bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short article: Retreatment of chronic hepatitis C virus infection after unsuccessful therapy with all-oral direct-acting antiviral regimens: a real-life experience
Authors: Milazzo Laura , Magni Carlo , Niero Fosca , Schiavini Monica , Lai Alessia , Cento Valeria , Binda Francesca , Antinori Spinello , Sollima Salvatore 
Published: September 2017

Objective
Few real-life data are available on the retreatment of patients who failed direct-acting antiviral (DAA)-regimens. We reported the outcome of retreatment with approved DAA regimens in a real-life cohort of patients who previously failed an all-oral DAAs combination and we analyzed the association with resistance substitutions (RASs) performed at the time of virological failure.

Aim and methods
Next-generation sequencing of the NS3, NS5A, and NS5B regions was performed by Illumina deep sequencing. The sequence reads were analyzed by an in-house pipeline.

Results
Of the 16/759 (2%) patients who failed to achieve a sustained virological response at 12 weeks to all-oral DAAs from December 2014 to January 2016, 10 were retreated with licensed DAAs regimens. In all the patients, retreatment was followed by sustained virological response at 12 weeks. Baseline NS3-RASs before retreatment were observed in two patients who failed a sofosbuvir/simeprevir regimen: D168V RAS was detected in a genotype-4 patient, whereas the complex RAS-pattern Q80K, I170V, R155K, D168E was observed in a genotype-1a patient. Only one of the two patients who previously failed ombitasvir, paritaprevir/ritonavir, and dasabuvir underwent RAS analysis at relapse and showed baseline NS5A RAS (M28V) before retreatment.

Conclusion
These real-life findings indicated a high efficacy of sofosbuvir+NS5A-inihbitors in retreating NS3-experienced patients and also NS5A-experienced patients by using a 24-week course ribavirin-containing regimen. The relevance of hepatitis C virus resistance testing before retreatment remains to be better defined to guide the choice of the new regimen before retreatment in DAA-experienced patients.
Incidence and Timing of Thromboembolic Events in Patients With Ovarian Cancer Undergoing Neoadjuvant Chemotherapy
Authors: Greco Patricia S. , Bazzi Ali A. , McLean Karen , Reynolds R. Kevin , Spencer Ryan J. , Johnston Carolyn M. , Liu J. Rebecca , Uppal Shitanshu 
Published: September 2017

(Abstracted from Obstet Gynecol 2017;129(6):979–985)
Thromboembolism in patients with ovarian and other cancers is associated with lower survival and poor quality of life. The estimated incidence of venous thromboembolism (VTE) among patients with ovarian cancer (OC) is 10% to 22%.
Comparative Perioperative Pain and Recovery in Women Undergoing Vaginal Reconstruction Versus Robotic Sacrocolpopexy
Authors: Westermann Lauren B. , Crisp Catrina C. , Mazloomdoost Donna , Kleeman Steven D. , Pauls Rachel N. 
Published: September 2017

(Abstracted from Female Pelvic Med Reconstr Surg 2017;23:95–100)
The preferred surgical route for optimal recovery of women with pelvic organ prolapse is minimally invasive surgery. Reconstruction of the apex following a minimally invasive hysterectomy may be performed with a vaginal suspension or a laparoscopic/robotic sacrocolpopexy.
Contending With Preplanned Death: Questions for Clinicians
Authors: YAGER JOEL 
Published: September 2017

Background and Objectives:
The goal of this column is to assist readers in reflecting on their attitudes and responses toward clinical and nonclinical situations involving preplanned deaths by decisionally capable individuals. Such circumstances range from encountering individuals in one’s personal and professional lives who desire and intend to end their lives under their own terms, to having such individuals request assistance with predeath and postdeath arrangements.

Methods:
Attending to pertinent literature, this essay uses Socratic inquiry to question conventional assumptions and attitudes, push readers’ thoughts beyond typical comfort zones, and consider alternative modes of responding to challenges posed by preplanned death.

Results:
Studies indicate that, for their own end-of-life circumstances, physicians would prefer a briefer, higher quality life to prolonged low-quality life, dignity in infirmity and death, and avoidance of terminal suffering. Lay people generally endorse similar preferences. Although contemporary society generally shuns contemplating preplanned death, cultural attitudes regarding preplanned death are rapidly evolving, and variations of “Death with Dignity” legislation have gained traction in increasing numbers of US states as well as internationally. As yet, no broad consensus exists as to how clinicians should manage circumstances involving preplanned death.

