bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numericware i: Identical in state matrix calculator
Authors: Kim Bongsong , Beavis William 
Published: September 2016

AbstractHerein we introduce software, Numericware i to compute a matrix consisting of all pairwise identical in state (IIS) coefficients from genotypic data. Since the emergence of high throughput technology for genotyping, calculating an IIS matrix between many pairs of entities has required large computer memory and lengthy processing times. Numericware i addresses these limitations with two algorithmic methods: multithreading and forward chopping. The multithreading feature allows computational routines to concurrently run on multiple CPU processors. The forward chopping addresses memory limitations by dividing the genotypic data into appropriately sized subsets. Numericware i allows researchers who need to estimate an IIS matrix for big genotypes to use typical laptop/desktop computers. For comparison with different software, we calculated genetic relationship matrices using Numericware i, SPAGeDi and TASSEL with the same small-sized data set. Numericware i measured kinship coefficients between zero and two, while the matrices from SPAGeDi and TASSEL produced different ranges of values, including negative values. The Pearson correlation coefficient between the matrices from Numericware i and TASSEL was high at 0.993, while SPAGeDi rarely showed correlation with Numericware i (0.088) and TASSEL (0.087). To compare the capacity with high dimensional data, we applied the three software to a simulated data set consisted of 500 entities by 1,000,000 SNPs. Numericware i spent 71 minutes using seven CPU cores on a laptop (DELL LATITUDE E6540), while SPAGeDi and TASSEL failed to start. Numericware i is freely available for Windows and Linux under CC-BY license athttps://figshare.com/s/f100f33a8857131eb2db.
Managing risk and building resilient organisations in a riskier world
Authors: Cheese Peter 
Published: September 2016

Purpose
There has been increasing attention given to the need to bring risk thinking into the field of HRM. The purpose of this paper is to explore the nature of risk in a rapidly changing context, examines the responses being made and indicates the characteristics of resilient and adaptive organisations.

Design/methodology/approach
The paper presents a categorisation of risk. It uses the volatile, uncertain, complex and ambiguous metaphor to lay out the likely shape of imminent business risks, and the concept of adaptation to present a case that there is scope for effective responses.

Findings
The paper argues we are at inflexion point that will force businesses to re-examine how they do business in ways that will impact customer expectations, product enhancement, collaborative innovation and ultimately organisational forms. In order to manage and mitigate risk organisations need to understand corporate cultures, operating models and organisational constructs, leadership and governance, as well as the more traditional talent management practices and processes.

Practical implications
Key to achieving resilience will be a focus on behaviour and culture. These issues have to be brought to the heart of strategy and the business model of every organisation. Organisation cultures need to be developed based on trust and respect and the need to avoid risk blindness. We need to challenge the mindset that people can only be trusted within narrow confines of rules, or limits of authority.

Social implications
As we continue to develop more heterogeneous employment models – flexi-working, contractors, self-employed consultants, secondees, agency staff, interns and volunteers, outsourcing, partnering and even crowdsourcing – attention needs to be given to the implications for skills, learning and development and the challenges of aligning behaviours.

Originality/value
The paper brings together a range of imminent business risks to build the case that these risks of course have potentially profound impacts on people management, but that their solution also brings HRM thinking to the heart of strategies, cultures and business models.
Diversity and biogeography of a species‐rich ant fauna of the Australian seasonal tropics
Authors: Andersen Alan N. , Hoffmann Benjamin D. , Oberprieler Stefanie 
Published: September 2016

