bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationships Between Components of Emotional Intelligence and Suicidal Behavior in Alcohol-dependent Patients
Authors: Kopera Maciej , Jakubczyk Andrzej , Klimkiewicz Anna , Suszek Hubert , Krasowska Aleksandra , Brower Kirk J. , Wojnar Marcin
Published: September 2017

Objectives:

The importance of investigating various emotional skills in assessment of suicide risk in alcohol-dependent (AD) individuals has recently become the focus of increasing interest. The objective of this study was to explore the relationships between self-reported components of emotional intelligence and lifetime prevalence of suicide attempts in a clinical sample of AD subjects.

Methods:

A group of 80 inpatients entering an alcohol treatment program in Warsaw, Poland, was recruited. Baseline information about demographics, psychopathological symptoms, personality, and severity of alcohol problems was obtained. The Schutte Self-Report Emotional Intelligence Test was utilized for assessment of emotional processing. Lifetime history of suicide attempts was obtained from the MINI International Neuropsychiatric Interview.

Results:

After accounting for affect-related suicide risk factors (severity of depression, anxiety, neuroticism), and also other significant predictors (eg, age, sex, history of childhood abuse), mood regulation/optimism deficits remained a significant correlate of lifetime suicide attempts in AD patients. In the mediation models, mood regulation appeared to fully mediate the relationship between history of suicide attempts and depression, and also neuroticism.

Conclusions:

The results of this study support the evidence that poor mood regulation might be related to the risk for suicidal behavior in AD individuals. These findings point towards the significance of addressing the issue of emotion-related skills in the therapy of those AD subjects who are at risk for suicide.
Obesity Increases Risk of Loss of Reduction After Casting for Diaphyseal Fractures of the Radius and Ulna in Children: An Observational Cohort Study
Authors: DeFrancesco Christopher J. , Rogers Benjamin H. , Shah Apurva S.
Published: September 2017

Objectives:

To determine if high body mass index (BMI) increases the risk of loss of reduction (LOR) following closed reduction and casting for displaced concomitant fractures of the radial and ulnar shafts in pediatric patients.

Design:

Retrospective cohort study.

Setting:

A single, tertiary care, urban children's hospital.

Patients/Participants:

Pediatric patients 2–18 years of age with closed, displaced, concomitant diaphyseal fractures of the radius and ulna (OTA/AO 22-A3) who underwent closed reduction and casting at the study site.

Main Outcome Measures:

BMI percentile of ≥95 was defined as obese. For nonobese patients, BMI percentile of ≥85 was defined as overweight. BMI percentile category, fracture angulation, sex, age, fracture location, and number of follow-up visits were recorded. Radiographs and health records were reviewed to note clinical and radiographic cases of LOR. The primary outcome was LOR (clinical or radiographic).

Results:

Overall, 124 subjects (74 male and 50 female subjects) underwent acceptable closed reduction and casting. Median patient age was 7.6 years (range, 2.2–17.8 years). There were 14 cases of LOR. LOR rates were 7.2%, 16.7%, and 44.4% for the nonoverweight, overweight, and obese cohorts, respectively (P = 0.005). Regression analysis revealed that LOR was positively associated with higher BMI category (odds ratio for overweight 4.49; P = 0.082; odds ratio for obese 7.52; P = 0.020) and patient age in years (odds ratio, 1.38; P = 0.001).

Conclusions:

Given the high risk of LOR in overweight and obese children with displaced concomitant fractures of the radial and ulnar shafts, our findings suggest that attentive and frequent follow-up is warranted. In these patients, the initial reduction should be closely scrutinized, and a lower threshold for surgical fixation may be considered.

Level of Evidence:

Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
External Validation of Six Pediatric Fever and Neutropenia Clinical Decision Rules
Authors: Haeusler Gabrielle M. , Thursky Karin A. , Slavin Monica A. , Mechinaud Francoise , Babl Franz E. , Bryant Penelope , De Abreu Lourenco Richard , Phillips Robert
Published: September 2017

Background:

Fever and neutropenia (FN) clinical decision rules (CDRs) are recommended to help distinguish children with cancer at high and low risk of severe infection. The aim of this study was to validate existing pediatric FN CDRs designed to stratify children with cancer at high or low risk of serious infection or medical complication.

