bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational prediction shines light on type III secretion origins
Authors: Goldberg Tatyana , Rost Burkhard , Bromberg Yana
Published: January 2016

Type III secretion system is a key bacterial symbiosis and pathogenicity mechanism responsible for a variety of infectious diseases, ranging from food-borne illnesses to the bubonic plague. In many Gram-negative bacteria, the type III secretion system transports effector proteins into host cells, converting resources to bacterial advantage. Here we introduce a computational method that identifies type III effectors by combining homology based inference withde novopredictions, reaching up to 3-fold higher performance than existing tools. Our work reveals that signals for recognition and transport of effectors are distributed over the entire protein sequence instead of being confined to the N-terminus, as was previously thought. Our scan of hundreds of prokaryotic genomes identified previously unknown effectors, suggesting that type III secretion may have evolved prior to the archaea/bacteria split. Crucially, our method performs well for short sequence fragments, facilitating evaluation of microbial communities and rapid identification of bacterial pathogenicity – no genome assembly required. pEffect and its data sets are available athttp://services.bromberglab.org/peffect.
Phenotypic spandrel: absolute discrimination and ligand antagonism
Authors: Francois Paul , Johnson Kyle A , Saunders Laura N
Published: January 2016

We consider the general problem of absolute discrimination between categories of ligands irrespective of their concentration. An instance of this problem is immune discrimination between self and not-self. We connect this problem to biochemical adaptation, and establish that ligand antagonism - the ability of sub threshold ligands to negatively impact response - is a necessary consequence of absolute discrimination.Thus antagonism constitutes a “phenotypic spandrel”: a phenotype existing as a necessary by-product of another phenotype. We exhibit a simple analytic model of absolute discrimination displaying ligand antagonism, where antagonism strength is linear in distance from threshold. This contrasts with proofreading based models, where antagonism vanishes far from threshold and thus displays an inverted hierarchy of antagonism compared to simple model. The phenotypic spandrel studied here is expected to structure many decision pathways such as immune detection mediated by TCRs and FceRIs.
Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves
Authors: Adams Rhys M. , Mora Thierry , Walczak Aleksandra M. , Kinney Justin B.
Published: January 2016

Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody’s amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called TiteSeq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects of antibody expression and stability that arise in standard deep mutational scanning assays. We demonstrate Tite-Seq on the CDR1H and CDR3H regions of a well-studied scFv antibody. Our data shed light on the structural basis for antigen binding affinity and suggests a role for secondary CDR loops in establishing antibody stability. Tite-Seq fills a large gap in the ability to measure critical aspects of the adaptive immune system, and can be readily used for studying sequence-affinity landscapes in other protein systems.
Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants
Authors: Artyomenko Alexander , Wu Nicholas C , Mangul Serghei , Eskin Eleazar , Sun Ren , Zelikovsky Alex
Published: January 2016

As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous “swarm” of mutant variants. The long read length offered by single-molecule sequencing technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this paper, we present 2SNV, a method able to tolerate the high error-rate of the single-molecule protocol and reconstruct mutant variants. 2SNV uses linkage between single nucleotide variations to efficiently distinguish them from read errors. To benchmark the sensitivity of 2SNV, we performed a single-molecule sequencing experiment on a sample containing a titrated level of known viral mutant variants. Our method is able to accurately reconstruct clone with frequency of 0.2% and distinguish clones that differed in only two nucleotides distantly located on the genome. 2SNV outperforms existing methods for full-length viral mutant reconstruction. The open source implementation of 2SNV is freely available for download athttp://alan.cs.gsu.edu/NGS/?q=content/2snv
Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus
Authors: Bos Kirsten I , Herbig Alexander , Sahl Jason , Waglechner Nicholas , Fourment Mathieu , Forrest Stephen A , Klunk Jennifer , Schuenemann Verena , Poinar Debi , Kuch Melanie , Golding Brian , Dutour Olivier , Keim Paul , Wagner David M , Holmes Edward C , Krause Johannes , Poinar Hendrik N
Published: January 2016

The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.
The Genealogical Sorting Index and species delimitations
Authors: Winter David J. , Trewick Steven A. , Waters Jon M. , Spencer Hamish G.
Published: January 2016

The Genealogical Sorting Index (gsi) has been widely used in species-delimitation studies, where it is usually interpreted as a measure of the degree to which each of several predefined groups of specimens display a pattern of divergent evolution in a phylogenetic tree. Here we show that thegsivalue obtained for a given group is highly dependent on the structure of the tree outside of the group of interest. By calculating thegsifrom simulated datasets we demonstrate this dependence undermines some of desirable properties of the statistic. We also review the use of thegsidelimitation studies, and show that thegsihas typically been used under scenarios in which it is expected to produce large and statistically significant results for samples that are not divergent from all other populations and thus should not be considered species. Our proposed solution to this problem performs better than thegsiin under these conditions. Nevertheless, we show that our modified approach can produce positive results for populations that are connected by substantial levels of gene flow, and are thus unlikely to represent distinct species. We stress that the properties ofgsimade clear in this manuscript must be taken into account if the statistic is used in species-delimitation studies. More generally, we argue that the results of genetic species-delimitation methods need to be interpreted in the light the biological and ecological setting of a study, and not treated as the final test applied to hypotheses generated by other data.
Robust Lineage Reconstruction from High-Dimensional Single-Cell Data
Authors: Giecold Gregory , Marco Eugenio , Trippa Lorenzo , Yuan Guo-Cheng
Published: January 2016

