bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel Bronchoscopic Management of Airway Bleeding With Absorbable Gelatin and Thrombin Slurry
Authors: Peralta A. Rolando , Chawla Mohit , Lee Robert P.
Published: January 2018

Background:

Airway bleeding, either spontaneous or as a result of bronchoscopy, is associated with significant morbidity and mortality. Multiple bronchoscopic techniques are available to achieve complete hemostasis or as a bridge to definitive therapies.

Methods:

We report our experience on the feasibility of endobronchial instillation of an absorbable gelatin and thrombin slurry (GTS) for the treatment of spontaneous hemoptysis and procedure-related bleeding.

Results:

We identified 13 cases in which GTS was used for endobronchial hemostasis when standard bronchoscopic measures like cold saline, epinephrine, and in some cases balloon occlusion were not successful. GTS was delivered through the working channel of the bronchoscope in 10 cases and through the distal port of a bronchial blocker in the remaining 3 cases. Median age was 69 years (range, 52 to 79 y). Eight cases corresponded to spontaneous hemoptysis and 5 cases to diagnostic or therapeutic procedures. Bleeding was considered severe in 9 (70%) cases. All but 1 case were associated with malignancy. Hemostasis was achieved in 10 (77%) cases by using standard measures in addition to GTS. No patient adverse events at 30 days or damage to the equipment were identified.

Conclusions:

Bronchoscopic instillation of an absorbable GTS is feasible and may be used in cases of spontaneous or procedure-related bleeding in addition to conventional measures. It can be delivered through the working channel of the bronchoscope or through the distal port available in some bronchial blockers. Controlled studies are necessary to determine the safety and efficacy of this novel technique.
Atypical Teratoid Rhabdoid Tumor of the Cauda Equina in a Child: Report of a Very Unusual Case
Authors: Shiflett James M. , Herrington Betty L. , Joyner David A. , Saad Ali G.
Published: January 2018

Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive malignant primitive neoplasms that commonly occur in children younger than 2 years of age. The prognosis is generally dismal with a median survival time of <1 year. The majority of AT/RT occur in the posterior fossa and less frequently the supratentorium. Primary pediatric spinal AT/RT are exceedingly rare and only 15 cases have been reported to date. Here we report a very unusual case of primary spinal AT/RT extensively involving the spinal cord from T11 down to the cauda equina. In this patient, the tumor was highly aggressive and resulted in extensive dissemination into the nerve roots and paraspinal soft tissue rapidly resulting in the patient’s death 1 month after diagnosis. to the best of our knowledge, this degree of involvement of the spine by a primary AT/RT has not been described before.
Use of Point-of-Care Ultrasound to Guide Pediatric Gastrostomy Tube Replacement in the Emergency Department
Authors: Myatt Toby C. , Medak Anthony J. , Lam Samuel H.F.
Published: January 2018

The presentation of a pediatric patient to the emergency department for a malfunctioning or dislodged gastrostomy tube (G-tube) is not uncommon. As such, these tubes are often replaced at the bedside. Improper placement can result in a number of complications, including perforation, fistula tract formation, peritonitis, and sepsis. The current criterion standard method to confirm proper G-tube placement is contrast-enhanced radiography. However, point-of-care ultrasound may be an alternative method to guide and confirm pediatric G-tube replacement in the emergency department. We report a series of cases on this novel point-of-care ultrasound application.
Video Recordings to Analyze Preventable Management Errors in Pediatric Resuscitation Bay
Authors: Borns Julia , Ersch Jörg , Dobrovoljac Milana , Staubli Georg , Brotschi Barbara
Published: January 2018

Objective

In treating patients of different ages and diseases in the pediatric resuscitation bay, management errors are common. This study aimed to analyze the adherence to advanced trauma life support and pediatric advanced life support guidelines and identify management errors in the pediatric resuscitation bay by using video recordings.

Methods

Video recording of all patients admitted to the pediatric resuscitation bay at University Children's Hospital Zurich during a 13-month period was performed. Treatment adherence to advanced trauma life support guidelines and pediatric advanced life support guidelines and errors per patient were identified.

Results

During the study period, 128 patients were recorded (65.6% with surgical, 34.4% with medical diseases). The most common causes for admission were traumatic brain injury (21.1%), multiple trauma (20.3%), and seizures (14.8%). There was a statistically significant correlation between accurate handover from emergency medical service to hospital physicians and adherence to airway, breathing, circulation, and disability sequence (correlation coefficient [CC], 0.205; P = 0.021), existence of a defined team leader and adherence to airway, breathing, circulation, and disability sequence (CC, 0.856; P < 0.001), and accurate hand over and existence of a defined team leader (CC, 0.186; P = 0.037). Unexpected errors were revealed. Cervical spine examination/stabilization was omitted in 40% of admitted surgical patients, even in 20% of patients with an injury of spine/limbs.