AbstractAlthough ants are an ecologically dominant and extensively studied faunal group throughout the tropics, there is a poor understanding of tropical ant diversity and distribution at large spatial scales. Here we use a collection developed from 3 decades of ant surveys to present the first analysis of ant diversity and biogeography of a large tropical region. Our objective was to document the species richness, composition, and biogeographic distributions of the ant fauna of the 400 000 km2 “Top End” of Australia's Northern Territory. The known Top End ant fauna comprises 901 native species from 59 genera. The richest genera are Pheidole (90 species), Melophorus (83), Monomorium (83), Camponotus (71), Meranoplus (63), Polyrhachis (57), Rhytidoponera (50), Tetramorium (43), Cerapachys (32), and Iridomyrmex (31). The fauna is the center of diverse radiations within species‐groups of genera such as Meranoplus, Rhytidoponera, and Leptogenys. It also includes IndoMalayan species that have likely bypassed the normal dispersal route into Australia through Cape York Peninsula in North Queensland. Faunistic similarity with other regions of far northern Australia is associated more with rainfall than with geographic proximity. Most (60%) of Top End ant species have not been recorded elsewhere, and, despite uncertainties relating to species delimitation and sampling intensity, this appears to be a credible estimate of the level of endemism. Such exceptionally high endemism can be attributed to the Top End's geographic isolation from other regions of northern Australia with comparably high rainfall.
Zymomonas mobilis as a model system for production of biofuels and biochemicals
Authors: Yang Shihui , Fei Qiang , Zhang Yaoping , Contreras Lydia M. , Utturkar Sagar M. , Brown Steven D. , Himmel Michael E. , Zhang Min 
Published: September 2016

SummaryZymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.
Prospective Investigation of a Novel Ultrasound‐assisted Lumbar Puncture Technique on Infants in the Pediatric Emergency Department
Authors: Gorn Michael , Kunkov Sergey , Crain Ellen F. 
Published: September 2016

AbstractObjectiveThe objective was to describe a novel ultrasound‐assisted lumbar puncture (UALP) technique and to compare it to standard lumbar puncture (SLP) technique in infants.MethodsA prospective, randomized, controlled study in infants 60 days old and younger undergoing a lumbar puncture (LP) in a pediatric emergency department. Patients with a spinal anomaly or ventriculoperitoneal shunt were excluded. Eligible infants were randomized to UALP or SLP. A spinal sonogram was performed on all patients by an investigator not involved in performing the LP. Spinal landmarks and maximum safe depth were identified for the UALP providers. Providers in the SLP group were blinded to sonographic measurements. A successful LP was defined as the collection of cerebrospinal fluid (CSF) with a red blood cell count of less than 10,000 cells/mm3. Statistical analysis included chi‐square, Mann‐Whitney U‐test, and number needed to treat (NNT).ResultsForty‐three patients were enrolled, 21 in the UALP group and 22 in the SLP group. Prematurity, weight, length, provider experience, anesthesia use, stylet technique, and number of attempts were similar between groups. The median age in the UALP group was 38 days (interquartile range [IQR] = 33 days) versus 45 days (IQR = 19 days) in the SLP group (p = 0.02). CSF was obtained in all UALP subjects (100%) versus in 18 of 22 (82%) in the SLP group (p = 0.04); 20 (95%) UALP subjects versus 15 (68%) SLP subjects met our definition of success (p = 0.023). The odds ratio of successful LP using UALP technique was 9.33 (95% confidence interval [CI] = 1.034 to 84.026) and the NNT was 3.7 (95% CI = 2.02 to 24.18).ConclusionThe UALP technique increases the rate of a successful LP in infants compared to standard technique.
AO pelvic fracture classification: can an educational package improve orthopaedic registrar performance?
Authors: Au John , Perriman Diana M. , Bolton Claire , Abbott Liz , Neeman Teresa , Smith Paul N. 
Published: September 2016

BackgroundThe unstable pelvic fracture has been described as the ‘killing fracture’ because of the risk of significant vascular compromise. The ability to correctly classify pelvic fractures may therefore be crucial in optimizing patient outcomes. Pelvic fracture classification is difficult and previous research has indicated that ability is suboptimal in orthopaedic registrars. The objective of this study was to examine the efficacy of an educational package in improving orthopaedic registrars’ ability to classify pelvic fractures.MethodsA total of 35 orthopaedic registrars were recruited in this classification study. An educational package was used to introduce the AO classification of pelvic fractures and teach the registrars how to classify pelvic fractures using pelvic X‐rays and computed tomography scans. A classification test assessed their classification ability before and after using the educational package. A third test was performed 2 weeks after the second to assess the stability of learning.ResultsThe mean score at baseline of 8.4 ± 0.46 increased to 10.5 ± 0.48 after using the educational package, and this was maintained in the follow‐up test (10.7 ± 0.54 (F(2,52) = 15.5, P < 0.001)). The proportion of registrars achieving a satisfactory score increased from 46% (16/35) to 77% (23/30) after training, and 90% (19/21) at follow‐up (χ2(2) = 6.74, P = 0.035).ConclusionThe reliability with which orthopaedic registrars classified pelvic fractures was improved using an educational package. An educational package on pelvic fracture classification may prove to be a valuable addition to the orthopaedic training programme.
Feasibility and utility of portable ultrasound during retrieval of sick term and late preterm infants
Authors: Browning Carmo Kathryn , Lutz Tracey , Berry Andrew , Kluckow Martin , Evans Nick 
Published: September 2016

