bluuebunny/crossref_metadata_2025 huggingface dataset:
Surgical Reconstruction of Traumatic Partial Ear Defects Based on a Novel Classification of Defect Sizes and Surrounding Skin Conditions
Authors: Li Datao , Xu Feng , Zhang Ruhong , Zhang Qun , Xu Zhicheng , Li Yiyuan , Wang Cheng , Li Tianya
Published: August 2016

Background:

Although a standard classification system and corresponding reconstruction methods are well described for microtia, establishing a classification system and corresponding surgical strategies for traumatic ear defects is difficult because the size, shape, and local skin conditions of each defect differ considerably. In this article, the authors describe a useful new classification system and corresponding surgical approaches.

Methods:

Ear defects were classified into four types according to defect size and surrounding skin conditions. Defects in which the postauricular skin is of good quality are classified as types I, II, and III. The rest are type IV defects. Four ears (type I defects) were reconstructed using conchal cartilage and posterior auricular flaps. In 51 ears, costal cartilage and posterior auricular flaps were used for single-stage (type II defects, n = 31) or two-stage (type III defects, n = 20) reconstructions. In five instances of severe posterior auricular cutaneous scarring (type IV defects), temporoparietal fascial flaps were created to cover costal cartilage frameworks.

Results:

Sixty subjects with traumatic partial ear defects were followed for 6 months to 6 years. Most (n = 55) were satisfied with their results. Two patients complained of an unnatural junction between the graft framework and residual ear stump. One was dissatisfied with the reduced ear size, caused by improper fixation and skin flap contraction. Another developed minor framework exposure because of skin necrosis, which healed with conservative management.

Conclusion:

Using our new classification system for partial traumatic ear defects based on defect size and contiguous skin condition, the corresponding surgical repair approach was applied consistently, yielding acceptable results and few complications.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
New Suturing Techniques to Reconstruct the Keystone Area in Extracorporeal Septoplasty
Authors: Rezaeian Farid , Gubisch Wolfgang , Janku Dirk , Haack Sebastian
Published: August 2016

Background:

Severe septal deformations require adequate treatment to restore shape and function using extracorporeal septoplasty. Because it has been criticized for being technically demanding to execute and has increased risk for aesthetic complications, the authors have developed two new suture techniques for refixation of the neoseptum.

Methods:

A retrospective analysis of multisurgeon consecutive extracorporeal septoplasties performed from January of 2014 to December of 2014 was conducted at a single institution using the criss-cross or transcutaneous transosseous cerclage suture (group 1) compared with fixation at the upper lateral cartilages only (group 2).

Results:

One hundred ten extracorporeal septoplasties were performed in 110 patients over 12 months. Group 1 consisted of 58 patients (53 percent), whether receiving the criss-cross [12 patients (21 percent)] or the transcutaneous transosseous cerclage suture [46 patients (79 percent)], and group 2 consisted of 52 patients (47 percent). The median follow-up was 11 months (range, 6 to 16 months). Operative revision because of complications at the dorsum or the keystone area had to be performed in no case in group 1 and in five cases (9.6 percent) in group 2, resulting in a statistically significant difference between the two groups (p = 0.0212). There were no complications such as bleeding or infection observed in any of the 110 cases.

Conclusions:

To facilitate and to reduce the complication rate after extracorporeal septoplasty, the authors have developed the criss-cross and transcutaneous transosseous cerclage suture to overcome the important and technically demanding reimplantation of the neoseptum. Thus, the authors believe that these new operative techniques are safe and reproducible procedures that may take a permanent place among extracorporeal septoplasty procedures.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Implementation and Operational Research: Cost and Efficiency of a Hybrid Mobile Multidisease Testing Approach With High HIV Testing Coverage in East Africa
Authors: Chang Wei , Chamie Gabriel , Mwai Daniel , Clark Tamara D. , Thirumurthy Harsha , Charlebois Edwin D. , Petersen Maya , Kabami Jane , Ssemmondo Emmanuel , Kadede Kevin , Kwarisiima Dalsone , Sang Norton , Bukusi Elizabeth A. , Cohen Craig R. , Kamya Moses , Havlir Diane V. , Kahn James G.
Published: August 2016

Background:

In 2013–2014, we achieved 89% adult HIV testing coverage using a hybrid testing approach in 32 communities in Uganda and Kenya (SEARCH: NCT01864603). To inform scalability, we sought to determine: (1) overall cost and efficiency of this approach; and (2) costs associated with point-of-care (POC) CD4 testing, multidisease services, and community mobilization.

Methods:

We applied microcosting methods to estimate costs of population-wide HIV testing in 12 SEARCH trial communities. Main intervention components of the hybrid approach are census, multidisease community health campaigns (CHC), and home-based testing for CHC nonattendees. POC CD4 tests were provided for all HIV-infected participants. Data were extracted from expenditure records, activity registers, staff interviews, and time and motion logs.