Conclusions

Video recording is a useful tool to evaluate patient management in the pediatric resuscitation bay. Analyzing errors of missing the adherence to the guidelines helps to pay attention and focus on specific items to improve patient care.
Trends in Severe Pediatric Emergency Conditions in a National Cohort, 2008 to 2014
Authors: Michelson Kenneth A. , Hudgins Joel D. , Burke Laura G. , Lyons Todd W. , Monuteaux Michael C. , Bachur Richard G. , Finkelstein Jonathan A.
Published: January 2018

Objective

The objective of this study was to determine the incidence and recent trends in serious pediatric emergency conditions.

Methods

We conducted a cross-sectional study of the Nationwide Emergency Department Sample from 2008 through 2014, and included patients with age below 18 years with a serious condition, defined as each diagnosis group in the diagnosis grouping system with a severity classification system score of 5. We calculated national incidences for each serious condition using annualized weighted condition counts divided by annual United States census child population counts. We determined the highest-incidence serious conditions over the study period and calculated percentage changes between 2008 and 2014 for each serious condition using a Poisson model.

Results

The 2008 incidence of serious conditions across the national child population was 1721 visits per million person-years (95% confidence interval, 1485–1957). This incidence increased to 2020 visits per million person-years (95% confidence interval, 1661–2379) in 2014. The most common serious conditions were serious respiratory diseases, septicemia, and serious neurologic diseases. Anaphylaxis was the condition with the largest change, increasing by 147%, from 101 to 249 visits per million person-years.

Conclusions

The most common serious condition in children presenting to United States emergency departments is serious respiratory disease. Anaphylaxis is the fastest increasing serious condition. Additional research attention to these diagnoses is warranted.
Pediatric Pelvic Fractures and Differences Compared With the Adult Population
Authors: de la Calva Carolina , Jover Nadia , Alonso Jaime , Salom Marta
Published: January 2018

Introduction

Although pelvic fractures in children are rare, because of anatomical differences between an adult's skeleton and a child's skeleton, these lesions in the pediatric population have specific characteristics that need to be borne in mind when dealing with them.

Materials and Methods

A retrospective chart review was performed on the pelvic fractures in skeletally immature patients treated in our hospital in the last 20 years.

Results

Eighty-one pelvic fractures in children were treated between 1993 and 2013. The mean age was 9.98 years, with 61.7%(50/81) boys and 38.2% (31/81) girls. A traffic accident was the main injury mechanism (74%, 60/81), and height fall was in second place (16%, 13/81). Following Tile pelvic fracture classification, type A2 was the most frequent (58.04%, 47/81); and following Torode and Zieg classification, type IIIA (45.68%, 37/81).

Associated injuries were present in 77.8% (63/81) of the patients; fractures of other bones and head trauma were the most frequent. An acetabular fracture was present in 13.5% (11/81) of the patients.

Nonsurgical treatment was chosen for all the pelvic fractures except in 4 patients, which required surgical management for their pelvic injuries. Blood transfusion was required in 32% (26/81) of the patients, and arterial embolization was not needed in any case. Furthermore, 11.1% (9/81) required a stay in the pediatric care unit, and the death rate was 8.64% (7/81).

The mean length of hospital stay was 12.4 days.

Conclusions

Because of the specific characteristics of pelvic fractures in children, fracture patterns are less severe than those of adults, but the injury mechanisms are high-energy traumas. The rate of associated injuries is very high, and a multidisciplinary management in pediatric trauma centers is needed to treat these patients.
Synergistic Impact of Training Followed by On-Site Support on HIV Clinical Practice: A Mixed-Design Study in Uganda With Pre/Post and Cluster-Randomized Trial Components
Authors: Burnett Sarah M. , Mubiru Norbert , Imani Peace , Mbonye Martin K. , Fisher Leigh , Colebunders Robert , Manabe Yukari C. , Weaver Marcia R.
Published: January 2018

Background:

Task shifting can expand antiretroviral therapy access, but little is known about effective approaches to improve clinical practice among midlevel practitioners (MLPs) such as clinical officers, nurses, and midwives. The Integrated Infectious Diseases Capacity Building Evaluation compared training alone with training combined with on-site support (OSS).

Methods:

Two MLPs each from 36 health facilities attended the 5-week Integrated Management of Infectious Disease training. After training, 18 facilities randomly assigned to arm A received OSS for 9 months, whereas 18 arm B facilities did not. Clinical faculty assessed MLP HIV clinical practice on 6 tasks: history taking, physical examination, laboratory investigations, diagnosis, treatment, and patient education. We analyzed the effect of training alone and training combined with OSS as the pre/post change within each arm. We analyzed the incremental effect of OSS with a difference-in-difference analysis that compared changes between arms.