Single-cell gene expression data provide invaluable resources for systematic characterization of cellular hierarchy in multi-cellular organisms. However, cell lineage reconstruction is still often associated with significant uncertainty due to technological constraints. Such uncertainties have not been taken into account in current methods. We present ECLAIR, a novel computational method for the statistical inference of cell lineage relationships from single-cell gene expression data. ECLAIR uses an ensemble approach to improve the robustness of lineage predictions, and provides a quantitative estimate of the uncertainty of lineage branchings. We show that the application of ECLAIR to published datasets successfully reconstructs known lineage relationships and significantly improves the robustness of predictions. In conclusion, ECLAIR is a powerful bioinformatics tool for single-cell data analysis. It can be used for robust lineage reconstruction with quantitative estimate of prediction accuracy.
A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos
Authors: Cheatle Jarvela Alys M. , Yankura Kristen A. , Hinman Veronica F.
Published: January 2016

How neural stem cells generate the correct number and type of differentiated neurons in appropriate places is an important question in developmental biology. Although nervous systems are diverse across phyla, many taxa have a larva that forms an anterior concentration of neurons, or apical organ. The number of neurons in these organs is highly variable. We show that neurogenesis in the sea star larvae begins withsoxc-expressing multipotent progenitors. These give rise to restricted progenitors that expresslhx2/9.Soxc- andlhx2/9-expressing cells are capable of undergoing both asymmetric divisions, which allow for progression towards a particular neural fate, and symmetric proliferative divisions. Nested concentric domains of gene expression along the anterior-posterior (AP) axis, which have been observed in a great diversity of metazoans, control neurogenesis in the sea star by promoting particular division modes and progression towards becoming a neuron. This work, therefore, explains how spatial patterning in the ectoderm controls progression of neurogenesis. Modification to the sizes of these AP territories provides a simple mechanism to explain the diversity of neuron number found among apical organs.

Summary Statement

The progression of apical organ neurogenesis in the sea star is controlled by regulatory anterior-posterior patterning domains.
Discharge against medical advice from a Tehran emergency department
Authors: Hadadi Azar , Khashayar Patricia , Karbakhsh Mojgan , Vasheghani Farahani Ali
Published: January 2016

Purpose

– The purpose of this paper is to identify the main reasons for discharge against medical advice (DAMA) in the emergency department (ED) of a teaching hospital in Tehran, Iran.

Design/methodology/approach

– This cross-sectional study was conducted on all the patients who left the ED of a referral teaching hospital against medical advice (AMA) in 2008. A questionnaire was filled out for each patient to determine the reasons behind patient leaving AMA.

Findings

– In total, 12.8 percent of the patients left the hospital AMA. Dissatisfaction with being observed in the ED, having a feeling of recovery and hospital personnel encouraging patients to leave the hospital were the main reasons for leaving the hospital AMA.

Practical implications

– Like many other centers, the results showed that poor communication skill and work overload were the main contributing factors to DAMA. The center managed to improve patient satisfaction and thus lowered DAMA rates following this study. Considering the similarities reported in the reports and that of other studies, it could be concluded that policy makers in other centers can also benefit from the results to adopt effective approaches to reduce DAMA rate.

Originality/value

– To the knowledge no study has evaluated the rate and the reasons behind DAMA in the Iranian EDs.
Measuring family satisfaction with inpatient rehabilitation care
Authors: Angelino Elisabetta , Gragnano Andrea , Miglioretti Massimo
Published: January 2016

Purpose

– The purpose of this paper is to investigate the psychometric characteristics of the Questionnaire of Family members’ Satisfaction about the Rehabilitation (QFSR), a new questionnaire assessing the satisfaction of patients’ families with the in-hospital rehabilitation service, i.e., the organizational procedure, medical treatment, relationship with nurses/other health workers, and outcome.

Design/methodology/approach

– The QFSR (13 items) was administered to 1,226 (F=60.4 percent; mean age=57.4, SD 15 years) family members of patients admitted to two units for inpatient rehabilitation, i.e., cardiovascular and neuromotor.

Findings

– Confirmatory factor analysis (CFA) confirmed the theoretical four-factor structure of the questionnaire in a subsample of 308 respondents randomly selected from the sample (SB χ² (61)=57.4, p=0.61; RMSEA=0.0; 90 percent CI [0.0, 0.031], CFI=1.00). The remaining 708 respondents (393 relatives of cardiovascular unit inpatients and 315 relatives of neuromotor unit inpatients) were used to test measurement invariance between the groups of family members with patients in the two units. The configurial, scalar, and strict factorial invariance provided a good fit to the data.

