bluuebunny/crossref_metadata_2025_split huggingface dataset:
HyAsP, a greedy tool for plasmids identification
Authors: Müller Robert , Chauve Cedric 
Published: May 2019

Abstract

Motivation
Plasmids are ubiquituous in bacterial genomes, and have been shown to be involved in important evolutionary processes, in particular the acquisition of antimicrobial resistance. However separating chromosomal contigs from plasmid contigs and assembling the later is a challenging problem.

Results
We introduce HyAsP, a tool that identifies, bins and assembles plasmid contigs following a hybrid approach based on a database of known plasmids genes and a greedy assembly algorithm. We test HyAsP on a large sample of bacterial datasets and observe that it generally outperforms other tools.

Availability and implementation
https://github.com/cchauve/HyAsP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cost-Effectiveness Analysis of Lung Cancer Screening Accounting for the Effect of Indeterminate Findings
Authors: Toumazis Iakovos , Tsai Emily B , Erdogan S Ayca , Han Summer S , Wan Wenshuai , Leung Ann , Plevritis Sylvia K 
Published: May 2019

Abstract

Background
Numerous health policy organizations recommend lung cancer screening, but no consensus exists on the optimal policy. Moreover, the impact of the Lung CT screening reporting and data system guidelines to manage small pulmonary nodules of unknown significance (a.k.a. indeterminate nodules) on the cost-effectiveness of lung cancer screening is not well established.

Methods
We assess the cost-effectiveness of 199 screening strategies that vary in terms of age and smoking eligibility criteria, using a microsimulation model. We simulate lung cancer-related events throughout the lifetime of US-representative current and former smokers. We conduct sensitivity analyses to test key model inputs and assumptions.

Results
The cost-effectiveness efficiency frontier consists of both annual and biennial screening strategies. Current guidelines are not on the frontier. Assuming 4% disutility associated with indeterminate findings, biennial screening for smokers aged 50–70 years with at least 40 pack-years and less than 10 years since smoking cessation is the cost-effective strategy using $100 000 willingness-to-pay threshold yielding the highest health benefit. Among all health utilities, the cost-effectiveness of screening is most sensitive to changes in the disutility of indeterminate findings. As the disutility of indeterminate findings decreases, screening eligibility criteria become less stringent and eventually annual screening for smokers aged 50–70 years with at least 30 pack-years and less than 10 years since smoking cessation is the cost-effective strategy yielding the highest health benefit.

Conclusions
The disutility associated with indeterminate findings impacts the cost-effectiveness of lung cancer screening. Efforts to quantify and better understand the impact of indeterminate findings on the effectiveness and cost-effectiveness of lung cancer screening are warranted.
Applicable Law Provisions in Investment Treaties: Forever Midnight Clauses?
Authors: Atanasova Dafina 
Published: May 2019

Abstract
Building on the growing awareness that applicable law determinations are one of the places where the balance between investor and state interests is struck in investment disputes, the article probes the capacity of applicable law provisions (ALPs) in investment treaties to contribute to its regulation. Based on a large scale survey of treaty texts (1000+ treaties), the article argues that there is a misunderstanding of ALPs by negotiators despite greater engagement with these provisions. The article uncovers a mismatch between the questions of choosing among different potentially applicable laws and their proper interpretation, which are salient in investment arbitration, and the focus of ALP drafting. Even recent ALPs seem primarily used as tools to circumscribe tribunals’ jurisdiction, which leads to their redundancy. To bridge this gap, the article argues for a structural change bringing ALPs in investment treaties closer to choice of law provisions proper.
What They Expect Is What You Get: The Role of Interviewer Expectations in Nonresponse to Income and Asset Questions
Authors: Friedel Sabine 
Published: May 2019

