-term disabilities with needs concerning social issues. There is relatively little consideration of social recovery of patients and the support required to return to work, receive social benefits, participate in daily life activities, maintain contact with family and friends and to organize financial affairs. In our study we aimed to investigate if existing tools record social needs adequately. We analyzed the current provision of social support provided in long-term care after stroke and whether unmet social needs were associated with quality of life, caregiver burden, overall function and degree of disability. Methods: Our analysis is part of the Managing Aftercare of Stroke study (MAS-I), a cross-sectional exploratory study of patient needs 2-3 years after initial stroke. Assessment tools included the Nikolaus-score (social situation), the EuroQoL (quality of life), the German Burden Scale for Family Caregivers (caregiver burden), the modified Rankin Scale (disability / dependence), Stroke Impact Scale (function and degree of disability) and the Stroke Survivor Needs Questionnaire (unmet needs). Results: Overall 57 patients were included in MAS-I, with ten patients classified in urgent need of socio-economic support according to the Nikolaus-score. Patients with lower than normal Nikolaus-score had a higher degree of disability. Thirty percent of all patients had never received professional social support. Social worker contact happened mostly during the stay in acute hospital or rehabilitation institution. Only four patients (11%) reported long-term support after discharge. Apart from social worker contact during acute care, 43% of patients had unmet needs in the long-term aftercare. Forty percent of all patients included in MAS-I were recommended for social work intervention after an in-depth analysis of their situation. Finally, we saw that unmet social needs were associated with lower quality of life and higher caregiver burden. Conclusions: Our data suggest significant unmet needs in social care in long-term stroke patients. Screening tools for unmet social needs such as the Nikolaus-score do not holistically report patients’ needs.
Risk of Stroke-Associated Pneumonia During Hospitalization: Predictive Ability of Combined A2DS2 Score and Hyperglycemia
Authors: Li Yang , Zhang Yu , Ma Sheng Lian , Niu Xiaoyuan , Chang Junsen 
Published: October 2019

Abstract
Background: Stroke-associated pneumonia (SAP) is a common complication of cerebrovascular disease. The A 2 DS 2 score has been used to predict the risk of SAP. However, hyperglycemia is not included in this scale. The purpose of the present study was to explore whether the A 2 DS 2 scoring system and hyperglycemia could predict the risk of SAP more effectively than the conventional A 2 DS 2 scale.
Methods: This retrospective study enrolled 2,552 patients with acute ischemic stroke. The A 2 DS 2 scores, fasting blood glucose level and blood glucose level on admission were collected. Regression analysis was used to identify the independent risk factors of SAP. ROC curve analysis was used to evaluate the specificity and sensitivity of the combined A 2 DS 2 score and fasting hyperglycemia for predicting SAP.
Results: Fasting hyperglycemia was an independent risk factor for SAP (OR=2.95; 95% confidence interval: 2.11-4.12; P< 0.001). The area under curve of the combined A 2 DS 2 score and fasting hyperglycemia was significantly higher than that of the A 2 DS 2 score alone (0.814 vs. 0.793; P =0.020).
Conclusion: Fasting hyperglycemia is an independent risk factor for predicting SAP. Compared with the A2DS2 score, the modified A2DS2 score (combined A2DS2 score and fasting hyperglycemia) is more effective in predicting the risk of SAP.
Keywords : Stroke-associated pneumonia; A 2 DS 2 score; Fasting hyperglycemia; Predictive value