Results:

The mean cost per adult tested for HIV was $20.5 (range: $17.1–$32.1) (2014 US$), including a POC CD4 test at $16 per HIV+ person identified. Cost per adult tested for HIV was $13.8 at CHC vs. $31.7 by home-based testing. The cost per HIV+ adult identified was $231 ($87–$1245), with variability due mainly to HIV prevalence among persons tested (ie, HIV positivity rate). The marginal costs of multidisease testing at CHCs were $1.16/person for hypertension and diabetes, and $0.90 for malaria. Community mobilization constituted 15.3% of total costs.

Conclusions:

The hybrid testing approach achieved very high HIV testing coverage, with POC CD4, at costs similar to previously reported mobile, home-based, or venue-based HIV testing approaches in sub-Saharan Africa. By leveraging HIV infrastructure, multidisease services were offered at low marginal costs.
Advances in diagnosis, treatment, and prevention of invasive Salmonella infections
Authors: MacFadden Derek R. , Bogoch Isaac I. , Andrews Jason R.
Published: August 2016

Purpose of review

Typhoidal and nontyphoidal Salmonella enterica serotypes are among the most common bacterial causes of acute febrile illnesses in the developing world. In this review, we discuss new advances in understanding of the burden, diagnostic approaches, treatment and vaccines for invasive Salmonella infections.

Recent findings

Recent estimates of the global burden of typhoidal and nontyphoidal Salmonella not only affirm the importance of these infections but also highlight the paucity of systematic incidence data from many regions. New data from Africa indicate that typhoidal Salmonella may be more common than previously considered. Novel diagnostic techniques for Salmonella include new serologic, molecular and metabolomic approaches, but blood culture – although slow and insensitive – remains the primary means of establishing a diagnosis. Antibiotic resistance, particularly to fluoroquinolones, continues to emerge and threatens to undermine treatment success for these infections. New vaccines for typhoid, including conjugate vaccines with longer duration of immunity than prior vaccines, represent a promising tool for prevention of enteric fever.

Invasive Salmonella infections are a major cause of morbidity and mortality worldwide. Increasing antibiotic resistance in Salmonella is concerning, and empiric oral options are being rapidly eroded. Where new effective antimicrobials are lacking, developments in vaccines offer hope for reducing the burden of Salmonella infections globally.
Simulation-based Randomized Comparative Assessment of Out-of-Hospital Cardiac Arrest Resuscitation Bundle Completion by Emergency Medical Service Teams Using Standard Life Support or an Experimental Automation-assisted Approach
Authors: Choi Bryan , Asselin Nicholas , Pettit Catherine C. , Dannecker Max , Machan Jason T. , Merck Derek L. , Merck Lisa H. , Suner Selim , Williams Kenneth A. , Jay Gregory D. , Kobayashi Leo
Published: August 2016

Introduction

Effective resuscitation of out-of-hospital cardiac arrest (OHCA) patients is challenging. Alternative resuscitative approaches using electromechanical adjuncts may improve provider performance. Investigators applied simulation to study the effect of an experimental automation-assisted, goal-directed OHCA management protocol on EMS providers' resuscitation performance relative to standard protocols and equipment.

Methods

Two-provider (emergency medical technicians (EMT)-B and EMT-I/C/P) teams were randomized to control or experimental group. Each team engaged in 3 simulations: baseline simulation (standard roles); repeat simulation (standard roles); and abbreviated repeat simulation (reversed roles, i.e., basic life support provider performing ALS tasks). Control teams used standard OHCA protocols and equipment (with high-performance cardiopulmonary resuscitation training intervention); for second and third simulations, experimental teams performed chest compression, defibrillation, airway, pulmonary ventilation, vascular access, medication, and transport tasks with goal-directed protocol and resuscitation-automating devices. Videorecorders and simulator logs collected resuscitation data.

Results

Ten control and 10 experimental teams comprised 20 EMT-B's; 1 EMT-I, 8 EMT-C's, and 11 EMT-P's; study groups were not fully matched. Both groups suboptimally performed chest compressions and ventilations at baseline. For their second simulations, control teams performed similarly except for reduced on-scene time, and experimental teams improved their chest compressions (P=0.03), pulmonary ventilations (P<0.01), and medication administration (P=0.02); changes in their performance of chest compression, defibrillation, airway, and transport tasks did not attain significance against control teams' changes. Experimental teams maintained performance improvements during reversed-role simulations.