AbstractAimTo determine the role of clinician performed ultrasound (CPU) during the retrieval and transport of critically ill term and near term newborns.MethodsA neonatologist with portable ultrasound accompanied a sample of newborn retrievals to perform cardiac and cerebral ultrasound before and after transportation.ResultsA total of fifty‐five babies were studied. Median birthweight: 3350 g (2220–5030 g). CPU led to a change in the planned receiving hospital in ten babies. Eleven babies were suspected congenital heart disease (CHD) prior to retrieval: eight confirmed CHD by CPU and three normal structure. One transported to a children's hospital for cardiology review was confirmed as having normal structure; one to a perinatal hospital where normal structure was confirmed and one baby died at the referring hospital and postmortem confirmed normal structure. In five babies with clinical pulmonary hypertension, CPU revealed unsuspected CHD. The destination was changed to a paediatric cardiology centre, avoiding a second retrieval. Eleven babies had evidence of haemodynamic compromise allowing targeting of inotropes.ConclusionThis is the first study of CPU during retrieval of high‐risk infants. Ultrasound in retrieval is feasible, allows accurate triage of babies to cardiac centres and may allow more accurate targeting of fluid and inotrope support.
Predictors of response to tenofovir disoproxil fumarate plus peginterferon alfa‐2a combination therapy for chronic hepatitis B
Authors: Marcellin P. , Ahn S. H. , Chuang W.‐L. , Hui A. J. , Tabak F. , Mehta R. , Petersen J. , Lee C.‐M. , Ma X. , Caruntu F. A. , Tak W. Y. , Elkhashab M. , Lin L. , Wu G. , Martins E. B , Charuworn P. , Yee L. J. , Lim S. G. , Foster G. R. , Fung S. , Morano L. , Samuel D. , Agarwal K. , Idilman R. , Strasser S. I. , Buti M. , Gaeta G. B. , Papatheodoridis G. , Flisiak R. , Chan H. L. Y. 
Published: September 2016

SummaryBackgroundIn patients with chronic hepatitis B, tenofovir disoproxil fumarate (TDF) plus pegylated interferon (PEG‐IFN) for 48‐weeks results in higher rates of hepatitis B surface antigen (HBsAg) loss than either monotherapy.AimTo identify baseline and on‐treatment factors associated with HBsAg loss at Week 72 and provide a model for predicting HBsAg loss in patients receiving combination therapy for 48 weeks.MethodsA secondary analysis of data from an open‐label study where patients were randomised to TDF (300 mg/day, oral) plus PEG‐IFN (PI, 180 μg/week, subcutaneous) for 48 weeks (TDF/PI‐48w); TDF plus PEG‐IFN for 16 weeks, TDF for 32 weeks (TDF/PI‐16w+TDF‐32w); TDF for 120 weeks (TDF‐120w) or PEG‐IFN for 48 weeks (PI‐48w). Logistic regression methods were used to identify models that best predicted HBsAg loss at Week 72.ResultsRates of HBsAg loss at Week 72 were significantly higher in the TDF/PI‐48w group (6.5%) than in the TDF/PI‐16w+TDF‐32w (0.5%), TDF‐120w (0%) and PI‐48w (2.2%) groups (P = 0.09). The only baseline factor associated with response was genotype A. HBsAg decline at Week 12 or 24 of treatment was associated with HBsAg loss at Week 72 (P < 0.001). HBsAg decline >3.5 log10 IU/mL at Week 24 in the TDF/PI‐48w group resulted in a positive predictive value of 85% and a negative predictive value of 99% for HBsAg loss at Week 72.ConclusionsHBsAg decline at Week 24 of TDF plus PEG‐IFN combination therapy may identify patients who, after completing 48 weeks of treatment, have a better chance of achieving HBsAg loss at Week 72.
Long‐term outcomes of high‐dose‐rate brachytherapy for intermediate‐ and high‐risk prostate cancer with a median follow‐up of 10 years
Authors: Yaxley John W. , Lah Kevin , Yaxley Julian P. , Gardiner Robert A. , Samaratunga Hema , MacKean James 
Published: September 2016