Originality/value

– The QFSR, specifically developed to measure the satisfaction of family members of patients undergoing rehabilitation, appears to be a promising brief questionnaire that can provide important indications for continuous improvement in the delivery of healthcare.
The role of information alignment and entrepreneurial traits on SME internationalization
Authors: Peschken Thomas , Shukla Paurav , Lennon John , Rate Shirley
Published: January 2016

Purpose

– The paper aims to explore the internationalisation decision-making of small- and medium-sized enterprise (SME) owner/managers. Specifically, structural alignment theory (SAT) and regulatory focus theory (RFT) are utilised to examine the concept of opportunity recognition in the context of internationalisation choices.

Design/methodology/approach

– This paper is conceptual in nature, and an integrative cognitive model of internationalisation choice decisions is developed based on SAT and RFT, underpinned by a critical review of the international entrepreneurship (IE) literature.

Findings

– Scenarios are identified in which the structure of available information may affect the decision-evaluation process in terms of cognitive resource requirements. Further, the SME owner/manager’s motivational goal orientation is suggested to moderate the role of the information structure in line with IE literature. A conceptual model and propositions are presented.

Research limitations/implications

– The conceptual model and the propositions arising from the discussion in this paper offer new directions of research to explore SME internationalisation.

Originality/value

– This paper offers a cognitive perspective of SME internationalisation. This paper offers insights for policymakers, SME owner/managers, practitioners and researchers alike. For internationalisation decisions, this paper highlights the potential impact of the structure of information that is made available to SME owner/managers by industry or policy bodies; further, the moderating influence of motivational goal orientation may inform policy on how information should be presented to SME owner/managers to aid their decision-making.
Delivering motivation for change at DUKES LONDON
Authors: Dhugga Debrah
Published: January 2016

Purpose

– DUKES LONDON Hotel was once a Mayfair favourite with the Queen Mother and the Princess of Wales – but had got to a stage where it was in danger of losing its five-star rating. New management meant an opportunity to re-engage with staff and use their strengths to create the best possible guest experience.

Design/methodology/approach

– An ongoing programme of leadership and engagement workshops was run to create a family-style culture within the hotel, re-connecting employees with the hotel’s ambitions and their part in the plans.

Findings

– The work has led to international awards for customer service, best hotel in London awards and increased profitability, and is now being used as the model to set up a new DUKES DUBAI hotel.

Originality/value

– The work at DUKES LONDON demonstrates the importance of translating organisational values and goals for staff at every level, making use of management development to ensure the messages are easily understood as day-to-day behaviours and consistently monitored and appraised.
The Curious Incident of Mr Cameron and the United Kingdom Defence Budget: A New Legacy?
Authors: Dorman Andrew M. , Uttley MattheW R. H. , Wilkinson Benedict
Published: January 2016

During 2015 Prime Minister Cameron found himself under intense domestic and international pressure over his apparent reluctance to maintain United Kingdom defence spending at the NATO target level of 2 per cent of GDP. Most commentators attributed this reluctance to the inevitability of defence cuts if the government wished to meet its deficit reduction targets. However, the aftermath of the general election saw a sudden decision to maintain UK defence spending at the NATO target level. This u‐turn is one of the more curious episodes in recent British defence policy. In this article we explore the reasons why, at a time of continuing cuts and austerity measures and against all the political signals, a decision was made to meet the 2 per cent target, and what this means for the UK's defence policy. In doing so, we analyse why most commentators assumed that defence cuts were inevitable, the domestic and international factors that explain the government's apparent u‐turn and what this revised defence budget settlement meant for the new 2015 National Security Strategy and Strategic Defence and Security Review.
Testing the Validity of Primary Care Physicians' Self‐Reported Acceptance of New Patients by Insurance Status
Authors: Coffman Janet M. , Rhodes Karin V. , Fix Margaret , Bindman Andrew B.
Published: January 2016

Objective

To compare physicians' self‐reported willingness to provide new patient appointments with the experience of research assistants posing as either a Medicaid beneficiary or privately insured person seeking a new patient appointment.

Data Sources/Study Setting

Survey administered to California physicians and telephone calls placed to a subsample of respondents.

Study Design

Cross‐sectional comparison.

Data Collection/Extraction Methods

All physicians whose California licenses were due for renewal in June or July 2013 were mailed a survey, which included questions about acceptance of new Medicaid and new privately insured patients. Subsequently, research assistants using a script called the practices of a stratified random sample of 209 primary care physician respondents in an attempt to obtain a new patient appointment. By design, half of the physicians selected for the telephone validation reported on the survey that they accepted new Medicaid patients and half indicated that they did not.