Conclusion

Simulation-based investigation into OHCA resuscitation revealed considerable variability and improvable deficiencies in small EMS teams. Goal-directed, automation-assisted OHCA management augmented select resuscitation bundle element performance without comprehensive improvement.
Examining the Feasibility and Predictive Validity of the SAGAT Tool to Assess Situation Awareness Among Medical Trainees
Authors: Gardner Aimee K. , Kosemund Matthew , Martinez Joseph
Published: August 2016

Introduction

Situational awareness (SA) describes a team's ability to perceive environmental elements, comprehend their meaning, and anticipate future events. Although SA is consistently described as a critical competency among surgical teams, there is a dearth of research identifying efficacious methods to assess and develop SA in such settings. The aim of this study was to investigate the feasibility of implementing an objective tool that has been used to measure SA in other intense and dynamic environments —the Situation Awareness Global Assessment Technique (SAGAT)—and to examine its ability to predict surgical trainee team performance.

Methods

Ten team-training sessions were conducted involving 2 standardized high-fidelity trauma simulation scenarios. Teams consisted of 4 or 5 participants, and roles were randomly assigned. Team situational awareness was assessed using the SAGAT method, which involves intermittent freezes to probe trainee awareness of the situation. Team performance was assessed using the Mayo High-Performance Teamwork Scale. Hierarchical regression was used to examine SA-performance relationships for each scenario.

Results

Forty-three third-year medical students participated in the training sessions. Team SA ranged from 45% to 79% and 46% to 97% for the first and second scenarios, respectively. Additionally, team SA significantly predicted team performance for both the first scenario (F(1, 42)=19.57; P<0.001; R
2=0.30) and second scenario (F(1,42)=26.18, P<0.001; R
2=0.38).

Conclusions

The SAGAT is a valid, reliable tool for assessing surgical trainee SA. Information provided by the SAGAT can help diagnose team performance problems, inform debriefing discussion points, and inform curriculum development endeavors.
Writing Instruction and Self-Regulation for Students With Autism Spectrum Disorders
Authors: Asaro-Saddler Kristie
Published: August 2016

Children with autism spectrum disorders (ASDs) may struggle to self-regulate their learning, and such difficulty may be especially notable in the area of written expression. One intervention that has explored self-regulation in writing is the self-regulated strategy development (SRSD) approach. In this article, a review of the research using SRSD to teach children with ASD to write is conducted. Investigation yielded 11 studies including 27 participants with ASD. Results of the review indicated that students with ASD taught using an SRSD approach can improve their overall quality of writing, their discourse elements (e.g., persuasive or story) utilized, and the length of their products. Self-regulatory abilities, such as self-monitoring and planning, were also noted to improve. Suggestions for practice and future research are provided.
Dental Procedures
Authors: Ramponi Denise R.
Published: August 2016

Dental problems are a common complaint in emergency departments in the United States. There are a wide variety of dental issues addressed in emergency department visits such as dental caries, loose teeth, dental trauma, gingival infections, and dry socket syndrome. Review of the most common dental blocks and dental procedures will allow the practitioner the opportunity to make the patient more comfortable and reduce the amount of analgesia the patient will need upon discharge. Familiarity with the dental equipment, tooth, and mouth anatomy will help prepare the practitioner for to perform these dental procedures.
Limb girdle muscular dystrophies: classification, clinical spectrum and emerging therapies
Authors: Vissing John
Published: August 2016

Purpose of review

The aim of the study was to describe the clinical spectrum of limb girdle muscular dystrophies (LGMDs), the pitfalls of the current classification system for LGMDs, and emerging therapies for these conditions.

Recent findings

Close to half of all LGMD subtypes have been discovered within the last 6 years of the 21-year-period in which the current classification system for LGMD has existed. The number of letters for annotation of new recessive LGMD conditions is exhausted, and multiple already classified LGMDs do not strictly fulfill diagnostic criteria for LGMD or are registered in other classification systems for muscle disease. On the contrary, diseases that fulfill classical criteria for LGMD have found no place in the LGMD classification system. These shortcomings call for revision/creation of a new classification system for LGMD. The rapidly expanding gene sequencing capabilities have helped to speed up new LGMD discoveries, and unveiled pheno-/genotype relations. Parallel to this progress in identifying new LGMD subtypes, emerging therapies for LGMDs are under way, but no disease-specific treatment is yet available for nonexperimental use.