Results:

Training alone and training combined with OSS significantly improved clinical practice in patient history taking (13% and 24% increase, respectively), physical examination (54% and 71%), laboratory investigations (32% and 20%), and diagnosis (31% and 51%). Combined training and OSS also improved patient education significantly (72% increase). Effect sizes for training combined with OSS were larger than for training alone except for laboratory investigations, and the effects were robust in sensitivity analyses. The incremental effect of OSS on diagnosis was significant [adjusted relative risk = 1.23; 95% confidence interval = 1.00 to 1.50].

Conclusions:

Combined training and OSS improved MLP HIV clinical practice over training alone and can contribute to continued expansion of access to antiretroviral therapy.
A New Robot-assisted Billroth-I Reconstruction: Details of the Technique and Early Results
Authors: Ceccarelli Graziano , Marano Luigi , Codacci-Pisanelli Massimo , Andolfi Enrico , Biancafarina Alessia , Fabozzi Massimiliano , Caruso Stefano , Patriti Alberto
Published: January 2018

Background:

Laparoscopic surgery for gastric tumor is considered a demanding procedure because of lymph node dissection and reconstruction. Billroth-I (B-I) reconstruction after laparoscopic distal gastrectomy is commonly performed extracorporeally because of the complexity of an intracorporeal procedure. Robotic surgery overcomes some limitations of laparoscopy, allowing to reproduce the basic maneuvers of open surgery. We describe a new technique to perform robotic B-I anastomosis.

Methods:

Between January 2012 and February 2015, 5 patients underwent distal gastrectomy with intracorporeal B-I-stapled anastomosis. Patient demographics, tumor characteristics, histopathologic features, and perioperative data were analyzed.

Results:

Median operative time was 170 minutes (145 to 180 min). There were no conversions. Contrast swallow was routinely performed on the third postoperative day. Median postoperative hospitalization was 7 days (range: 6 to 8). No major complications or mortality were observed.

Conclusions:

Robotic distal gastrectomy with intracorporeal B-I anastomosis is a safe and promising technique in selected cases of gastric tumors.
Coevolution of male and female mate choice can destabilize reproductive isolation
Authors: Aubier Thomas G. , Kokko Hanna , Joron Mathieu
Published: January 2018

Sexual interactions play an important role in the evolution of reproductive isolation, with important consequences for speciation. Theoretical studies have focused on the evolution of mate preferences in each sex separately. However, mounting empirical evidence suggests that premating isolation often involves mutual mate choice. Here, using a population genetic model, we investigate how female and male mate choice coevolve under a phenotype matching rule and how this affects reproductive isolation. We show that the evolution of female preferences increases the mating success of males with reciprocal preferences, favouring mutual mate choice. However, the evolution of male preferences weakens indirect selection on female preferences and, with weak genetic drift, the coevolution of female and male mate choice leads to periodic episodes of random mating with increased hybridization (deterministic ‘preference cycling’ triggered by stochasticity). Thus, counterintuitively, the process of establishing premating isolation proves rather fragile if both male and female mate choice contribute to assortative mating.
The Delirium and Population Health Informatics Cohort study protocol: ascertaining the determinants and outcomes from delirium in a whole population
Authors: Davis Daniel , Richardson Sarah , Hornby Joanne , Bowden Helen , Hoffmann Katrin , Weston-Clarke Maryse , Green Fenella , Chaturvedi Nishi , Hughes Alun , Kuh Diana , Sampson Elizabeth , Mizoguchi Ruth , Cheah Khai Lee , Romain Melanie , Sinha Abhi , Jenkin Rodric , Brayne Carol , MacLullich Alasdair
Published: January 2018

Background

Delirium affects 25% of older inpatients and is associated with long-term cognitive impairment and future dementia. However, no population studies have systematically ascertained cognitive function before, cognitive deficits during, and cognitive impairment after delirium. Therefore, there is a need to address the following question: does delirium, and its features (including severity, duration, and presumed aetiologies), predict long-term cognitive impairment, independent of cognitive impairment at baseline?

Methods

The Delirium and Population Health Informatics Cohort (DELPHIC) study is an observational population-based cohort study based in the London Borough of Camden. It is recruiting 2000 individuals aged ≥70 years and prospectively following them for two years, including daily ascertainment of all inpatient episodes for delirium. Daily inpatient assessments include the Memorial Delirium Assessment Scale, the Observational Scale for Level of Arousal, and the Hierarchical Assessment of Balance and Mobility. Data on delirium aetiology is also collected. The primary outcome is the change in the modified Telephone Interview for Cognitive Status at two years.