Methods:

Pediatric CDRs suitable for validation were identified from a literature search. Relevant data were extracted from an existing data set of 650 retrospective FN episodes in children with cancer. The sensitivity and specificity of each of the CDR were compared with the derivation studies to assess reproducibility.

Results:

Six CDRs were identified for validation: 2 were designed to predict bacteremia and 4 to predict adverse events. Five CDRs exhibited reproducibility in our cohort. A rule predicting bacteremia had the highest sensitivity (100%; 95% confidence interval (CI): 93%–100%) although poor specificity (17%), with only 15% identified as low risk. For adverse events, the highest sensitivity achieved was 84% (95% CI: 75%–90%), with specificity of 29% and 27% identified as low risk. A rule intended for application after a 24-hour period of inpatient observation yielded a sensitivity of 80% (95% CI: 73–86) and specificity of 46%, with 44% identified as low risk.

Conclusions:

Five CDRs were reproducible, although not all can be recommended for implementation because of either inadequate sensitivity or failure to identify a clinically meaningful number of low-risk patients. The 24-hour rule arguably exhibits the best balance between sensitivity and specificity in our population.
Spinal Epidural Abscess Caused by Gardnerella vaginalis and Prevotella amnii
Authors: Stewart Leslie , Sinha Saurabh , Madsen Peter J. , Glaser Laurel , Chen H. Isaac , Culyba Matthew J.
Published: September 2017

We report a case of spinal epidural abscess in a 58-year-old woman who had recently been diagnosed with gonococcal infection, but did not receive guideline-recommended therapy. She presented with back pain as well as signs and symptoms of pelvic inflammatory disease (PID). Magnetic resonance imaging of the spine demonstrated epidural abscess extending from T10 to L4/L5. She underwent T10/L1 and L3/L4 laminectomies for evacuation of the abscess and Gardnerella vaginalis and Prevotella amnii were isolated from the abscess fluid cultures. Our case demonstrates spinal epidural abscess as a rare, but morbid complication of PID and highlights the pathogenic potential of the anaerobic flora associated with PID.
Exploring the Perceived Value of a Personalized Informatics Tool to Anticipate and Mitigate Patient Risk
Authors: Kneeland Michael D. , Ivory Catherine H. , Bloomingburg Phebe , Choma Neesha N.
Published: September 2017

Health care systems are implementing a myriad of strategies to improve patient outcomes and reduce both adverse events and unplanned readmissions. These approaches include interventions related to people, processes, and technology. This article describes the development of a technology-based model in the form of an actionable risk profile, which was used by one inpatient surgical unit (people) during a daily care team briefing (process). The risk profile was evaluated for its perceived value to the care team as a method of organizing care and anticipating patients' needs. Preliminary findings of the proof of concept are presented along with recommendations for practice and research.
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.
Project HANDS
Authors: Crowell Judybeth , O'Neil Karen , Drager Leslie
Published: September 2017

Increasing short peripheral catheter (SPC) dwell time is becoming common practice. A number of variables lead to unscheduled restarts and significant complications with SPCs. Preventing complications is important to patient outcomes as dwell time increases. This quality improvement project compared the use of a manufactured securement device versus tape and transparent occlusive dressing while instituting a standardized insertion and care bundle with a 96-hour dwell time. Major findings included no statistically significant difference in restart rates in SPCs secured with a device compared with those secured with tape and transparent occlusive dressing (P = .06). These results differ from other published studies and may be due to the traditional nature of the hospital's infusion team and patients' average length of stay.
Understanding the Patient Experience of Peripherally Inserted Central Catheter-Related Deep Vein Thrombosis Using Interpretive Phenomenology
Authors: Meyer Britt M.
Published: September 2017