The field of LGMD is rapidly developing from a diagnostic and therapeutic viewpoint, but a uniform and universally agreed classification system for LGMDs is needed.
Encephalitis With Antibodies to GluN2B During Administration of Clozapine
Authors: Gon Junji , Takehisa Yasushi , Yada Yuji , Kishi Yoshiki , Oshima Etsuko , Takahashi Yukitoshi , Takaki Manabu
Published: August 2016

Clozapine's immunomodulatory properties may contribute to its effect on schizophrenia as well as various adverse effects. However, a possible relationship between N-methyl-d-aspartate-type glutamate receptor antibodies, refractory schizophrenia, and clozapine has not been reported. We experienced a patient who developed refractory schizophrenia that mimicked an exacerbation of encephalitis with antibodies to N-methyl-d-aspartate–type glutamate receptor (GluN2B) after administration of clozapine for 26 days. We performed plasma exchange 5 times and subsequent steroid pulse therapy. The level of consciousness improved within a few weeks, but involuntary movement as well as psychotic symptoms remained. The production of anti-GluN2B antibodies may have contributed to the patient's resistance to the antipsychotic effects of clozapine in addition to mediating the encephalitis. When we administer clozapine to patients with refractory schizophrenia, we should be careful to differentiate between a diagnosis of refractory schizophrenia and encephalitis with antibodies to GluN2B.
Two-dimensional inorganic analogues of graphene: transition metal dichalcogenides
Authors: Jana Manoj K. , Rao C. N. R.
Published: August 2016

The discovery of graphene marks a major event in the physics and chemistry of materials. The amazing properties of this two-dimensional (2D) material have prompted research on other 2D layered materials, of which layered transition metal dichalcogenides (TMDCs) are important members. Single-layer and few-layer TMDCs have been synthesized and characterized. They possess a wide range of properties many of which have not been known hitherto. A typical example of such materials is MoS2. In this article, we briefly present various aspects of layered analogues of graphene as exemplified by TMDCs. The discussion includes not only synthesis and characterization, but also various properties and phenomena exhibited by the TMDCs.

This article is part of the themed issue ‘Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene’.
Competing consumers: contrasting the patterns and impacts of fire and mammalian herbivory in Africa
Authors: Archibald Sally , Hempson Gareth P.
Published: August 2016

Fire and herbivory are the two consumers of above-ground biomass globally. They have contrasting impacts as they differ in terms of selectivity and temporal occurrence. Here, we integrate continental-scale data on fire and herbivory in Africa to explore (i) how environmental drivers constrain these two consumers and (ii) the degree to which each consumer affects the other. Environments conducive to mammalian herbivory are not necessarily the same as those conducive to fire, although their spheres of influence do overlap—especially in grassy ecosystems which are known for their frequent fires and abundance of large mammalian herbivores. Interactions between fire and herbivory can be competitive, facultative or antagonistic, and we explore this with reference to the potential for alternative ecosystem states. Although fire removes orders of magnitude more biomass than herbivory their methane emissions are very similar, and in the past, herbivores probably emitted more methane than fire. We contrast the type of herbivory and fire in different ecosystems to define ‘consumer-realms’.

This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.
Reforestation or conservation? The attributes of old growth grasslands in South Africa
Authors: Zaloumis Nicholas P. , Bond William J.
Published: August 2016

Deforestation as a result of burning and land conversion in the tropics and subtropics has been widely studied and active restoration of forests has been widely promoted. Besides other benefits, reforestation can sequester carbon thereby reducing CO
2
emissions to the atmosphere. However, before grasslands are targeted for ‘reforestation', it is necessary to distinguish whether they are ancient natural grasslands or secondary vegetation colonizing deforested areas. Here we report the results of a study comparing primary grasslands in South Africa with 4–40 year old secondary grasslands recovering from afforestation with
Pinus
species. Primary grasslands had significantly higher plant species richness overall, especially of forb species. Ground cover of primary grasslands was more evenly distributed among species than secondary grasslands which tended to mono-dominance. Forbs with underground storage organs (USOs) were common in primary grasslands but conspicuously absent in the recovering systems. Comparison of secondary grasslands of different ages (up to 40 years) showed negligible recovery of the original species composition. Three key features distinguish old growth primary from secondary grasslands: total and forb species numbers, evenness of species contributions to cover and the presence of USOs. Old growth grasslands also differed in their fire response, showing significant post-burn resprouting and fire-stimulated flowering in contrast to secondary grasslands. Though similar contrasting attributes of ancient and secondary grasslands have been reported in South America, more studies are needed to explore their generality in other geographical regions.

This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.
The future distribution of the savannah biome: model-based and biogeographic contingency
Authors: Moncrieff Glenn R. , Scheiter Simon , Langan Liam , Trabucco Antonio , Higgins Steven I.
Published: August 2016

The extent of the savannah biome is expected to be profoundly altered by climatic change and increasing atmospheric CO
2
concentrations. Contrasting projections are given when using different modelling approaches to estimate future distributions. Furthermore, biogeographic variation within savannahs in plant function and structure is expected to lead to divergent responses to global change. Hence the use of a single model with a single savannah tree type will likely lead to biased projections. Here we compare and contrast projections of South American, African and Australian savannah distributions from the physiologically based Thornley transport resistance statistical distribution model (TTR-SDM)—and three versions of a dynamic vegetation model (DVM) designed and parametrized separately for specific continents. We show that attempting to extrapolate any continent-specific model globally biases projections. By 2070, all DVMs generally project a decrease in the extent of savannahs at their boundary with forests, whereas the TTR-SDM projects a decrease in savannahs at their boundary with aridlands and grasslands. This difference is driven by forest and woodland expansion in response to rising atmospheric CO
2
concentrations in DVMs, unaccounted for by the TTR-SDM. We suggest that the most suitable models of the savannah biome for future development are individual-based dynamic vegetation models designed for specific biogeographic regions.