Conclusions:
Considerations regarding preplanned deaths merit greater professional and public discussion. Many options exist for improving how professionals address the quality of human experiences surrounding death.
The Ideal Hospital Discharge Summary: A Survey of U.S. Physicians
Authors: Sorita Atsushi , Robelia Paul M. , Kattel Sharma B. , McCoy Christopher P. , Keller Allan Scott , Almasri Jehad , Murad Mohammad Hassan , Newman James S. , Kashiwagi Deanne T. 
Published: September 2017

Background
Hospital discharge summaries enable communication between inpatient and outpatient physicians. Despite existing guidelines for discharge summaries, they are frequently suboptimal.

Objective
The aim of this study was to assess physicians’ perspectives about discharge summaries and the differences between summaries’ authors (hospitalists) and readers (primary care physicians [PCPs]).

Methods
A national survey of 1600 U.S. physicians was undertaken. Primary measures included physicians’ preferences in discharge summary standardization, content, format, and audience.

Results
A total of 815 physicians responded (response rate = 51%). Eighty-nine percent agreed that discharge summaries “should have a standardized format.” Most agreed that summaries should “document everything that was done, found, and recommended in the hospital” (64%) yet “only include details that are highly pertinent to the hospitalization” (66%). Although 74% perceived patients as an important audience of discharge summaries, only 43% agreed that summaries “should be written in language that patients…can easily understand,” and 68% agreed that it “should be written solely for provider-to-provider communication.” Compared with hospitalists, PCPs preferred comprehensive summaries (68% versus 59%, P = 0.002). More PCPs agreed that separate summaries should be created for patients and for provider-to-provider communication than hospitalists (60% versus 47%, P < 0.001). Compared with PCPs, more hospitalists believe that “hospitalists are too busy to prepare a high-quality discharge summary” (44% versus 23%, P < 0.001) and “PCPs have insufficient time to read an entire discharge summary” (60% versus 38%, P < 0.001).

Conclusions
Physicians believe that discharge summaries should have a standardized format but do not agree on how comprehensive or in what format they should be. Efforts are necessary to build consensus toward the ideal discharge summary.
The Effectiveness of Oxidized Regenerated Cellulose as a Graft Material in Transalveolar Osteotome Sinus Lift Procedure
Authors: Hussein Laith A. , Hassan Thair A.L. 
Published: September 2017

Abstract
The posterior maxilla is challenged with postextraction alveolar bone resorption and pneumatization drive of the Schneiderian membrane that reduces the subantral distance. To overcome such anatomic obstacle a sinus augmentation procedure was introduced either via lateral or crestal approach depending on residual ridge height. The current study evaluated oxidized regenerated cellulose (ORC) as a grafting material versus osteon II by measuring bone gain and graft density, 24 weeks postoperatively. Twenty consecutive patients (24 cases) aged from 20 to 65 years were considered eligible after clinical and radiographic evaluation. These patients were allocated in 2 groups (study and control) that underwent transcrestal osteotome antral membrane balloon elevation and surgical void augmentation with ORC in the study group, while the control group grafted with collagen membrane and osteon II with simultaneous dental implant placement in both groups and were followed up for 1 year. Cone beam computed tomography was taken for all patients preoperatively and postoperatively to verify neoformed bone and density in Hounsfield units (HU). The mean gained height of the bone was 6.48 mm (5.94 mm in the study and 7.02 mm in the control). The mean density of graft above implant apex was 497.99 HU (434.23 HU in the study and 561.75 HU in the control). Apart from Schneider membrane thickening in 2 patients from the control group, there were no serious complications reported throughout the study. These results demonstrate that ORC is a reasonable grafting material with comparable outcomes when compared to osteon II with less postoperative complications.
Ethylene Glycol Poisoning Should Not Contraindicate Liver Donation
Authors: Burman Alisha , Watson Christopher J. E. , Kosmoliaptsis Vasilis 
Published: September 2017

Abstract
As the number of patients waiting to receive transplants increases, there is a need to explore all possible donation opportunities. In this case report, we describe the transplantation of a liver from a donor who died after ethylene glycol poisoning into a woman with alcoholic liver disease with cirrhosis and associated ascites. Donor management, including ethanol, fomepizol and haemodialysis, hastened clearance of ethylene glycol from the circulation, and after liver transplantation, the recipient exhibited no adverse effects suggestive of ethylene glycol toxicity, although recipient hepatic artery dissection and thrombosis necessitated retransplantation. Our experience suggests that donor death due to ethylene glycol intoxication should not contraindicate liver transplantation, particularly after appropriate donor management.
Diagnostic Utility of Repetitive Nerve Stimulation in a Large Cohort of Patients With Myasthenia Gravis
Authors: Amandusson Åsa , Elf Kristin , Grindlund Margareta E. , Punga Anna R. 
Published: September 2017

Purpose:
Optimizing the diagnostic utility of repetitive nerve stimulation in myasthenia gravis (MG) may include tailoring the examination to clinical phenotype. Therefore, we analyzed all available repetitive nerve stimulation parameters in a large cohort of patients with confirmed MG diagnosis.