The purpose of this interpretive phenomenological study was to determine what it means to patients to live with a peripherally inserted central catheter (PICC)-related deep vein thrombosis and to describe the influence of the experience on the individual's quality of life. The sample included 11 adult patients from an acute care setting who developed a PICC-related symptomatic thrombus between November 2014 and March 2016, using purposive sampling. Three distinct themes emerged from the data in this study: a loss of trust in health care providers, additional burdens to existing problems, and a yearning for understanding.
High-Dose Subcutaneous Immunoglobulin in Patients With Multifocal Motor Neuropathy
Authors: Rasutis Vilija M. , Katzberg Hans D. , Bril Vera
Published: September 2017

Multifocal motor neuropathy (MMN), an immune neuromuscular condition causing progressive weakness, usually responds to immune-mediated treatments, including intravenous immunoglobulin (IVIG). Fifteen patients with MMN receiving IVIG were enrolled in an open-label, single-center trial and switched to 20% subcutaneous immunoglobulin (SCIG) using a smooth transition protocol (ie, changing the therapy without interruption or impact on the intended outcome of the therapy). Patients received individualized training and support based on motivation and ability to learn, follow directions, and maintain compliance. Although some patients required assistance during the training phase, most managed self-infusion and reported satisfaction in managing therapy autonomously. Educating patients with neuropathies to self-infuse high-dose SCIG at home and with flexibility in dosing schedules was successfully demonstrated in this patient group.
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

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

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.
Sneeze to leave: African wild dogs (Lycaon pictus) use variable quorum thresholds facilitated by sneezes in collective decisions
Authors: Walker Reena H. , King Andrew J. , McNutt J. Weldon , Jordan Neil R.
Published: September 2017

In despotically driven animal societies, one or a few individuals tend to have a disproportionate influence on group decision-making and actions. However, global communication allows each group member to assess the relative strength of preferences for different options among their group-mates. Here, we investigate collective decisions by free-ranging African wild dog packs in Botswana. African wild dogs exhibit dominant-directed group living and take part in stereotyped social rallies: high energy greeting ceremonies that occur before collective movements. Not all rallies result in collective movements, for reasons that are not well understood. We show that the probability of rally success (i.e. group departure) is predicted by a minimum number of audible rapid nasal exhalations (sneezes), within the rally. Moreover, the number of sneezes needed for the group to depart (i.e. the quorum) was reduced whenever dominant individuals initiated rallies, suggesting that dominant participation increases the likelihood of a rally's success, but is not a prerequisite. As such, the ‘will of the group’ may override dominant preferences when the consensus of subordinates is sufficiently great. Our findings illustrate how specific behavioural mechanisms (here, sneezing) allow for negotiation (in effect, voting) that shapes decision-making in a wild, socially complex animal society.
Plant defences limit herbivore population growth by changing predator–prey interactions
Authors: Kersch-Becker Mônica F. , Kessler André , Thaler Jennifer S.
Published: September 2017

Plant quality and predators are important factors affecting herbivore population growth, but how they interact to regulate herbivore populations is not well understood. We manipulated jasmonate-induced plant resistance, exposure to the natural predator community and herbivore density to test how these factors jointly and independently affect herbivore population growth. On low-resistance plants, the predator community was diverse and abundant, promoting high predator consumption rates. On high-resistance plants, the predator community was less diverse and abundant, resulting in low predator consumption rate. Plant resistance only directly regulated aphid population growth on predator-excluded plants. When predators were present, plant resistance indirectly regulated herbivore population growth by changing the impact of predators on the herbivorous prey. A possible mechanism for the interaction between plant resistance and predation is that methyl salicylate, a herbivore-induced plant volatile attractive to predators, was more strongly induced in low-resistance plants. Increased plant resistance reduced predator attractant lures, preventing predators from locating their prey. Low-resistance plants may regulate herbivore populations via predators by providing reliable information on prey availability and increasing the effectiveness of predators.
Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs
Authors: Li Hu , Leavengood John M. , Chapman Eric G. , Burkhardt Daniel , Song Fan , Jiang Pei , Liu Jinpeng , Zhou Xuguo , Cai Wanzhi
Published: September 2017

Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats.
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

Background

The 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).