Principal Findings

The percentage of callers posing as Medicaid patients who could schedule new patient appointments was 18 percentage points lower than the percentage of physicians who self‐reported on the survey that they accept new Medicaid patients. Callers were also less likely to obtain appointments when they posed as patients with private insurance.

Conclusions

Physicians overestimate the extent to which their practices are accepting new patients, regardless of insurance status.
Transition From Heparin to Citrate Anticoagulation for Continuous Renal Replacement Therapy: Safety, Efficiency, and Cost
Authors: Gutierrez‐Bernays David , Ostwald Matthew , Anstey Chris , Campbell Victoria
Published: January 2016

Regional citrate anticoagulation (RCA) for continuous renal replacement therapy (CRRT) has recently been recommended as first‐line over heparin. Evidence suggests that RCA prolongs filter life and may reduce bleeding risk, but there is little research on the benefits to dialysis dose delivery or cost, or the effectiveness of transitioning to RCA first‐line. The aim of the present study was to assess the effect on dialysis delivery, cost and safety when transitioning from systemic heparin to RCA for first‐line anticoagulation for CRRT. A single‐center, retrospective observational study was conducted from 2006 to 2012, during which a transition from heparin to a simplified RCA protocol occurred. Demographic and dialysis data, pathology results and costs were obtained. Data were analyzed for both heparin and RCA, and for before and after the transition. 166 patients had 992 dialysis days (heparin 334 vs. RCA 658); demographics were well matched; RCA used less filters per day (P = 0.03), had more days when prescribed dialysis was achieved (85% vs. 60%, P < 0.001), and less filter “down‐time” per day (2.4 vs. 6.1 h, P = 0.02). RCA was estimated to cost AU$487 per day, compared to heparin at $479 per day. When the data were analyzed, comparing before and after the transition, these results remained statistically significant. There was no statistical difference in clinical safety events. Transition to first‐line RCA was safe, provided more time on filter and consumed less filter circuits using a simple and user friendly protocol. The adjusted cost difference appears negligible.
THE POLITICS, AND PLACE, OF GENDER IN RESEARCH ON CRIME*
Authors: KRUTTSCHNITT CANDACE
Published: January 2016

The study of gender and crime has grown exponentially over the past 40 years, but in some fundamental respects, it remains underdeveloped. Few scholars have considered both the similarities and the differences in the predictors of offending among males and females and the implication of this for middle‐range theories. Victimization has been put forth as a major explanatory factor for female offending; yet the study of female victimization has been ghettoized because it has failed to address the ways in which it is related to the larger literature of victimization. Female inmates have always been characterized as having special needs, but the basic necessities (housing and employment) inmates require once they are released from prison are in fact gender neutral. These bodies of research all have suggested that the salience of gender varies in different contexts and is intermixed with other forms of stratification. As such, we would do well to attend to those situations and relational processes that foreground gender and focus our efforts on where gender‐based paradigms are important and can have a real impact.
Cross‐selling in the US home video industry
Authors: Cabral Luís , Natividad Gabriel
Published: January 2016

We identify significant cross‐selling effects in the home video industry: a 10% increase in the demand for a studio's old titles leads to a 4.7% increase in new title sales. We argue this is due to supply‐side effects: studios with strong titles are better able to “push” other titles through retailers; and the latter “push” these additional supplies to consumers by means of lower prices and/or heavier advertising. Our strategy for identifying causality is based on “star power” effects: increases in old movie demand caused by recent success of movies with a similar cast and/or director.
Project selection and execution in teams
Authors: Blanes i Vidal Jordi , Möller Marc
Published: January 2016

We use a mechanism‐design approach to study a team whose members select a joint project and exert individual efforts to execute it. Members have private information about the qualities of alternative projects. Information sharing is obstructed by a trade‐off between adaptation and motivation. We determine the conditions under which first‐best project and effort choices are implementable and show that these conditions can become relaxed as the team grows in size. We also characterize the second‐best mechanism and find that it may include a “motivational bias,” that is, a bias in favor of the team's initially preferred project, and higher‐than‐optimal effort by uninformed team members.
Etomidate exposure in early infant mice (P10) does not induce apoptosis or affect behaviour
Authors: Nyman Y. , Fredriksson A. , Lönnqvist P.‐A. , Viberg H.
Published: January 2016

Background

Numerous animal studies have shown that all commonly used intravenous anaesthetic drugs and volatile agents may cause neuronal apoptosis following exposure in early life. Most studies have focussed on detecting increased apoptosis but their methods are not always readily transferrable to humans.

The lipid formulation of etomidate represents an alternative to the currently established intravenous anaesthetic agents but there is no animal or human data on apoptosis or long‐term behavioural changes. The aim of our study was to investigate the effects of etomidate on cerebral neuronal apoptosis and long‐term behavioural effects using an established mouse model that represents the clinically relevant period of anaesthesia during early infancy in humans.