ObjectiveTo evaluate the long‐term outcomes of high‐dose‐rate (HDR) brachytherapy for patients with intermediate‐ and high‐risk prostate cancer.Subjects and MethodsWe retrospectively analysed a prospective longitudinal cohort database including a single‐surgeon series of 507 consecutive men treated with external beam radiotherapy and an HDR prostate brachytherapy boost between August 2000 and December 2009. The risk factors used were based on the D'Amico classification. We measured the incidence of no biochemical evidence of disease (bNED) based on the Phoenix definition of failure (nadir PSA + 2 ng/mL). We also reviewed the incidence of urethral stricture in this cohort.ResultsWith minimum and median follow‐ups of 6 and 10.3 years, respectively, the bNED rates for men with intermediate‐ and high risk disease were 93.3% and 74.2%, respectively, at 5 years and 86.9% and 56.1%, respectively, at 10 years. The 10‐year bNED rate for men with only one intermediate‐risk factor was 94%, whereas for patients with all three high‐risk factors it was 39.5%. The overall urethral stricture rate was 13.6%. Before 2005, the urethral stricture rate was 28.9% and after January 2005 it was 4.2%. For the 271 men with a minimum follow‐up of 10 years the actuarial 10‐year prostate cancer‐specific survival rate was 90.8% and the actuarial overall survival rate was 86.7%.ConclusionsFor men with intermediate‐ or high‐risk prostate cancer features, who are considered not suitable for, or wish to avoid a radical prostatectomy, HDR prostate brachytherapy remains an appropriate treatment option. From December 2004, prevention strategies decreased the risk of post‐brachytherapy urethral strictures.
Health and social care practitioners’ experiences of assessing mental capacity in a community learning disability team
Authors: Ratcliff Daniel , Chapman Melanie 
Published: September 2016

Accessible summary

The Mental Capacity Act says when and how to assess someone's ability to make a decision and how best to support them to do this.

Eight workers in community learning disability teams were interviewed about their experiences of assessing people's ability to make decisions.

The workers said that there were a number of areas that they felt were important and which helped them to do good assessments. They also said there were some things that they found difficult.

We suggest some changes that could be made to help workers when assessing people's ability to make decisions.

It is important to help people make decisions for themselves where they can and to help them when they cannot.

AbstractBackground: The study explored experiences of health and social care practitioners within a community learning disability team in undertaking mental capacity assessments with people with learning disabilities.Materials and Methods: Eight practitioners were interviewed using a semi‐structured interview schedule.Results: The information gained was analysed using thematic network analysis. Twelve basic themes emerged which fit into five organising themes labelled: ‘systemic barriers to assessment’; ‘capacity assessing as a process’; ‘person‐specific challenges’; ‘protective practices’; and ‘protection of a fundamental human right’. A global theme, ‘freedom of action versus restrictions on action’, was identified.Conclusions: The themes highlighted that there were a range of organisational, systemic and person‐specific factors that impacted on the perceived quality of and assessors’ confidence in their assessments of mental capacity. Furthermore, these factors appeared to create a range of tensions for assessors increasing the likelihood of cognitive dissonance. Practice implications surround maintaining knowledge, ensuring adequate skills in the practical application of knowledge and reducing organisational barriers.
The nature and rate of behaviour that challenges in individuals with intellectual disabilities who have hearing impairments/deafness (a longitudinal prospective cohort survey)
Authors: Buskermolen Willem Meindert , Hoekman Joop , Aldenkamp Albert Pierre 
Published: September 2016

Accessible summary

Behaviour that challenges among people with both an intellectual disability and hearing impairment or deafness is common. The aim of our study was to identify factors influencing behaviour (that challenges).