Methods:
All repetitive nerve stimulation examinations at the Uppsala University Hospital rendering an MG diagnosis during 1996 to 2014 were analyzed. The deltoid, trapezius, anconeus, nasalis, abductor digiti quinti, and frontalis muscles were examined.

Results:
Two hundred one patients with MG were diagnosed. Abnormal amplitude decrement was found in 54% of patients with ocular MG, 77% of patients with predominantly bulbar fatigue, and in 83% of patients with predominantly limb fatigue. The deltoid muscle had the highest sensitivity in all MG subtypes, with a mean of 77% sensitivity in all clinical subtypes, and the most pronounced decrement for amplitude (P = 0.0002) and area (P < 0.0001). Technical issues were rare.

Conclusions:
These data contribute to further optimization of repetitive nerve stimulation strategies regarding muscle selection and technical performance in the electrodiagnostic workup of MG.
Dose-dependent effects of inhaled corticosteroids on bone mineral density in postmenopausal women with asthma or COPD: A registry-based cohort study
Authors: Chen Wenjia , Johnson Kate M. , FitzGerald J. Mark , Sadatsafavi Mohsen , Leslie William D. 
Published: September 2017

ABSTRACTBackgroundThe effect of long-term inhaled corticosteroid (ICS) therapy on the bone health of older adults remains unclear due to its possible impact on bone mineral density (BMD).ObjectiveTo evaluate, cross-sectionally and longitudinally, the impact of ICS use on BMD in postmenopausal women with asthma or chronic obstructive pulmonary disease (COPD).MethodsWe used a population-based bone densitometry registry linked with administrative health data of the province of Manitoba, Canada (1999–2013), to identify women with diagnosed asthma or COPD. ICS use was defined as cumulative dispensed days prior to baseline BMD (cross-sectional analysis), and medication possession ratio (MPR) between two BMD measurements (longitudinal analysis). Results were adjusted for multiple covariates including the underlying respiratory diagnosis and its severity.ResultsIn the cross sectional analysis, compared with non-users, women with the highest tertile of prior ICS exposure had lower baseline BMD at the femoral neck (-0.09 standard deviations [SD] below a healthy young adult, 95% CI: −0.16, −0.02) and total hip (-0.14 SD, 95% CI: −0.22, −0.05), but not at the lumbar spine. Longitudinally, the highest tertile of ICS exposure was associated with a slight decline in total hip BMD relative to non-users (-0.02 SD/year, 95% CI: −0.04, −0.01), with no significant effect at the femoral neck and lumbar spine. Middle and lower tertiles of ICS use had no significant effects.ConclusionHigh exposure to ICS was associated with a small adverse effect on baseline hip BMD and total hip BMD loss in post-menopausal women with asthma or COPD.
Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome
Authors: Rahman Sumayah F. , Olm Matthew R. , Morowitz Michael J. , Banfield Jillian F. 
Published: September 2017

AbstractAntibiotic resistance in pathogens is extensively studied, yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leverage genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We find that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly,Clostridium difficilestrains harboring this gene are at higher abundance in formula-fed infants compared toC. difficilelacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have faster replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism’s direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data into five principal components classified by boosted decision trees. Among the genes involved in predicting if an organism increased in relative abundance after treatment are those that encode for subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics and predict how organisms in the gut microbiome will respond to antibiotic administration.ImportanceThe process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows for unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome. Using genomes from metagenomes, we built a machine learning model to predict how organisms in the gut microbial community respond to perturbation by antibiotics. This may eventually have clinical and industrial applications.
CDK1 and PLK1 co-ordinate the disassembly and re-assembly of the Nuclear Envelope in vertebrate mitosis
Authors: de Castro Ines J , Sales Gil Raquel , Ligammari Lorena , Di Giacinto Maria Laura , Vagnarelli Paola 
Published: September 2017