Abstract
Personal income and assets are sensitive topics to discuss. This phenomenon is reflected in high rates of nonresponse to financial questions in surveys. In face-to-face surveys, item nonresponse is influenced by interviewers. Although interviewers are trained to conduct standardized interviews, some obtain a higher number of item nonresponses than others. This study examines interviewer effects on nonresponse to questions about household income, bank balances, and interest and dividend income in the Survey of Health, Ageing and Retirement in Europe (SHARE). It first investigates the extent to which interviewers affect nonresponse to income and asset questions and second whether interviewers’ prior expectations regarding respondents’ likelihood to provide information about their income predict actual nonresponse rates. Results of multilevel modeling show that interviewer influence on nonresponse to the income and asset questions was significant at the five percent level. In addition, interviewer expectations were significantly correlated with “don’t know” responses and “refusals.” These results indicate that interviewer expectations matter in the context of income and asset questions and that survey practitioners should take this into account when designing interviewer training.
Multiple Independent Recruitment of Sodefrin Precursor-Like Factors in Anuran Sexually Dimorphic Glands
Authors: Bossuyt Franky , Schulte Lisa M , Maex Margo , Janssenswillen Sunita , Novikova Polina Yu , Biju S D , Van de Peer Yves , Matthijs Severine , Roelants Kim , Martel An , Van Bocxlaer Ines 
Published: May 2019

AbstractChemical signaling in animals often plays a central role in eliciting a variety of responses during reproductive interactions between males and females. One of the best-known vertebrate courtship pheromone systems is sodefrin precursor-like factors (SPFs), a family of two-domain three-finger proteins with a female-receptivity enhancing function, currently only known from salamanders. The oldest divergence between active components in a single salamander species dates back to the Late Paleozoic, indicating that these proteins potentially gained a pheromone function earlier in amphibian evolution. Here, we combined whole transcriptome sequencing, proteomics, histology, and molecular phylogenetics in a comparative approach to investigate SPF occurrence in male breeding glands across the evolutionary tree of anurans (frogs and toads). Our study shows that multiple families of both terrestrially and aquatically reproducing frogs have substantially increased expression levels of SPFs in male breeding glands. This suggests that multiple anuran lineages make use of SPFs to complement acoustic and visual sexual signaling during courtship. Comparative analyses show that anurans independently recruited these proteins each time the gland location on the male’s body allowed efficient transmission of the secretion to the female’s nares.
Vulpes chama (Carnivora: Canidae)
Authors: Lavoie Maxime , Renard Aurélie , Pitt Justin A , Larivière Serge 
Published: May 2019

AbstractVulpes chama (Smith, 1833), commonly called the Cape fox, is 1 of 11 species of Vulpes. It is the only species of Vulpes occurring in southern Africa, and is endemic to that region. It occurs in southern Angola, Botswana, Namibia, South Africa, and southwestern Zimbabwe. V. chama is a slender-built fox and its pelage is silvery gray throughout, back of pinna is tawny, and white hairs occur in the front along pinna edge. It tends to occupy arid and semiarid open habitats and feeds mainly on small mammals and insects, but also consumes birds, small reptiles, and fruits. V. chama is not of conservation concern and is listed as “Least Concern” by the International Union for the Conservation of Nature and Natural Resources.
Change in mutation frequency at a TP53 hotspot during culture of ENU-mutagenised human lymphoblastoid cells
Authors: Watanabe Masahiko , Toudou Masae , Uchida Taeko , Yoshikawa Misato , Aso Hiroaki , Suemaru Katsuya 
Published: May 2019

AbstractMutations in oncogenes or tumour suppressor genes cause increases in cell growth capacity. In some cases, fully malignant cancer cells develop after additional mutations occur in initially mutated cells. In such instances, the risk of cancer would increase in response to growth of these initially mutated cells. To ascertain whether such a situation might occur in cultured cells, three independent cultures of human lymphoblastoid GM00130 cells were treated with N-ethyl-N-nitrosourea to induce mutations, and the cells were maintained for 12 weeks. Mutant frequencies and spectra of the cells at the MspI and HaeIII restriction sites located at codons 247–250 of the TP53 gene were examined. Mutant frequencies at both sites in the gene exhibited a declining trend during cell culture and reached background levels after 12 weeks; this was also supported by mutation spectra findings. These results indicate that the mutations detected under our assay conditions are disadvantageous to cell growth.
A large-scale drug screen identifies selective inhibitors of class I HDACs as a potential therapeutic option for SHH medulloblastoma
Authors: Pak Ekaterina , MacKenzie Ethan L , Zhao Xuesong , Pazyra-Murphy Maria F , Park Paul M C , Wu Lei , Shaw Daniel L , Addleson Emily C , Cayer Suzanne S , Lopez Begoña G-C , Agar Nathalie Y R , Rubin Lee L , Qi Jun , Merk Daniel J , Segal Rosalind A 
Published: May 2019

Abstract

Background
Medulloblastoma (MB) is one of the most frequent malignant brain tumors of children, and a large set of these tumors is characterized by aberrant activation of the sonic hedgehog (SHH) pathway. While some tumors initially respond to inhibition of the SHH pathway component Smoothened (SMO), tumors ultimately recur due to downstream resistance mechanisms, indicating a need for novel therapeutic options.