Discussion

DELPHIC is the first population sample to assess older persons before, during and after hospitalisation. The cumulative incidence of delirium in the general population aged ≥70 will be described. DELPHIC offers the opportunity to quantify the impact of delirium on cognitive and functional outcomes. Overall, DELPHIC will provide a real-time public health observatory whereby information from primary, secondary, intermediate and social care can be integrated to understand how acute illness is linked to health and social care outcomes.
Timing of Cyclic Estradiol Treatment Differentially Affects Cognition in Aged Female Rhesus Monkeys
Authors: Baxter Mark G. , Santistevan Anthony C. , Bliss-Moreau Eliza , Morrison John H.
Published: January 2018

Some evidence suggests that there may be a limited "window of opportunity" for beneficial effects of hormone therapy on physiology after menopause in women. We tested, in aged, surgically menopausal (ovariectomized) rhesus monkeys, whether the timing of cyclic estradiol (E2) treatment impacted its effect on cognitive function. Monkeys were assigned to one of four treatment conditions after ovariectomy: either vehicle or E2 treatment for the duration of the protocol, vehicle for the first 2 years of the protocol followed by E2 for the remainder (delayed treatment), or E2 for the first year of the protocol followed by vehicle for the remainder (withdrawn treatment). Delayed treatment addressed the hypothesis that E2 treatment initiated more than 2 years after ovariectomy would have a reduced effect on cognitive function. Withdrawn treatment mirrors current clinical advice to women to use hormone therapy in the initial post-menopausal period then discontinue it. Two periods of cognitive testing assessed treatment effects on cognition over time. E2 treatment predominantly affected a prefrontal cortex-dependent test of spatiotemporal working memory (delayed response). Monkeys with delayed E2 treatment improved in delayed response performance over time, whereas vehicle-treated monkeys declined. Monkeys with withdrawn E2 treatment maintained their performance across assessments, as did monkeys treated with E2 across the entire protocol. These findings suggest that a "window of opportunity" for hormone treatment after cessation of ovarian function, if present in nonhuman primates, lasts longer than 2 years. It also supports the notion that beneficial effects of hormone therapy may persist after discontinuation of treatment.
Astrocyte networks and intercellular calcium propagation
Authors: Lallouette Jules , De Pittà Maurizio , Berry Hugues
Published: January 2018

Astrocytes organize in complex networks through connections by gap junction channels that are regulated by extra‐ and intracellular signals. Calcium signals generated in individual cells, can propagate across these networks in the form of intercellular calcium waves, mediated by diffusion of second messengers molecules such as inositol 1,4,5-trisphosphate. The mechanisms underpinning the large variety of spatiotemporal patterns of propagation of astrocytic calcium waves however remain a matter of investigation. In the last decade, awareness has grown on the morphological diversity of astrocytes as well as their connections in networks, which seem dependent on the brain area, developmental stage, and the ultrastructure of the associated neuropile. It is speculated that this diversity underpins an equal functional variety but the current experimental techniques are limited in supporting this hypothesis because they do not allow to resolve the exact connectivity of astrocyte networks in the brain. With this aim we present a general framework to model intercellular calcium wave propagation in astrocyte networks and use it to specifically investigate how different network topologies could influence shape, frequency and propagation of these waves.
An evolutionary innovation is contingent on maintaining adaptive potential until competition subsides
Authors: Leon Dacia , D'Alton Simon , Quandt Erik M. , Barrick Jeffrey E.
Published: January 2018

After 15 years of the Lenski experiment one of twelveEscherichia colipopulations evolved the ability to utilize an abundant but previously untapped carbon source, citrate. Mutations responsible for the appearance of rudimentary citrate utilization (Cit+phenotype) and for refining this ability have been characterized. However, the complete nature of the genetic and/or ecological events that set the stage for this key innovation remain unknown. We found that there was a slight fitness benefit for introducing an activatedcitTcassette that mimics the mutation causing Cit+into the ancestor of the evolution experiment and strains isolated from the population close to when it evolved. However, there was no benefit or even a large deleterious effect in intermediate strains. We conclude that achieving Cit+was contingent on both an evolutionary trajectory that maintained a potentiated genetic state and the slowing rate of adaptation in this population late in the experiment.
marge: An API for Analysis of Motifs Using HOMER in R
Authors: Amezquita Robert A.
Published: January 2018

Profiling of open chromatin regions through the assay for transposase-accessible chromatin (ATAC) and transcription factor binding via chromatin immunoprecipitation (ChIP) sequencing has increased our ability to resolve patterns of putative transcription factor binding sites at the genome-wide level. Popular tools such as [HOMER (http://homer.ucsd.edu/homer/) and [MEME] (http://meme-suite.org/) have driven forward the analyses of sequence composition, deriving de novo motifs and searching for the enrichment of known motifs. However, their interfaces do not allow for the construction of parallel inquiries of multiple datasets. Furthermore, their results do not conform to formats amenable to ‘tidy’ analyses, presenting a significant bottleneck in motif analysis. Here, I present ‘marge’, a companion ‘R’ package that interfaces with HOMER to facilitate the construction of queries and to tidy results for further downstream analyses.
Global fingerprint of humans on the distribution ofBartonellabacteria in mammals
Authors: Frank Hannah K. , Hadly Elizabeth A.
Published: January 2018