This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.
Woody encroachment and its consequences on hydrological processes in the savannah
Authors: Honda Eliane A. , Durigan Giselda
Published: August 2016

Woody encroachment due to changes in climate or in the disturbance regimes (fire and herbivory) has been observed throughout the savannah biome over the last century with ecological, hydrological and socioeconomic consequences. We assessed changes in tree density and basal area and estimated changes in rain interception by the canopies across a 5-year period over a biomass gradient in Cerrado vegetation protected from fire. We modelled throughfall, stemflow and net rainfall on the basis of tree basal area (TBA). Tree density increased by an average annual rate of 6.7%, basal area at 5.7% and rain interception by the canopies at 0.6% of the gross rainfall. Independent of the vegetation structure, we found a robust relationship of 0.9% less rainfall reaching the ground as TBA increases by 1 m
2
ha
−1
. Increases in tree biomass with woody encroachment may potentially result in less water available for uptake by plants and to recharge rivers and groundwater reserves. Given that water is a seasonally scarce resource in all savannahs, woody encroachment may threaten the ecosystem services related to water resources.

This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.
Charcoal production in the Mopane woodlands of Mozambique: what are the trade-offs with other ecosystem services?
Authors: Woollen Emily , Ryan Casey M. , Baumert Sophia , Vollmer Frank , Grundy Isla , Fisher Janet , Fernando Jone , Luz Ana , Ribeiro Natasha , Lisboa Sá N.
Published: August 2016

African woodlands form a major part of the tropical grassy biome and support the livelihoods of millions of rural and urban people. Charcoal production in particular is a major economic activity, but its impact on other ecosystem services is little studied. To address this, our study collected biophysical and social datasets, which were combined in ecological production functions, to assess ecosystem service provision and its change under different charcoal production scenarios in Gaza Province, southern Mozambique. We found that villages with longer histories of charcoal production had experienced declines in wood suitable for charcoal, firewood and construction, and tended to have lower perceived availabilities of these services. Scenarios of future charcoal impacts indicated that firewood and woody construction services were likely to trade-off with charcoal production. However, even under the most extreme charcoal scenario, these services were not completely lost. Other provisioning services, such as wild food, medicinal plants and grass, were largely unaffected by charcoal production. To reduce the future impacts of charcoal production, producers must avoid increased intensification of charcoal extraction by avoiding the expansion of species and sizes of trees used for charcoal production. This is a major challenge to land managers and policymakers in the area.

This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.
Testing for local adaptation and evolutionary potential along 1 altitudinal gradients in rainforestDrosophila: beyond laboratory estimates
Authors: O’Brien Eleanor K. , Higgie Megan , Reynolds Alan , Hoffmann Ary A. , Bridle Jon R.
Published: August 2016

Predicting how species will respond to the rapid climatic changes predicted this century is an urgent task. Species Distribution Models (SDMs) use the current relationship between environmental variation and species’ abundances to predict the effect of future environmental change on their distributions. However, two common assumptions of SDMs are likely to be violated in many cases: (1) that the relationship of environment with abundance or fitness is constant throughout a species’ range and will remain so in future, and (2) that abiotic factors (e.g. temperature, humidity) determine species’ distributions. We test these assumptions by relating field abundance of the rainforest fruit flyDrosophila birchiito ecological change across gradients that include its low and high altitudinal limits. We then test how such ecological variation affects the fitness of 35D. birchiifamilies transplanted in 591 cages to sites along two altitudinal gradients, to determine whether genetic variation in fitness responses could facilitate future adaptation to environmental change. Overall, field abundance was highest at cooler, high altitude sites, and declined towards warmer, low altitude sites. By contrast, cage fitness (productivity)increasedtowards warmer, lower altitude sites, suggesting that biotic interactions (absent from cages) drive ecological limits at warmer margins. In addition, the relationship between environmental variation and abundance varied significantly among gradients, indicating divergence in ecological niche across the species’ range. However, there was no evidence for local adaptation within gradients, despite greater productivity of high altitude than low altitude populations when families were reared under laboratory conditions. Families also responded similarly to transplantation along gradients, providing no evidence for fitness trade-offs that would favour local adaptation. These findings highlight the importance of (1) measuring genetic variation of key traits under ecologically relevant conditions, and (2) considering the effect of biotic interactions when predicting species’ responses to environmental change.
recount: A large-scale resource of analysis-ready RNA-seq expression data
Authors: Collado-Torres Leonardo , Nellore Abhinav , Kammers Kai , Ellis Shannon E. , Taub Margaret A. , Hansen Kasper D. , Jaffe Andrew E. , Langmead Ben , Leek Jeffrey T.
Published: August 2016