Methods
Here we performed a targeted small-molecule screen on a stable, SHH-dependent murine MB cell line (SMB21). Comprehensive isotype profiling of histone deacetylase (HDAC) inhibitors was performed, and effects of HDAC inhibition were evaluated in cell lines both sensitive and resistant to SMO inhibition. Lastly, distinct mouse models of SHH MB were used to demonstrate pharmacologic efficacy in vivo.

Results
A subset of the HDAC inhibitors tested significantly inhibit tumor growth of SMB21 cells by preventing SHH pathway activation. Isotype profiling of HDAC inhibitors, together with genetic approaches suggested that concerted inhibition of multiple class I HDACs is necessary to achieve pathway inhibition. Of note, class I HDAC inhibitors were also efficacious in suppressing growth of diverse SMO inhibitor‒resistant clones of SMB21 cells. Finally, we show that the novel HDAC inhibitor quisinostat targets multiple class I HDACs, is well tolerated in mouse models, and robustly inhibits growth of SHH MB cells in vivo as well as in vitro.

Conclusions
Our data provide strong evidence that quisinostat or other class I HDAC inhibitors might be therapeutically useful for patients with SHH MB, including those resistant to SMO inhibition.
Atraumatic Sylvian Fissure Split: Nuances and Pitfalls
Authors: Cohen-Gadol Aaron A 
Published: May 2019

Abstract
An appropriately wide, efficient, and atraumatic split of the Sylvian fissure is technically challenging; this task does not often receive the respect or attention it deserves. Mastering efficient fissure dissection is imperative for protecting the cerebrovascular structures and using dynamic retraction for optimal exposure of the lesions within the peri-insular region and around the circle of Willis.
Construction of an ICF core set and ICF-based questionnaire assessing activities and participation in patients with systemic sclerosis
Authors: Papelard Agathe , Daste Camille , Alami Sophie , Sanchez Katherine , Roren Alexandra , Segretin François , Lefèvre-Colau Marie-Martine , Rannou François , Mouthon Luc , Poiraudeau Serge , Nguyen Christelle 
Published: May 2019

Abstract

Objectives
To develop an International Classification of Functioning, Disability and Health (ICF) core set for SSc and to conceive a patient-centred ICF-based questionnaire assessing activities and participation in patients with SSc.

Methods
The construction of the ICF core set followed two steps. In the first step, meaningful concepts related to SSc were collected using data source triangulation from patients (n = 18), experts (n = 10) and literature (n = 174 articles). In the second step, concepts were linked to the best-matching ICF categories by one reviewer according to prespecified linking rules. Finally, patient-reported activities and participation categories of the ICF core set were translated into understandable questions.

Results
After linking concepts to ICF categories, 150 ICF categories were collected from focus groups, 22 from experts and 82 from literature. After fusion of the sources and removal of duplicates, the ICF core set included 164 categories: one at the first level, 157 at the second level and six at the third level, with 50 categories on body functions, 15 on body structures, 52 on activities and participation, and 47 on environmental factors. Patient-reported ICF categories on activities and participation were translated into a patient-centred ICF-based 65-item questionnaire.

Conclusion
The present study proposes an ICF core set that offers a conceptual framework for SSc patients’ care and health policy. Using a patient-centred approach, a patient-centred ICF-based questionnaire, the Cochin Scleroderma ICF-65 questionnaire, assessing activities and participation in patients with SSc, was conceived.

Trial registration
ClinicalTrials.gov, http://clinicaltrials.gov, NCT01848418.
Prenatal Practice Staff Perceptions of Three Substance Use Screening Tools for Pregnant Women
Authors: Trocin Kathleen E. , Weinstein Nicole I. , Oga Emmanuel A. , Mark Katrina S. , Coleman-Cowger Victoria H. 
Published: May 2019

Objective:
There is a need to identify an acceptable and comprehensive substance use screening tool for pregnant women in the United States. This qualitative study sought to better understand prenatal practice staff perceptions of three existing substance use screening tools for use among pregnant women in an outpatient practice setting.