As humans alter habitats and move themselves and their commensal animals around the globe they change the disease risk for themselves, their commensal animals and wildlife.Bartonellabacteria are prevalent in many mammalian taxa, responsible for numerous human infections and presumed to be an important emerging group of zoonoses. Understanding how this genus has evolved and passed between host taxa in the past can reveal not only how current patterns were established but identify potential mechanisms for future cross-species transmission. We analyzed patterns ofBartonellatransmission and likely sources of spillover using the largest collection ofBartonella gltAgenotypes assembled, 860 unique genotypes ofBartonellaglobally. We provide support for the hypothesis that this pathogenic genus originated as an environmental bacterium before becoming an insect commensal and finally vertebrate pathogen. We show that rodents and domestic animals serve as the reservoirs or at least key proximate host for mostBartonellagenotypes in humans. We also find evidence of exchange ofBartonellabetween domestic animals and wildlife and between domestic animals, likely due to increased contact between all groups.Bartonellais a useful infection for tracing potential zoonoses and demonstrates another major impact of humans on the planet. Care should be taken to avoid contact between humans, domestic animals and wildlife to protect the health of all.
Attentional set to safety recruits the medial prefrontal cortex
Authors: Yao Shuxia , Qi Song , Kendrick Keith M. , Mobbs Dean
Published: January 2018

During threat assessment, the early detection of danger is highly adaptive, yet the fast orientation towards safety is also key to survival. The present study aimed to explore how the human brain searches for safety by manipulating subjects’ attentional set to cues associated with shock probability. Subjects were asked to judge random dots motion (RDM) direction and could be shocked for incorrect responses (RDM task) while keeping alert in detecting the shock probability cues (cue detection task). In contrast to the safe condition, where subjects searched for cues associated with no shock probability, incorrect responses to ‘dangerous+’ (D+) cues would increase the shock probability and correct responses to ‘dangerous-’ (D-) cues would decrease shock probability. In the RDM task, results showed that relative to the D+, the safe attentional set resulted in stronger activation in the ventral medial prefrontal cortex (vmPFC), a core region involved in flexible threat assessment and safety signalling. The vmPFC was also recruited by the D-compared to the D + attentional set. In the cue detection task, shorter response times and greater accuracy were observed for D+ compared to D‐ and safe cues. Correspondingly, at the neural level D+ cues induced increased activity in the frontoparietal attention network including the inferior parietal lobule and intraparietal sulcus. Overall, our findings demonstrate that attentional set for searching safety recruits the vmPFC, while detection of threat elicits activity in the frontoparietal attention network, suggesting a new role for these regions in human defensive survival circuitry.

Significance Statement

While early detection of threat is highly adaptive, the fast orientation towards safety is also key to survival. However, little is known about neural mechanisms underlying attentional set to safety. Using a novel dots motion paradigm combined with fMRI, we explored how human brain prepares for safety searching by manipulating subjects’ attentional set to cues associated with shock probability. Relative to the dangerous attentional set associated with increasing shock probability, the safe attentional set resulted in stronger activity in the ventral medial prefrontal cortex, a core region involved in flexible threat assessment and safety signalling, suggesting a new role for this region in human defensive survival system in encoding stimuli with survival significance.
Partially methylated domains are hallmarks of a cell specific epigenome topology
Authors: Salhab Abdulrahman , Nordström Karl , Kattler Kathrin , Ebert Peter , Ramirez Fidel , Arrigoni Laura , Müller Fabian , Cadenas Cristina , Hengstler Jan G. , Lengauer Thomas , Manke Thomas ,   DEEP Consortium, Walter Jörn
Published: January 2018

Background

Partially methylated domains, PMDs, are extended regions in the genome exhibiting a reduced average DNA-methylation level. PMDs cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. Here, we present a first comprehensive comparative analysis of PMDs across more than 190 WGBS methylomes of human and mouse cells providing a deep insight into structural and functional features associated with PMDs.

Results

PMDs are ubiquitous signatures covering up to 75% of the genome in human and mouse cells irrespective of their tissue or cell origin. Additionally, each cell type comes with a distinct set of specific PMDs, and genes expressed in such PMDs show a strong cell type effect. Demethylation strength varies in PMDs with a tendency towards a more pronounced effect in differentiating and replicating cells. The strongest demethylation is observed in highly proliferating and immortal cancer cell lines. A decrease of DNA-methylation within PMDs tends to be linked to an increase in heterochromatic histone marks and a decrease of gene expressions. Characteristic combinations of heterochromatic signatures in PMDs are linked to domains of early, middle and late DNA-replication.