Methods

Six groups of 10 day old mice (P10) were injected with either etomidate 0.3, 3 or 10 mg/kg, propofol 60 mg/kg, ketamine 50 mg/kg or placebo only. Apoptosis in the cerebral cortex and hippocampus was assessed 24 h after treatment (activated caspase‐3). Late behavioural effects were tested at 2 months of age (spontaneous activity in a new environment).

Results

No evidence was found of differences in activated caspase 3‐concentrations among the study groups. Significant late behavioural changes were only observed in the ketamine group.

Conclusion

A single dose of etomidate in early infant mice at P10 did not produce evidence of cerebral apoptosis or impaired adult motor behaviour.
Bone mineral density, osteoporosis, and fractures among people with eating disorders: a systematic review and meta‐analysis
Authors: Solmi M. , Veronese N. , Correll C. U. , Favaro A. , Santonastaso P. , Caregaro L. , Vancampfort D. , Luchini C. , De Hert M. , Stubbs B.
Published: January 2016

Objective

To provide meta‐analytical evidence of bone mineral density (BMD), fractures, and osteoporosis rates in eating disorders (ED) vs. healthy controls (HCs).

Method

Three independent authors searched major electronic databases from inception till August 2015 for cross‐sectional studies reporting BMD in people with ED (anorexia nervosa, (AN); bulimia nervosa, (BN); eating disorders not otherwise specified, (EDNOS)) vs. HCs. Standardized mean differences (SMDs) ±95% and confidence intervals (CIs) were calculated for BMD, and odds ratios (ORs) for osteopenia, osteoporosis, and fractures.

Results

Overall, 57 studies were eligible, including 21 607 participants (ED = 6485, HCs = 15 122). Compared to HC, AN subjects had significantly lower BMD values at lumbar spine (SMD = −1.51, 95% CI = −1.75, −1.27, studies = 42), total hip (SMD = −1.56, 95%CI = −1.84, −1.28, studies = 23), intertrochanteric region (SMD = −1.80, 95%CI = −2.46, −1.14, studies = 7), trochanteric region (SMD = −1.05, 95%CI = −1.44, −0.66, studies = 7), and femoral neck (SMD = −0.98, 95%CI = −1.12, −0.77, studies = 20). Reduced BMD was moderated by ED illness duration and amenorrhea (P < 0.05). AN was associated with an increased likelihood of osteoporosis (OR = 12.59, 95%CI = 3.30–47.9, P < 0.001, studies = 4) and fractures (OR = 1.84, 95% CI = 1.17–2.89, I2 = 56, studies = 6). No difference in BMD was found between BN and EDNOS vs. HC.

Conclusion

People with AN have reduced BMD, increased odds of osteoporosis and risk of fractures. Proactive monitoring and interventions are required to ameliorate bone loss in AN.
Rosacea or photodamaged skin? Use of brimonidine gel in differentiating erythema in the two conditions
Authors: Oon Hazel H , Lim Ziying Vanessa
Published: January 2016

In this case report, we detail the response of a 37‐year‐old Caucasian man with an overlap of erythematotelangiectatic rosacea and telangiectatic photoaging to brimonidine tartrate gel. With the application of brimonidine only on half of his face, skin analysis images, clinician's and patient's assessment showed that there was significant improvement in the erythema. This case has lent insight into how brimonidine can be used to assess the extent of photoaging by eliminating the erythema of rosacea to some degree. We propose that it can be used as a non‐invasive test to differentiate between the two conditions, sparing patients from skin biopsies and molecular analysis.
Tacrolimus vs. anti‐tumour necrosis factor agents for moderately to severely active ulcerative colitis: a retrospective observational study
Authors: Yamamoto T. , Shimoyama T. , Umegae S. , Matsumoto K.
Published: January 2016

Background

There have been no comparative studies of tacrolimus vs. anti‐tumour necrosis factor (anti‐TNF) agents to determine which treatment is safer or more effective in refractory ulcerative colitis (UC).

Aim

To compare short‐term safety and efficacy of tacrolimus vs. anti‐TNF agents for active UC.

Methods

One hundred patients with moderate‐to‐severe active UC were studied. Fifty patients were treated with oral tacrolimus (TAC group). The other 50 patients were treated with anti‐TNF agents (anti‐TNF group): 40 with infliximab and 10 with adalimumab. Primary endpoints were clinical response and remission rates, colectomy rate, and the incidence of adverse events during 12 weeks.

Results

The incidence of adverse events was 12% in the TAC vs. 18% in the anti‐TNF groups (P = 0.58). At week 12, clinical remission rate was 40% in the TAC vs. 28% in the anti‐TNF groups (P = 0.29). Clinical response (including remission) rate was 62% in the TAC vs. 64% in the anti‐TNF groups (P > 0.99). Five patients (10%) in the TAC and 8 (16%) in the anti‐TNF groups required colectomy (P = 0.55). In a subgroup analysis restricted to severely active UC, the response rate was 50% in the TAC vs. 25% in the anti‐TNF groups (P = 0.24). In severely active UC, the response rate tended to be higher in patients treated with tacrolimus, albeit not statistically significant.