Methods:
Eight focus groups with 40 total participants were conducted with clinical and administrative staff of 2 diverse Maryland prenatal practices to determine the acceptability and usability of 3 substance use screening tools (4P's Plus, NIDA-Modified Alcohol, Smoking and Substance Involvement Screening Test, and the Substance Use Risk Profile-Pregnancy scale). The focus groups were digitally recorded, transcribed, coded, and analyzed using thematic analysis.

Results:
Participant perceptions of screening tools were dependent upon screening tool length, tone, comprehensiveness, subjectivity, time frame of questions, and scoring and clinician instructions. Most participants preferred the 4P's Plus screening tool because it is brief, comprehensive, easy for the patient to understand, and excludes judgmental language and subjective questions.

Conclusions:
These results provide valuable insight into the specific needs and preferences of prenatal practice staff as it relates to prenatal substance use screening and provides evidence that the 4P's Plus may be a preferred screening tool for standardized use in prenatal care.
ONE-YEAR OUTCOMES OF A NOVEL SURGICAL TECHNIQUE FOR SUTURELESS INTRASCLERAL FIXATION OF A THREE-PIECE INTRAOCULAR LENS USING A 30-GAUGE NEEDLE
Authors: Bonnell Alyssa C. , Polo Richard N. , Shah Sumit P. , Fine Howard F. , Prenner Jonathan L. 
Published: May 2019

Purpose:
To present the 1-year results of a surgical technique for the sutureless intrascleral fixation of a 3-piece intraocular lens using a 30-gauge needle.

Methods:
A retrospective chart review of a consecutive series of 9 eyes of 8 patients who underwent sutureless intrascleral fixation of posterior chamber intraocular lens using a 30-gauge needle was performed. Patients were required to have at least 1 year of follow-up to be included in the analysis. Short-term data were collected 1 month after surgery, and long-term data were collected 1 year after surgery. Data collected included visual acuity, lens stability, intraocular pressure, and the development of complications.

Results:
Visual acuity improved from Snellen 20/309 preoperatively to Snellen 20/27 at postoperative Month 12 (P = 0.03). Short-term complications included increased intraocular pressure (n = 4) and corneal edema (n = 2). Long-term complications included exposed superior haptic (n = 1) and recurrent anterior chamber inflammation (n = 1).

Conclusion:
The novel surgical technique for sutureless intrascleral fixation of a 3-piece intraocular lens is well tolerated 1 year after surgery.
CENTRAL RETINAL VEIN OCCLUSION IN OTHERWISE HEALTHY CHILDREN AND ADOLESCENTS
Authors: Bremond-Gignac Dominique , Daruich Alejandra , Gallet Marlène , Menoud Pierre Alain , Nowomiejska Katarzyna , Rejdak Robert , Behar-Cohen Francine , Benkhalifa Moncef , Copin Henri 
Published: May 2019

Purpose:
To report cases of central retinal vein occlusion in otherwise healthy children showing combined genetic variants of thrombophilia.

Methods:
Ophthalmological, pediatric records and genetic analyses of thrombophilia-associated variants were retrospectively reviewed in four children diagnosed with central retinal vein occlusion. Genetic screening, including Factor XII, platelet glycoprotein (GP) IIIa PlA1/A2 (rs5918), and GPIa/IIa C807T (rs1126643) and G873A (rs1062535) mutations, was performed by PCR amplification and Sanger sequencing of PCR products. The genotyping of prothrombin G20210A, Leiden Factor V G1691A, methylenetetrahydrofolate reductase (MTHFR) C677T/A1298C mutations, and plasminogen activator inhibitor-1 4G/5G polymorphisms was performed by real-time PCR with Fluorescence Resonance Energy Transfer (FRET) probes.