Conclusion

PMDs are prominent signatures of long-range epigenomic organization. Integrative analysis identifies PMDs as important general, lineage- and cell-type specific topological features. PMD changes are hallmarks of cell differentiation. Demethylation of PMDs combined with increased heterochromatic marks is a feature linked to enhanced cell proliferation. In combination with broad histone marks PMDs demarcate distinct domains of late DNA-replication.
Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing
Authors: Das Sarbashis , Pettersson B. M. Fredrik , Behra Phani Rama Krishna , Mallick Amrita , Cheramie Martin , Shirreff Lisa , DuCote Tanner , Dasgupta Santanu , Ennis Don G. , Kirsebom Leif. A.
Published: January 2018

Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the “M”- and the “Aronson”-type. We suggest that these two clusters should be considered, if not two separate species, at least two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to that M. marinum occupy different ecological niches.
Real-space refinement in Phenix for cryo-EM and crystallography
Authors: Afonine Pavel V. , Poon Billy K. , Read Randy J. , Sobolev Oleg V. , Terwilliger Thomas C. , Urzhumtsev Alexandre , Adams Paul D.
Published: January 2018

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 Å or better shows significant improvement of models and the fit of these models to the target maps.

Synopsis

A description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models.
Achieving radical change
Authors: Hyndman Noel , Liguori Mariannunziata
Published: January 2018

Purpose

The purpose of this paper is to focus on strategies and “spoken discourses” used to construct legitimation around change at the individual level. Comparing changes in financial accounting, budgeting and performance management at two government levels (Westminster and Scotland), it explores the use of legitimation strategies in the implementation of accounting change and its perceived outcomes.

Design/methodology/approach

Drawing on semi-structured interviews, six legitimation/delegitimation strategies are used to code the transcribed data. Patterns with the perceived outcomes of change are explored.

Findings

Changes introduced to enhance “rational” decision making are often received as pushed by some source of authority. Regardless of the interviewees’ background and level, the results suggest that for radical accounting change to embed, it is necessary for it to be perceived as rational, rather than merely driven by authorisation-based pressures. Conversely, incremental change is associated with modest legitimation via rationalisation and delegitimation based on pathos and rationalisation.

Research limitations/implications

The study deals with actors’ legitimation strategies and perceptions of change. These may not correspond to actual substantial change. Taken-for-granted ideas often remain “under the radar”, therefore care must be taken in interpreting the results. The focus of the empirical study is on the UK, therefore conclusions are restricted to this context.

Originality/value

Existing studies struggle to explain organisations’ heterogeneity and practice variation; this study sheds light on how individual legitimation, which may lead to different organisational results, occurs. Differences in how actors interpret changes may be based on their position (central vs devolved administration) and on their ownership of the changes.
Corporate political connection and corporate social responsibility disclosures
Authors: Muttakin Mohammad Badrul , Mihret Dessalegn Getie , Khan Arifur
Published: January 2018

Purpose

The purpose of this paper is to examine the association of corporate political connection with the level of voluntary corporate social responsibility (CSR) disclosures to determine how the relationships between the state and the corporate sector influence CSR engagement.

Design/methodology/approach

Based on a neo-pluralist view of legitimacy theory, which conceptualizes the state as a concentration of power amenable to exploitation by the corporate sector, the study develops and empirically tests a hypothesis that CSR disclosures are inversely associated with political connection. A sample of 936 firm-year observations is used with data collected from annual reports of companies listed on the Dhaka Stock Exchange in Bangladesh from 2005 to 2013.

Findings

Results indicate that corporate political connection is associated with reduced CSR disclosures. This finding suggests that the perceived need for CSR disclosures as a legitimation strategy diminishes for politically connected firms. The finding supports a neo-pluralist argument that political connection could enable firms to eschew stakeholder pressure associated with potential legitimacy threats originating from poor CSR performance. This conclusion challenges the pluralist view of legitimacy theory that considers the state as a neutral arbiter resolving conflict among stakeholder groups in society.

Originality/value

The study makes a significant contribution to the literature by developing a neo-pluralist theorization of voluntary CSR disclosures within legitimacy theory and empirically testing it. Because prior empirical CSR disclosure research is largely underpinned by the pluralistic conception of society, examining this phenomenon from a neo-pluralist perspective enables a more complete understanding of CSR disclosure behaviors of firms.
Accounting as capital and doxa: exploring power and resistance in World Bank projects in Tonga
Authors: Fukofuka Peni , Jacobs Kerry
Published: January 2018

Purpose

The purpose of this paper is to explore the fluid role of accounting both as a form of power and resistance in the context of World Bank projects in the Island Kingdom of Tonga.