Objective

To evaluate, cross-sectionally and longitudinally, the impact of ICS use on BMD in postmenopausal women with asthma or chronic obstructive pulmonary disease (COPD).

Methods

We 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.

Results

In 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.

Conclusion

High 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

Antibiotic 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.

Importance

The 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

Micronuclei (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

In 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

Interactions 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.
Enabling rapid cloud-based analysis of thousands of human genomes via Butler
Authors: Yakneen Sergei , Waszak Sebastian M. , Gertz Michael , Korbel Jan O.
Published: September 2017

We present Butler, a computational framework developed in the context of the international Pan-cancer Analysis of Whole Genomes (PCAWG)1 project to overcome the challenges of orchestrating analyses of thousands of human genomes on the cloud. Butler operates equally well on public and academic clouds. This highly flexible framework facilitates management of virtual cloud infrastructure, software configuration, genomics workflow development, and provides unique capabilities in workflow execution management. By comprehensively collecting and analysing metrics and logs, performing anomaly detection as well as notification and cluster self-healing, Butler enables large-scale analytical processing of human genomes with 43% increased throughput compared to prior setups. Butler was key for delivering the germline genetic variant call-sets in 2,834 cancer genomes analysed by PCAWG1.
Solid-phase reverse transfection for intracellular delivery of functionally active proteins
Authors: Bulkescher Ruben , Starkuviene Vytaute , Erfle Holger
Published: September 2017

Delivery of large and functionally active biomolecules across cell membranes presents a challenge in cell biological experimentation. For this purpose, we developed a novel solid-phase reverse transfection method that is suitable for the intracellular delivery of proteins into mammalian cells with preservation of their function. We show results for diverse application areas of the method, ranging from antibody-mediated inhibition of protein function to CRISPR/Cas9-based gene editing in living cells. Our method enables prefabrication of “ready to transfect” substrates carrying diverse proteins. This allows their easy distribution and standardization of biological assays across different laboratories.
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.
Double surrogate modeling usage in PSO
Authors: Pehlivanoglu Volkan Yasin
Published: September 2017

Purpose

The purpose of this paper is to improve the efficiency of particle optimization method by using direct and indirect surrogate modeling in inverse design problems.

Design/methodology/approach

The new algorithm emphasizes the use of a direct and an indirect design prediction based on local surrogate models in particle swarm optimization (PSO) algorithm. Local response surface approximations are constructed by using radial basis neural networks. The principal role of surrogate models is to answer the question of which individuals should be placed into the next swarm. Therefore, the main purpose of surrogate models is to predict new design points instead of estimating the objective function values. To demonstrate its merits, the new approach and six comparative algorithms were applied to two different test cases including surface fitting of a geographical terrain and an inverse design of a wing, the averaged best-individual fitness values of the algorithms were recorded for a fair comparison.

Findings

The new algorithm provides more than 60 per cent reduction in the required generations as compared with comparative algorithms.

Research limitations/implications

The comparative study was carried out only for two different test cases. It is possible to extend test cases for different problems.

Practical implications

The proposed algorithm can be applied to different inverse design problems.

Originality/value

The study presents extra ordinary application of double surrogate modeling usage in PSO for inverse design problems.
How family firms execute open innovation strategies: the Loccioni case
Authors: Casprini Elena , De Massis Alfredo , Di Minin Alberto , Frattini Federico , Piccaluga Andrea
Published: September 2017

Purpose

This paper aims to shed light on how family firms execute open innovation strategies by managing internal and external knowledge flows.

Design/methodology/approach

First, through a comprehensive literature review, the paper identifies the barriers to the acquisition and transfer of knowledge in open innovation processes. Second, it presents and discusses the results of an exploratory case study on Loccioni, an Italian family firm providing high-tech measurement solutions, highlighting how this family firm managed to overcome the barriers in executing an open innovation strategy.