Results:
The genotyping analysis identified combined genetic variants of thrombophilia in each patient. Mutations for MTHFR (C677T) and GPIIIa PlA1/A2 were detected in Case 1, mutations for MTHFR (C677T), GPIIIa PlA1/A2, and GPIa/IIa in Case 2, mutations for MTHFR (C677T) and GPIa/IIa in Case 3, and mutation for MTHFR (A12986C), GPIIIa Pl A1/A2, and GPIa/IIa in Case 4. Preventive low-dose aspirin therapy was prescribed to all patients. During a follow-up of 5 and 8 years, neither central retinal vein occlusion recurrence nor any other thrombotic event was observed in Cases 1 and 2, respectively.

Conclusion:
In otherwise healthy children presenting central retinal vein occlusion, genetic investigations for thrombophilia-associated variants should be considered, given the possible long-term benefit of aspirin prophylaxis.
Surgery for adhesive small-bowel obstruction is associated with improved long-term survival mediated through recurrence prevention: A population-based, propensity-matched analysis
Authors: Behman Ramy , Nathens Avery B. , Haas Barbara , Look Hong Nicole , Pechlivanoglou Petros , Karanicolas Paul 
Published: May 2019

BACKGROUND
Adhesive small-bowel obstruction (aSBO) is among the most common reasons for admission to a surgical service. While operative intervention for aSBO is associated with a lower risk of recurrence, current guidelines continue to advocate a trial of nonoperative management. The impact of the increased risk for recurrence on long-term survival is unknown. We sought to explore the potential for improved survival with operative management through the prevention of admissions for recurrence of aSBO and the associated risks.

METHODS
This is a population-based retrospective cohort study using administrative data. We identified patients admitted to hospital for their first episode of aSBO from 2005 to 2014 and created a propensity-matched cohort to compare survival of patients managed operatively with those managed nonoperatively. To test whether survival differences were mediated by recurrence prevention, a competing risk regression was used to model the subdistribution hazard of death when accounting for the risk of recurrence. An instrumental variable approach was used as a secondary analysis to compare survival while accounting for unmeasured confounding.

RESULTS
There were 27,904 patients admitted for their first episode of aSBO between 2005 and 2014. The mean age was 61.2 years (std dev, 13.6), and 51% were female. Operative management was associated with a significantly lower risk of death (hazard ratio, 0.80; 95% confidence interval, 0.75–0.86), which was robust to instrumental variable analyses, and a lower risk of recurrence (hazard ratio, 0.59; 95% confidence interval, 0.54–0.65). When adjusting for the risk of recurrence, operative intervention was not associated with improved survival, suggesting that the survival benefit is mediated through prevention of recurrences of aSBO.

CONCLUSION
In patients admitted for their first episode of aSBO, operative intervention is associated with a significant long-term survival benefit. This survival benefit appears to be mediated through the prevention of recurrences of aSBO.

STUDY TYPE
Retrospective cohort study.

LEVEL OF EVIDENCE
Therapeutic study, Level II.
Adaptive post-transcriptional reprogramming of metabolism limits response to targeted therapy in BRAFV600 melanoma
Authors: Smith Lorey K , Parmenter Tiffany , Kleinschmidt Margarete , Kusnadi Eric P , Kang Jian , Martin Claire A , Lau Peter , Lorent Julie , Trigos Anna , Ward Teresa , Rao Aparna D , Lelliott Emily J , Sheppard Karen E , Goode David , Hicks Rodney J , Tiganis Tony , Simpson Kaylene J , Larsson Ola , Cullinane Carleen , Wickramasinghe Vihandha O , Pearson Richard B , McArthur Grant A 
Published: May 2019

AbstractDespite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by a residual disease that results in relapse. This residual disease is characterized by drug-induced adaptation, that in melanoma includes altered metabolism. Here, we examined how targeted therapy reprograms metabolism in BRAF-mutant melanoma cells using a genome-wide RNAi screen and global gene expression profiling. This systematic approach revealed post-transcriptional regulation of metabolism following BRAF inhibition, involving selective mRNA transport and translation. As proof of concept we demonstrate the RNA binding kinase UHMK1 interacts with mRNAs that encode metabolic proteins and selectively controls their transport and translation during adaptation to BRAF targeted therapy. Inactivation of UHMK1 improves metabolic response to BRAF targeted therapy and delays resistance to BRAF and MEK combination therapy in vivo. Our data support a model wherein post-transcriptional gene expression pathways regulate metabolic adaptation underpinning targeted therapy response and suggest inactivation of these pathways may delay disease relapse.