Design/methodology/approach

Bourdieu’s concepts of doxa and capital provided the framework for problematizing the fluidity of practices of accounting as both a form of power and of resistance. The authors used a qualitative field study design based on a combination of a documentary analysis of these loan agreements and interviews with key actors and informants.

Findings

The role of accounting in relation to subaltern groups is mediated by the doxic rules and existing capital arrangements at the national and the local or village level. Understanding accounting as both capital and as doxa explains why it can be both a form of power and of resistance.

Practical implications

This study provides policy makers and foreign donors of Tonga and other Pacific Islands a deeper understanding on the struggles to implement and the impacts of accounting at local level as accounting is deployed as part of struggles in various social contexts each with its own doxa and capital arrangements.

Originality/value

This study contributes to the growing accounting body of work that seeks to better understand accounting by proposing that role of accounting as a tool for domination is mediated in various social settings by the doxic value and the existing capital arrangements in those settings.
Strategic practices of subsidiary positioning in business networks
Authors: Laari-Salmela Sari , Mainela Tuija , Pernu Elina , Puhakka Vesa
Published: January 2018

Purpose

The purpose of this paper is to examine subsidiary positioning within the dynamic business networks in the context of multinational companies (MNCs). The research question of the study is: How does the positioning of a subsidiary emerge through strategic practices in the dynamic business networks of an MNC?

Design/methodology/approach

The study relies on the IMP view on strategy with a focus on market positioning activity and the strategy-as-practice approach. Positioning is seen as a question of strategic practices in the interactive spheres of the subsidiaries. In the empirical part of the study, the authors examine the practices of a forest machine industry multinational through longitudinal interview and archival data on three of its sales subsidiaries in Sweden, Russia and the USA.

Findings

The study defines core tensions in subsidiary interactive spheres and the related strategic practices that shape the positioning of the subsidiaries. The study models the practice-based network positioning of MNC subsidiaries as a dynamic play of relationship tensions.

Originality/value

Prior research has focused either on the internal organizing of the MNCs or embeddedness of subsidiaries in their local environment. Less attention has been paid to the practices of positioning through which the subsidiaries deal with the inevitable tensions at the intersection of the internal and external networks.
Academic libraries and student learning outcomes
Authors: Blummer Barbara , Kenton Jeffrey M.
Published: January 2018

Purpose

The purpose of this paper is to examine the literature on student learning outcomes and academic libraries. An analysis of 81 papers revealed the following themes: outcomes assessment of library skills instruction, tools for assessing students’ achievement of learning outcomes, institutional accreditation and student learning outcomes, academic libraries’ impact on student learning outcomes, and the creation of learning outcomes. An understanding of these themes highlights how student learning outcomes are created, assessed, and valued in the academy.

Design/methodology/approach

The methodology centered on a literature review of student learning outcomes and academic libraries from 2001 to the present. To identify relevant articles on this topic, the authors searched the library literature with various combinations of the following keywords: learning outcomes, library, academic, university, college, and higher education.

Findings

An analysis of 81 papers on student learning outcomes and academic libraries revealed the following five themes: outcomes assessment of library skills instruction, assessment tools for student learning outcomes, institutional accreditation and student learning outcomes, academic libraries’ impact on student learning outcomes, and the creation of learning outcomes.

Research limitations/implications

The research was limited to articles published in English and after 2000.

Practical implications

The findings can be utilized to inform instructional librarians about creating and assessing student learning outcomes. In addition, the paper can assist librarians in forging partnerships with academic departments and faculty in creating student learning outcomes to support course and departmental outcomes and accreditation efforts.

Originality/value

The research offers librarians opportunities to incorporate student learning outcomes in library instruction as well as collaborate with faculty in creating student learning outcomes.
Regional dynamics of ownership structure and their impact on firm performance and firm valuation
Authors: Ali Awais , Qiang Fu , Ashraf Sadia
Published: January 2018

Purpose

The purpose of this paper is to analyse the impact of ownership structure on firm valuation and performance across different geographical regions within mainland China.

Design/methodology/approach

The authors classify China in six geographical regions and use cross-sectional data of companies with A-shares listed on domestic stock exchanges in China for the year-end 2015. Using data from CSMAR and Wind database, they use multivariate regression technique and analytically compare the consistency of relationship between operational variables of ownership structure with corporate performance and evaluation.

Findings

The authors find that institutional ownership and state ownership negatively affect market valuation throughout various geographical regions of China. Further, in East, Northwest, South Central and Southwestern parts of China, managerial ownership and concentration of shareholding among top ten shareholders positively influence return on equity (ROE). Interestingly, institutional shareholding negatively affects return on assets (ROA), while institutional ownership has a neutral effect on profitability margin in Northeast China. Although in northern part of China, this relationship is slightly positive. In East China region, state ownership and ownership concentration are directly proportional to profitability margin.