recountis a resource of processed and summarized expression data spanning nearly 60,000 human RNA-seq samples from the Sequence Read Archive (SRA). The associatedrecountBio-conductor package provides a convenient API for querying, downloading, and analyzing the data. Each processed study consists of meta/phenotype data, the expression levels of genes and their underlying exons and splice junctions, and corresponding genomic annotation. We also provide data summarization types for quantifying novel transcribed sequence including base-resolution coverage and potentially unannotated splice junctions. We present workflows illustrating how to use recount to perform differential expression analysis including meta-analysis, annotation-free base-level analysis, and replication of smaller studies using data from larger studies. recount provides a valuable and user-friendly resource of processed RNA-seq datasets to draw additional biological insights from existing public data. The resource is available athttps://jhubiostatistics.shinyapps.io/recount/.
Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations
Authors: Evoli Stefania , Mobley David L. , Guzzi Rita , Rizzuti Bruno
Published: August 2016

Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S– isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow’s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

Graphical abstract

Focus

Alchemical free energy methods can identify favored binding modes of a ligand within a large protein with multiple binding sites

Highlights

Human serum albumin binds the anti-inflammatory drug ibuprofen in multiple sites

Alchemical free energy calculations predicted favored binding modes of ibuprofen

Bound geometry, affinity and protonation state of the ligand were determined

Simulations identified a number of previously undetected binding sites for ibuprofen

Free energy methods can be used to study large proteins with multiple binding sites
Modeling and predicting of aeronautical thin-walled sheet metal parts riveting deformation
Authors: Chang Zhengping , Wang Zhongqi , Jiang Bo , Zhang Jinming , Guo Feiyan , Kang Yonggang
Published: August 2016

Purpose

Riveting deformation is inevitable because of local relatively large material flows and typical compliant parts assembly, which affect the final product dimensional quality and fatigue durability. However, traditional approaches are concentrated on elastic assembly variation simulation and do not consider the impact of local plastic deformation. This paper aims to present a successive calculation model to study the riveting deformation where local deformation is taken into consideration.

Design/methodology/approach

Based on the material constitutive model and friction coefficient obtained by experiments, an accurate three-dimensional finite element model was built primarily using ABAQUS and was verified by experiments. A successive calculation model of predicting riveting deformation was implemented by the Python and Matlab and was solved by the ABAQUS. Finally, three configuration experiments were conducted to evaluate the effectiveness of the model.

Findings

The model predicting results, obtained from two simple coupons and a wing panel, showed that it was a good compliant with the experimental results, and the riveting sequences had a significant effect on the distribution and magnitude of deformation.

Practical implications

The proposed model of predicting the deformation from riveting process was available in the early design stages, and some efficient suggestions for controlling deformation could be obtained.

Originality/value

A new predicting model of thin-walled sheet metal parts riveting deformation was presented to help the engineers to predict and control the assembly deformation more exactly.
Internal customer satisfaction improvement with QFD technique
Authors: Camgöz-Akdağ Hatice , İmer H. Pınar , Ergin K. Nazlı
Published: August 2016

Purpose

– The purpose of this paper is to employ quality function deployment (QFD) method for translating internal customer needs and expectations into appropriate service specifications to perform existing process assessments in relation to quality characteristics for increasing internal customer satisfaction.

Design/methodology/approach

– The integration of SERVQUAL into QFD has been used to set the success factors to improve quality in the textile industry. One of the largest textile companies in Turkey provided the sample. A SERVQUAL-type of questionnaire was used and a total of 32,938 questionnaires were distributed both manually and online, 24,551 usable were received, comprising a response rate of 77.31 percent.

Findings

– Findings of the QFD application suggest internal customer focus as having the highest weight score of almost 12 percent improvement. In addition, improvements in technical requirements of politeness and process communication have a 9 percent impact each on internal customer satisfaction criteria.

Research limitations/implications

– QFD technique is able to provide companies with a better understanding of internal customer expectations and translate these into appropriate service specifications and perform existing process assessment.