ABSTRACTMicronuclei (MN) arise from chromosomes or fragments that fail to be incorporated into the primary nucleus after cell division. These structures are a major source of genetic instability caused by DNA repair and replication defects coupled to aberrant Nuclear Envelope (NE). These problems ultimately lead to a spectrum of chromosome rearrangements called chromothripsis, a phenomenon that is a hallmark of several cancers. Despite its importance, the molecular mechanism at the origin of this instability is still not understood. Here we show that lagging chromatin, although it can efficiently assemble Lamin A/C, always fails to recruit Nuclear Pore Complexes (NPCs) proteins and that Polo-Like Kinase (PLK1) negatively regulates the NPC assembly. We also provide evidence for the requirement of PLK1 activity for the disassembly of NPCs, but not Lamina (A/C), at mitotic entry. Altogether this study reveals the existence of independent regulatory pathways for Lamin A/C and NPC reorganization during mitosis where Lamin A targeting to the chromatin is controlled by CDK1 activity (a clock-based model) while the NPC loading is also spatially monitored by PLK1.
Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements
Authors: Lewis Samuel H. , Quarles Kaycee A. , Yang Yujing , Tanguy Melanie , Frézal Lise , Smith Stephen A. , Sharma Prashant P. , Cordaux Richard , Gilbert Clément , Giraud Isabelle , Collins David H. , Zamore Phillip D. , Miska Eric A. , Sarkies Peter , Jiggins Francis M. 
Published: September 2017

AbstractIn animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were likely present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and mRNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders, scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.
The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis)
Authors: Menon Mitra , Bagley Justin C. , Friedline Christopher , Whipple Amy V. , Schoettle Anna W. , leal-Saenz Alejandro , Wehenkel Christian , Molina-Freaner Francisco , Flores-Renteria Lluvia , Gonzalez-Elizondo M. Socorro , Sniezko Richard A. , Cushman Samuel A. , Waring Kristen M. , Eckert Andrew J. 
Published: September 2017

AbstractInteractions between extrinsic factors, such as disruptive selection, and intrinsic factors, such as genetic incompatibilities among loci, can contribute to the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow throughout their divergence history. We investigated the process of speciation and the maintenance of species boundaries betweenPinus strobiformisandP.flexilis. Utilizing ecological niche modeling, demographic modeling, and genomic cline analyses, we illustrated a history of divergence with continuous gene flow between these species. We found an abundance of advanced generation hybrids and a lack of loci exhibiting large allele frequency differences across the hybrid zone. Additionally, we found evidence for climate-associated variation in the hybrid index and niche divergence between parental species and the hybrid zone. Our results are consistent with extrinsic factors, such as climate, being an important isolating mechanism for these species. A buildup of intrinsic incompatibilities and of co-adapted gene complexes is also apparent in our results, although these appear to be in the earliest stages of development. This supports previous work in coniferous species demonstrating the importance of extrinsic factors in creating and enforcing species boundaries. Overall, we lend support to the hypothesis that varying strengths and directions of selection pressures across the long lifespans of conifers, in combination with their life history strategies, delay the evolution of strong intrinsic incompatibilities.
Take-off and landing control for a coaxial ducted fan unmanned helicopter
Authors: Chen Zhi , Wang Daobo , Zhen Ziyang , Wang Biao , Fu Jian 
Published: September 2017

Purpose
This paper aims to present a control strategy that eliminates the longitudinal and lateral drifting movements of the coaxial ducted fan unmanned helicopter (UH) during autonomous take-off and landing and reduce the coupling characteristics between channels of the coaxial UH for its special model structure.

Design/methodology/approach
Unidirectional auxiliary surfaces (UAS) for terminal sliding mode controller (TSMC) are designed for the flight control system of the coaxial UH, and a hierarchical flight control strategy is proposed to improve the decoupling ability of the coaxial UH.

Findings
It is demonstrated that the proposed height control strategy can solve the longitudinal and lateral movements during autonomous take-off and landing phase. The proposed hierarchical controller can decouple vertical and heading coupling problem which exists in coaxial UH. Furthermore, the confronted UAS-TSMC method can guarantee finite-time convergence and meet the quick flight trim requirements during take-off and landing.

Research limitations/implications
The designed flight control strategy has not implemented in real flight test yet, as all the tests are conducted in the numerical simulation and simulation with a hardware-in-the-loop (HIL) platform.

Social implications
The designed flight control strategy can solve the common problem of coupling characteristics between channels for coaxial UH, and it has important theoretical basis and reference value for engineering application; the control strategy can meet the demands of engineering practice.

Originality/value
In consideration of the TSMC approach, which can increase the convergence speed of the system state effectively, and the high level of response speed requirements to UH flight trim, the UAS-TSMC method is first applied to the coaxial ducted fan UH flight control. The proposed control strategy is implemented on the UH flight control system, and the HIL simulation clearly demonstrates that a much better performance could be achieved.