Conclusions

Both tacrolimus and anti‐TNF agents appeared to be safe and effective in the management of moderate‐to‐severe active UC. However, randomised controlled trials are warranted to confirm the results obtained in this study.
Discrepancy between the composition of some commercial cat foods and their package labelling and suitability for meeting nutritional requirements
Authors: Gosper EC , Raubenheimer D , Machovsky‐Capuska GE , Chaves AV
Published: January 2016

Objective

To investigate if the label information and nutrient composition of commercial cat foods are accurate and compliant with the Australian Standard (AS 5812–2011) and if they meet the nutritional requirements of an adult cat.

Methods

A chemical analysis of 10 wet and 10 dry commercial cat foods labelled as ‘nutritionally complete’ for the adult cat was performed. The results were compared with the package composition values, the Australian Standard and the unique dietary requirements of the cat. In addition, the results of the chemical analysis were compared with the nutrient requirements published by the Association of the American Feed Control Officials and the National Research Council.

Results

When compared with the Australian Standard, 9 of the 20 cat foods did not adhere to their ‘guaranteed analysis’ and 8 did not adhere to the standards for nutrient composition. Also, various deficiencies and excesses of crude protein, crude fat, fatty acid and amino acid were observed in the majority of the cat foods.

Conclusions

The results of this study highlight a need for an improved method of ensuring that label information and nutrient composition are accurate and comply with the Australian Standard (AS 5812–2011) to ensure the adult cat's unique dietary requirements are being met by commercial adult cat food.
Emergency Contraceptives and the Beginning of Human Animals
Authors: Paez Eze
Published: January 2016

Emergency contraceptives may sometimes prevent implantation, thereby causing the death of the embryo. According to some positions contrary to abortion, because the embryo is a human animal, there are usually decisive moral reasons not to use them. In this article, I will show that objecting to the use of emergency contraceptives on those grounds is unjustified. If organisms are real existents, then according to the most plausible conception of what is required for a group of cells to compose one, the embryo cannot qualify as a single organism. On the other hand, if organisms are virtual objects, then whether or not the embryo qualifies as one is morally irrelevant. I conclude that even if those positions are right about the morality of abortion, they are not entitled to oppose the use of emergency contraceptives.
Bulfin, Scott et al ed (2015) Critical perspectives on technology and educationPalgrave Macmillan (Basingstoke & St Martin's, New York) isbn 978‐1‐137‐38544‐4 265 pp £65 http://www.palgrave.com/page/detail/critical‐perspectives‐on‐technology‐and‐education‐scott‐bulfin/?K=9781137385451
Authors: Dettori Giuliana
Published: January 2016

This is an important book—but a dense and highly conceptual one—for researchers and scholars in learning technology (lt). Its purpose is to highlight critical perspectives on the field and broaden it by such means as opening up new topics, developing new theory, imagining how the field can advance, and working towards an informed agenda. Do you think the content of this book is likely to be relevant to you? If so, I advise that probably you will find only parts of interest.

Giuliana Dettori
Rubie‐Davis, Christine (2015) Becoming a high expectation teacherRoutledge (New York & London) isbn 978‐0‐415‐71337‐5 254 pp £25.99 https://www.routledge.com/products/9780415713375
Authors: Cowan John
Published: January 2016

Here is a rich and inspiring source book for those school (and other) teachers who have, and hope to realise, high expectations of all their students. It offers comprehensive coverage of the research in this field, all written in a clear, reader‐friendly style with a helpful index. I recommend that you buy a copy if you'd like to become a more inspired and more effective teacher.

John Cowan
Reduced intensity VEPEMB regimen compared with standard ABVD in elderly Hodgkin lymphoma patients: results from a randomized trial on behalf of the Fondazione Italiana Linfomi (FIL)
Authors: Zallio Francesco , Tamiazzo Stefania , Monagheddu Chiara , Merli Francesco , Ilariucci Fiorella , Stelitano Caterina , Liberati Anna Marina , Mannina Donato , Vitolo Umberto , Angelucci Emanuele , Rota Scalabrini Delia , Vallisa Daniele , Bellei Monica , Bari Alessia , Ciccone Giovannino , Salvi Flavia , Levis Alessandro
Published: January 2016