Originality/value

– This paper is a first attempt that applies this integrative approach to a different type of industry, thus offering practical and applied information for professionals engaged in academia and as practitioners.
Leadership for change
Authors: Arif Seema
Published: August 2016

Purpose

– The purpose of this paper is to explore the scope of application of systems thinking and cybernetics for change management by presenting the case of a private university of Pakistan. Six Sigma has been tested as a possible solution to the problems faced by the institution.

Design/methodology/approach

– Stafford Beer’s approach of running the system on trial at five levels has been used to estimate system’s efficacy. The system analysis helped to identify lapses in the system as well as the leverage points for quality improvement. Six Sigma DMAIC tools have been applied for the possible improvement in the process of course management in a private university of Pakistan.

Findings

– Private universities in Pakistan are operated as a business and the business owners are busy to keep their system stable unmindful for the protocol for sustainability. What will make the system viable and sustainable is yet to be learnt by the private universities of Pakistan. There exists a sharp divide between bottom line approach of businessmen and the academia’s confidence in the quality improvement. However, it has been learned that the organizational development is the job of every academic manager, and managing the process through creative innovation is the only solution.

Originality/value

– The case study is a unique contribution in theory and principles of quality management for checking the application of Six Sigma and lean techniques for organizational development of a private university.
On sustainable development of organization
Authors: Myszewski Jan M.
Published: August 2016

Purpose

– The subjects considered in this research paper form the basic prerequisites for improving the effectiveness of organizational development. The author assumes that the effectiveness of any process depends on the size of the reserve of capacity of the resources used in the process (for details, see Appendix). The purpose of this paper is to determine the conditions for the effectiveness of improvement projects.

Design/methodology/approach

– The author has constructed an algorithm (called ABC) to control the capacity of resources. With its help, the author defines the strategy for improvement in an organization. The basic principle of this strategy is continuous improvement, and tactics to control resources refers to the ABC algorithm.

Findings

– The author shows that continuous improvement is a prerequisite for the effectiveness of this strategy. It is shown that the features of this strategy reflect sustainable development of the organization. Along with the algorithm ABC, it forms a basis for the sustainable development strategy. The author shows conditions for effectiveness and explains how the strategy shapes the sustainable development of the organization. The author also explains why commitment of top management is necessary, what it is, and how it can benefit the organization.

Practical implications

– This effort is symbolized by the involvement of resources in projects conducted to improve organizational functions. The result of the capacity growth is increased ability to confront new challenges.

Originality/value

– The author claims that the strategy for sustainable development is shaping the conditions for a gradual increase in the capacity of the resources used in the improvement process. The growth in resource capacity in the repeatedly run improvement projects can serve as a model of organizational learning. The learning process requires effort.
Differential reporting of social and environmental disclosures between local and foreign oil companies in Nigeria
Authors: Odera Odhiambo , Scott Albert , Gow Jeff
Published: August 2016

Purpose

This study aims to identify the differences between local and foreign companies’ social and environmental disclosures (SEDs) practices operating in the Nigerian oil sector. It aims at distinguishing SED levels by comparing local and foreign companies operating in the oil sector.

Design/methodology/approach

The paper analyses annual reports through content analysis. SED extent and type are measured by the number of sentences. SEDs are further classified into three subcategories according to whether they are negative, neutral or positive disclosures and then their proportions are compared through descriptive analysis. To better understand SED differences, the Kruskal–Wallis and Mann–Whitney–Wilcoxon tests are used.

Findings

Local companies are found to provide more content and a wider variety of SED than foreign companies. The majority of the total SEDs in both local and foreign companies are positive with very little evidence of negative news.

Research limitations/implications

The measurement of SEDs focuses on only annual reports, without consideration of other disclosure media such as standalone reports and corporate websites. SEDs are assumed to be voluntary for the companies and they may choose not to disclose any information in annual reports, as there are no regulations or disclosure guidelines in Nigeria to be followed.

Originality/value

The main contribution of this study lies in identifying the factors that have led to diversity and uniqueness in SED between local and foreign oil companies. As such, this study seeks to contribute to the development of understanding multiple factors that could give rise to changing patterns of SED.
Corporate social responsibility and organizational attractiveness: implications for talent management
Authors: Story Joana , Castanheira Filipa , Hartig Silvia
Published: August 2016

Purpose

Talent management is a twenty-first-century concern. Attracting talented individuals to organizations is an important source for firm competitive advantage. Building on signaling theory, this paper proposes that corporate social responsibility (CSR) can be an important tool for talent recruitment.

Design/methodology/approach

Across two studies, this paper found support for this hypothesized relationship. In Study 1, a job advertisement was manipulated to include information about CSR and tested it in two groups of 120 master’s degree students who would be in the job market within the year. It was found that CSR was an important factor that increased organizational attractiveness. In Study 2, with 532 external talented stakeholders of 16 organizations, our findings were replicated and advanced by testing whether perceptions of CSR practices (internal and external) influenced perceptions of organizational attractiveness and if this relationship was mediated by organizational reputation.