Findings

The case study shows that Loccioni faced specific challenges in acquiring and transferring knowledge in its open innovation processes and developed two idiosyncratic capabilities – labelled imprinting and fraternization – that helped the firm overcome the barriers to knowledge acquisition and transfer. The analysis shows that these two capabilities are enabled by the distinctive goals and social capital characterizing family firms.

Originality/value

The paper creates a link between open innovation and family business research with an empirically grounded model illustrating how the idiosyncratic capabilities of a family firm help overcome the critical barriers to the acquisition and transfer of knowledge in executing an open innovation strategy.
Post‐Sovereignty and the European Legal Space
Authors: Gibbs Nathan
Published: September 2017

The political constitution of the European polity has become strained in recent years by insistent pressures on its institutional capacity to resolve social problems. The article examines the EU's polity crisis in the context of the development of a distinctive modern conception of secular constitutional authority, focused on the ideal of sovereign self‐determination. As the work of Neil MacCormick illustrates, the EU provides a radical challenge to the on‐going capacity of the concept of sovereignty to provide a framework to address problems of legitimacy. The article explores the nature of this challenge, its historical context and its consequences with reference to debates over the nature of constitutional pluralism. It sets out a path to the renewal of the European constitutional debate through a re‐consideration of secular constitutional authority and the necessity of its connection to the idea of sovereignty. The article seeks to re‐engage in the task of ‘questioning sovereignty’.
Ex Turpi Causa: Reformation not Revolution
Authors: Lim Ernest
Published: September 2017

Seldom has an area of law been so afflicted with uncertainties and contradictions as the illegality defence and rarely have judicial opinions been so sharply divided as in the Supreme Court decision in Patel v Mirza where nine Justices examined the issue of the correct approach to the illegality defence. Six of them endorsed the ‘range of factors’ approach, whereas three condemned it. This paper defends the majority's approach against the minority's criticisms but argues that refinements should be made to it in order to address the uncertainty that may arise from its application.
A Director's Duty of Loyalty and the Relevance of the Company's Scope of Business: Cheng Wai Tao v Poon Ka Man Jason
Authors: Koh Pearlie
Published: September 2017

The Hong Kong Court of Final Appeal has utilised a ‘scope of business’ inquiry to delineate the boundaries of the no‐conflict rule for the company director. Such an inquiry is directed at discerning the realistic ability of the company to exploit any particular business opportunity and a strict capacity approach is eschewed, at least where the no‐conflict rule is concerned. The decision is premised on a bifurcation between the no‐conflict and no‐profit rules, suggesting that the tests to determine breach of these fiduciary rules are not necessarily the same, thus permitting a more nuanced consideration of directorial breaches.
Reputational leadership and preference similarity: Explaining organisational collaboration in bank policy networks
Authors: JAMES SCOTT , CHRISTOPOULOS DIMITRIS
Published: September 2017

This article contributes to our understanding of the formation of policy networks. Research suggests that organisations collaborate with those that are perceived to be influential in order to access scarce political resources. Other studies show that organisations prefer to interact with those that share core policy beliefs on the basis of trust. This article seeks to develop new analytical tools for testing these alternative hypotheses. First, it measures whether perceptions of reputational leadership affect the likelihood of an organisation being the target or instigator of collaboration with others. Second, it tests whether the degree of preference similarity between two organisations makes them more or less likely to collaborate. The article adopts a mixed‐methods approach, combining exponential random graph models (ERGM) with qualitative interviews, to analyse and explain organisational collaboration around United Kingdom banking reform. It is found that reputational leadership and preference similarity exert a strong, positive and complementary effect on network formation. In particular, leadership is significant whether this is measured as an organisational attribute or as an individually held perception. Evidence is also found of closed or clique‐like network structures, and heterophily effects based on organisational type. These results offer significant new insights into the formation of policy networks in the banking sector and the drivers of collaboration between financial organisations.