Survival rates for elderly Hodgkin Lymphoma (HL) have not improved substantially in recent years, mainly because of a lack of prospective randomized studies, due to difficulties in enrolling patients. Between 2002 and 2006, 54 untreated HL patients, aged between 65 and 80 years and considered ‘non‐frail’ according to a comprehensive geriatric evaluation, were enrolled into a phase III randomized trial to compare a reduced‐intensity regimen (vinblastine, cyclophosphamide, procarbazine, prednisone, etoposide, mitoxantrone, bleomycin; VEPEMB) with standard ABVD (adriamycin, bleomycin, vinblastine, dacarbazine). Primary endpoint was progression‐free survival (PFS). Seventeen patients were in early stage (I‐IIA), while 37 were advanced stage. Median age was 72 years and median follow‐up was 76 months. Five‐year PFS rates were 48% vs. 70% [adjusted Hazard ratio (HR) = 2·19, 95% confidence interval (CI) = 0·94–5·10, P = 0·068] and 5‐year overall survival (OS) rates were 63% vs. 77% (adjusted HR = 1·67, 95% CI = 0·69–4·03, P = 0·254) for VEPEMB compared to ABVD. Overall treatment‐related mortality was 4%. World Health Organization grade 4 cardiac and lung toxicity occurred in four patients treated with ABVD versus no cases in the VEPEMB arm. Standard ABVD regimen resulted in better PFS and OS than the VEPEMB, although the differences were not statistically significant. The low toxicity of both treatments was probably attributable to stringent selection of patients based on a Comprehensive Geriatric Assessment that excluded frail patients.
The game is afoot: A response to three insightful commentaries
Authors: Wu Wenjie , Sheppard Elizabeth , Mitchell Peter
Published: January 2016

This is an author response to commentaries on our original article (Wu, Sheppard & Mitchell, 2016). We abstract two main themes from the commentaries, and they are as follows: (1) What kind of clues in target behaviour allow perceivers to infer target EQ? And related with this, by what process do perceivers infer the target's EQ? (2) Do features of the target group naturally lead to a U‐shaped function, whereby it is easy for perceivers to identify those at the extremes but not those in the middle of the continuum?
Effects of P2Y12 receptor antagonists beyond platelet inhibition – comparison of ticagrelor with thienopyridines
Authors: Nylander Sven , Schulz Rainer
Published: January 2016

The effect and clinical benefit of P2Y12 receptor antagonists may not be limited to platelet inhibition and the prevention of arterial thrombus formation. Potential additional effects include reduction of the pro‐inflammatory role of activated platelets and effects related to P2Y12 receptor inhibition on other cells apart from platelets. P2Y12 receptor antagonists, thienopyridines and ticagrelor, differ in their mode of action being prodrugs instead of direct acting and irreversibly instead of reversibly binding to P2Y12. These key differences may provide different potential when it comes to additional effects. In addition to P2Y12 receptor blockade, ticagrelor is unique in having the only well‐documented additional target of inhibition, the equilibrative nucleoside transporter 1. The current review will address the effects of P2Y12 receptor antagonists beyond platelets and the protection against arterial thrombosis. The discussion will include the potential for thienopyridines and ticagrelor to mediate anti‐inflammatory effects, to conserve vascular function, to affect atherosclerosis, to provide cardioprotection and to induce dyspnea.
Influence of platelet‐derived growth factor on osseous remodeling properties of a variable‐thread tapered dental implant in vivo
Authors: Kämmerer Peer W. , Schiegnitz Eik , Palarie Victor , Dau Michael , Frerich Bernhard , Al‐Nawas Bilal
Published: January 2016

Objectives

To evaluate the effect of platelet‐derived growth factor (rhPDGF‐BB) on the promotion of osteogenesis around variable‐thread tapered implants in an animal model.

Material and methods

Twenty‐four variable‐thread tapered implants were inserted in the tibia of 12 rabbits. Twelve sites received additional rhPDGF‐BB released from a presoaked xenogenic bone block that was fixed supracrestally. Primary outcomes were bone‐to‐implant contact (BIC; in % ± SD) and percentage of medullary bone fill around the implants (PMF; in % ± SD) after 3 weeks (PDGF n = 6, no PDGF n = 6) and 6 weeks (PDGF n = 6, no PDGF n = 6).

Results

Considerable crestal and medullary bone remodeling could be found around all implants. After 3 weeks, both BIC and PMF values were higher in the no PDGF group (BIC: 63% ± 10 with PDGF vs. 85% ± 5 with no PDGF; PMF: 57% ± 10 with PDGF vs. 74% ± 4 with no PDGF). After 6 weeks, the BIC difference between the two groups was less distinct (BIC: 78% ± 17 with PDGF vs. 72% ± 25 with no PDGF), whereas the PDGF group showed higher PMF values (PMF: 77% ± 5 with PDGF vs. 56% ± 10 with no PDGF).