Practical implications

As some of the findings exhibit weak state of market efficiency in some regions, the study may also be useful in identifying arbitrage opportunities across different regions. Moreover, this study suggests that regions with the same business environment and conditions anywhere around the globe invite same or similar ownership structure for better firm performance and valuation.

Originality/value

The study provides unique understanding of relationship between ownership structure, market valuation and firm performance in various parts of China and will be an addition to the relevant literature. Given a change in company’s ownership structure and considering its region of incorporation, this study will help investment analysts in assessing performance and market valuation of the firm. It will also assist several classes of investors, financial institutions and international businesses in making their investment decisions.
HpaP, a novel regulatory protein with ATPase and phosphatase activity, contributes to full virulence in Xanthomonas campestris pv. campestris
Authors: Cui Ping , Li Rui‐Fang , Zhang Da‐Pei , Tang Ji‐Liang , Lu Guang‐Tao
Published: January 2018

The ability of the bacterial phytopathogen Xanthomonas campestris pv. campestris (Xcc) to cause disease is dependent on the type III secretion system (T3SS). Proteins of the Xcc T3SS are encoded by hrp (hypersensitive response and pathogenicity) genes and whose expression is mainly controlled by the regulators HrpG and HrpX. Here, we describe the identification and characterization of a previously unknown regulatory protein (named HpaP), which plays important role in hrp gene expression and virulence in Xcc. Clean deletion of hpaP demonstrated reduced virulence and HR (hypersensitive response) induction of Xcc and alterations in cell motility and stress tolerance. Global transcriptome analyses revealed that most hrp genes were down regulated in the hpaP mutant, suggesting HpaP positively regulates hrp genes. GUS activity assays implied that HpaP regulates the expression of hrp genes via controlling the expression of hrpX. Biochemical analyses revealed that HpaP protein had both ATPase and phosphatase activity. While further site‐directed mutagenesis of conserved residues in the PTP loop (a protein tyrosine phosphatase signature) of HpaP resulted in the loss of both phosphatase activity and regulatory activity in virulence and HR. Taken together, the findings identify a new regulatory protein that controls hrp gene expression and virulence in Xcc.
Towards Multi‐Dimensional Ethnography
Authors: HAINES JULIA KATHERINE
Published: January 2018

In this paper, I argue for the value of multi‐dimensional ethnography. I explore the potential for ethnography to venture beyond sites, into different dimensions. As an example of work moving in this direction, I present a new approach, dubbed TRACES, which emphasizes the assemblages that constitute our lives, interweaving digital, embodied, and internal experiences. Various data streams and sources provide different vantage points for analysis and synthesis. I illustrate how we have used these to gain greater insight into the human lives we study, with different data sources providing different perspectives on a world, then delve into our use of tools, data sources, and methods from other traditions and other fields, which, combined, give us not only a more holistic picture, but a truer one, which refutes the false dichotomy of the digital and the real. I argue that we must continue to adapt and extend ethnography today into such spaces, and that reformulating the sites of ethnography as dimensions enables us to envision future subjects and objects of study in different ways.
Changing the Perspective of Government
Authors: SAUNDERS EMMA , STORMON‐TRINH MAILYNN , BUCKLAND STEPHANI
Published: January 2018

This case study highlights the value of ethnography in changing a client's perspective. New Zealand's productivity has been deceasing, and the government wants to reverse that trend. Empathy's government client believed that macro‐level forces were having a major impact on the productivity of small businesses, and wanted to suggest ways for small businesses to directly combat those forces. Empathy conducted ethnographic research, and the results required the client to change their perspective. While the government client saw increased productivity as a means to increase the standard of living, ethnographic research revealed some small businesses see increased productivity as a threat to their values and standard of living. If the government wanted to increase productivity, they were going to have to change tact completely and start talking to and supporting small businesses in a way that took their fears, motivations, beliefs and values to heart.
What is the Value of a Perspective?
Authors: FERRARI TAYLOR
Published: January 2018

How do you place a value on a perspective? Well, that depends on what you're seeking to accomplish. During this Pecha Kucha I journey of our current paradigm of Value to explore the role of the ethnographer in mediating business interests and human + planetary wellness. Outside of the metropolitan areas where can't afford to use an app to have someone come do their laundry, there lies an entire universe of perspectives that often go ignored, undervalued. What are the worldly consequences of excluding these perspectives when conducting business ethnography?
Instax as Objects of Record
Authors: SIMON DAVID PETER
Published: January 2018

Instant camera images can act as a physical‐digital assistant and craft richer ethnographic records. The author particularly underlines the importance of photography for design field research, drawing upon his fieldwork work in Uganda. Starting by briefly contextualizing the history of photography in research practice he introduces the concept of Spradley's “objects of record” (1979). How can we optimize the use of instant photography with participants, and make operable projects in corporate contexts.