Findings

This study found that perceptions of internal CSR practices were directly related to both organizational attractiveness and firm reputation. However, perceptions of external CSR practices were related only to organizational attractiveness through organizational reputation.

Research limitations/implications

The article’s one of the main limitations has to do with generalizability of the results and the potential common method variance bias.

Practical implications

The findings demonstrate that CSR can play an effective role in attracting potential employees, through enhancement of organizational reputation and organizational attractiveness. If organizations are willing to implement practices that protect and develop their employees, along with practices that improve the quality of the natural environment and the well-being of the society, they can become an employer-of-choice.

Originality/value

This study expands on previous studies by including an experimental design, including two types of CSR practices and a mediating variable in this field study.
Does Warsaw Stock Exchange value corporate social responsibility?
Authors: Lipiec Jacek
Published: August 2016

Purpose

This paper aims to examine the performance of corporate social responsibility (CSR) portfolio at the Warsaw Stock Exchange.

Design/methodology/approach

This paper uses the CSR portfolio of public companies that was selected in a three-step procedure. In total, 23 companies were selected and formed a CSR portfolio that is traded on the Warsaw Stock Exchange under the Respect Index. The Capital Asset Pricing Model (CAPM) is used to compare returns of CSR companies with respect to the market. The performance of this portfolio is measured in the period from 2010 to 2012.

Findings

This paper finds that the CSR portfolio measured under the Respect Index outperformed market in all time periods from 2010 to 2012. In addition, in 2010, the CSR portfolio exceptionally outperformed the market by almost 80 per cent. In 2011, even though the market was down, the CSR portfolio reported lesser losses: −0.93 vs −1.73 per cent. In the following year, the market regained and the CSR portfolio again outperformed the market by 14 per cent. This paper also finds that the CSR portfolio is more sensitive to systematic risk than to specific risk. In addition, the CSR securities move according to the market trend.

Research limitations/implications

The limitation of this paper is attributed to a cause-and-effect relationship. In other words, it did not answer whether adopting CSR led to higher profitability or profitability reflected an awareness of market conditions that favored the adoption of CSR. The future research should focus on this issue and indicate whether investors prioritize CSR over profits or vice versa.

Practical implications

The results indicate that investments in CSR portfolio companies bring abnormal returns to investors. In addition, the CSR portfolio may resist market downturns and even bring exceptional profits to investors.

Originality/value

This study explains the CSR portfolio’s performance on the Warsaw Stock Exchange by using the CAPM.
Accelerometers can measure total and activity‐specific energy expenditures in free‐ranging marine mammals only if linked to time‐activity budgets
Authors: Jeanniard‐du‐Dot Tiphaine , Guinet Christophe , Arnould John P.Y. , Speakman John R. , Trites Andrew W.
Published: August 2016

Energy expenditure is an important component of foraging ecology, but is extremely difficult to estimate in free‐ranging animals and depends on how animals partition their time between different activities during foraging. Acceleration data have emerged as a new way to determine energy expenditure at a fine scale but this needs to be tested and validated in wild animals.

This study investigated whether vectorial dynamic body acceleration (VeDBA) could accurately predict the energy expended by marine predators during a full foraging trip. We also aimed to determine whether the accuracy of predictions of energy expenditure derived from acceleration increased when partitioned by different types of at‐sea activities (i.e. diving, transiting, resting and surface activities).

To do so, we equipped 20 lactating northern (Callorhinus ursinus) and 20 lactating Antarctic fur seals (Arctocephalus gazella) with GPS, time‐depth recorders and tri‐axial accelerometers and obtained estimates of field metabolic rates using the doubly labelled water (DLW) method. VeDBA was derived from tri‐axial acceleration, and at‐sea activities (diving, transiting, resting and surface activities) were determined using dive depth, tri‐axial acceleration and travelling speed.

We found that VeDBA did not accurately predict the total energy expended by fur seals during their full foraging trips (R2 = 0·36). However, the accuracy of VeDBA as a predictor of total energy expenditure increased significantly when foraging trips were partitioned by activity and when activity‐specific VeDBA was paired with time‐activity budgets (R2 = 0·70). Activity‐specific VeDBA also accurately predicted the energy expenditures of each activity independent of each other (R2 > 0·85).

Our study confirms that acceleration is a promising way to estimate energy expenditures of free‐ranging marine mammals at a fine scale never attained before. However, it shows that it needs to be based on the time‐activity budgets that make up foraging trips rather than being derived as a single measure of VeDBA applied to entire foraging trips. Our activity‐based method provides a cost‐effective means to accurately calculate energy expenditures of fur seals using acceleration and time‐activity budgets, that can be transfered to studies on other species.