We used the Individual Behaviour and Observation Rating Scale to observe and rate behaviour during a period of one year. In this article, we focus on possible relationships between internal factors and behaviour that challenges.

We found that social independence, delay of communication and comorbidity of an autism spectrum disorder are possible important risk factors in developing behaviour that challenges.

This is important because in clinical practice, we should focus on daily care. Training should be aimed at stimulating social independence and communication skills. Individual training programmes aimed at these skills are therefore essential.

AbstractBackground: In this article, we describe our study of the prevalence of behaviour that challenges and which internal factors are related to behaviour that challenges in 21 people (fourteen are male, seven are female, varying in age from 12.4 to 42 years; mean 26.6, SD 7.27) with intellectual disabilities who have hearing impairments.Materials and Methods: Data were obtained by recording behaviour on a daily basis during one year using the ‘Individual Behaviour Observation and Rating Scale’ that was developed especially for this study.Results: It was found that 100% of the participants in this study showed behaviour that challenges, although this was not observed every day in each participant. Prevalence rates during a year varied from 1.8% to 77.3%. On average, the prevalence rate was 28.9%. We found a significantly negative correlation between behaviour that challenges and delay of communication as well as the level of social independence. We also found that in people with autism spectrum disorder, the prevalence of behaviour that challenges was significantly higher than in people without autism spectrum disorder. The level of intellectual disability as well as the level of hearing impairments was not related to the prevalence of behaviour that challenges.Conclusion: Because there are several patterns of increasing and decreasing behaviour that challenges throughout the day, it is not possible to draw one conclusion on this issue for the whole group. However, where certain individual patterns can be recognised, it is possible to make individual plans for the clients. This could mean an improvement in daily care and as a result an improvement in the quality of life for people with intellectual disability who have hearing impairments. Implications for clinical practice are discussed.
Selective targeting of CREB‐binding protein/β‐catenin inhibits growth of and extracellular matrix remodelling by airway smooth muscle
Authors: Koopmans Tim , Crutzen Stijn , Menzen Mark H , Halayko Andrew J , Hackett Tillie‐Louise , Knight Darryl A , Gosens Reinoud 
Published: September 2016

Background and PurposeAsthma is a heterogeneous chronic inflammatory disease, characterized by the development of structural changes (airway remodelling). β‐catenin, a transcriptional co‐activator, is fundamentally involved in airway smooth muscle growth and may be a potential target in the treatment of airway smooth muscle remodelling.Experimental ApproachWe assessed the ability of small‐molecule compounds that selectively target β‐catenin breakdown or its interactions with transcriptional co‐activators to inhibit airway smooth muscle remodelling in vitro and in vivo.Key ResultsICG‐001, a small‐molecule compound that inhibits the β‐catenin/CREB‐binding protein (CBP) interaction, strongly and dose‐dependently inhibited serum‐induced smooth muscle growth and TGFβ1‐induced production of extracellular matrix components in vitro. Inhibition of β‐catenin/p300 interactions using IQ‐1 or inhibition of tankyrase 1/2 using XAV‐939 had considerably less effect. In a mouse model of allergic asthma, β‐catenin expression in the smooth muscle layer was found to be unaltered in control versus ovalbumin‐treated animals, a pattern that was found to be similar in smooth muscle within biopsies taken from asthmatic and non‐asthmatic donors. However, β‐catenin target gene expression was highly increased in response to ovalbumin; this effect was prevented by topical treatment with ICG‐001. Interestingly, ICG‐001 dose‐dependently reduced airway smooth thickness after repeated ovalbumin challenge, but had no effect on the deposition of collagen around the airways, mucus secretion or eosinophil infiltration.Conclusions and ImplicationsTogether, our findings highlight the importance of β‐catenin/CBP signalling in the airways and suggest ICG‐001 may be a new therapeutic approach to treat airway smooth muscle remodelling in asthma.