Conclusions

The addition of rhPDGF‐BB decreases early osseous crestal and medullar healing properties around dental implants. In a later phase, an increase in the cortical area as well as an increased medullar bone formation was seen. This response is likely to provide stronger secondary stability and stability in suboptimal situations involving poor‐quality bone.
Pulmonary Langerhans cell histiocytosis: radiologic resolution following cessation of second hand smoking
Authors: Sawalha Leith , Kumar Abhishek , Arshad Ayesha , Mador Martin Jeffery
Published: January 2016

We present a 65‐year‐old male former smoker with past medical history of renal cell carcinoma. Surveillance chest CT scan showed numerous progressive bilateral upper lobe predominant nodular cystic densities. A Video Assisted Thoracoscopic Surgery lung biopsy was diagnostic of Pulmonary Langerhans Cell Histiocytosis. Further questioning of the patient revealed exposure to second hand smoke from his wife. A repeat chest CT scan 6 months following cessation of all smoking exposure showed near complete resolution of the nodular densities. Our case report highlights the importance of early identification of second hand smoke exposure. Timely elimination of the exposure led to near complete radiologic resolution.
Diagnostic utility of SOX11 immunohistochemistry in differentiating cutaneous spread of mantle cell lymphoma from primary cutaneous B‐cell lymphomas
Authors: Hsi Andy C. , Hurley M. Yadira , Lee Sena J. , Rosman Ilana S. , Pang Xiaofan , Gru Alejandro , Schaffer András
Published: January 2016

Background

Mantle cell lymphoma (MCL) is associated with the worst prognosis among low‐grade B‐cell lymphomas. While cutaneous involvement by nodal or systemic MCL is uncommon, its differentiation from primary cutaneous B‐cell lymphoma (CBCL) or cutaneous involvement by other extra‐cutaneous BCL is challenging as neither histomorphology nor immunophenotype can be absolutely specific. We analyzed the diagnostic utility of SOX11 immunohistochemistry in differentiating secondary cutaneous MCL from other low‐grade CBCL.

Methods

Immunohistochemical staining with anti‐SOX11 antibody was performed on 8 cases of secondary cutaneous MCL, 16 secondary cutaneous CLL, 20 primary cutaneous MZL, 12 cutaneous FCL (6 primary, 6 secondary), 7 primary cutaneous DLBCL, leg type, 5 systemic DLBCL and 3 B‐ALL. SOX11 and cyclin D1 staining were compared in secondary cutaneous MCL.

Results

Nuclear SOX11 staining was seen in seven of eight cases (88%) of secondary cutaneous MCL, including a case with minimal cyclin D1 expression. All other CBCL lacked detectable nuclear SOX11 expression. The sensitivity and specificity for SOX11 in MCL were 87.5 and 100%, respectively. Both the sensitivity and specificity for combined SOX11 and cyclin D1 immunohistochemistry were 100%.

Conclusion

SOX11 immunohistochemistry could be a useful adjunct in distinguishing secondary cutaneous MCL from other CBCL.
Interobserver reliability of the Australian Spasticity Assessment Scale (ASAS)
Authors: Love Sarah , Gibson Noula , Smith Nadine , Bear Natasha , Blair Eve ,   the Australian Cerebral Palsy Register Group
Published: January 2016

Aim

The aim of this paper is to present the Australian Spasticity Assessment Scale (ASAS) and to report studies of its interrater reliability. The ASAS identifies the presence of spasticity by confirming a velocity‐dependent increased response to rapid passive movement and quantifies it using an ordinal scale.

Method

The rationale and procedure for the ASAS is described. Twenty‐two participants with spastic CP (16 males; age range 1y 11mo–15y 3mo) who had not had botulinum neurotoxin‐A within 4 months, or bony or soft tissue surgery within 12 months, were recruited from the spasticity management clinic of a tertiary paediatric teaching hospital. Fourteen muscles in each child were assessed by each of three experienced independent raters. ASAS was recorded for all muscles. Interrater reliability was calculated using the weighted kappa statistic (quadratic weighting; κqw) for individual muscles, for upper limbs, for lower limbs, and between raters.

Results

The weighted kappa ranged between 0.75 and 0.92 for individual muscle groups and was 0.87 between raters.

Interpretation

The ASAS complies with the definition of spasticity and is clinically feasible in paediatric settings. Our estimates of interrater reliability for the ASAS exceed that of the most commonly used spasticity scoring systems.
COMBAT EXPOSURE, CIGARETTE CONSUMPTION, AND SUBSTANCE USE
Authors: Cesur Resul , Chesney Alexander , Sabia Joseph J.
Published: January 2016

This study estimates the relationship between combat exposure and several risky health behaviors: cigarette consumption, binge drinking, and drug use. We find that the U.S. active duty military personnel deployed to combat zones with enemy firefight are more likely to subsequently smoke cigarettes, consume alcohol, and use illicit drugs than their counterparts deployed to noncombat operations. Our results suggest that the mental health effects of combat can explain up to two‐thirds of the estimated association between combat exposure and risky health behaviors. (JEL H56, I12)
Defence‐related gene expression of Hevea brasiliensis clones in response to the white rot pathogen, Rigidoporus microporus
Authors: Oghenekaro A. O. , Omorusi V. I. , Asiegbu F. O.
Published: January 2016

Gene expression levels of pathogenesis‐related proteins (PR1, PR3, PR5, PR8 and PR9), cell wall modification genes (PAL and expansin), signal transduction genes (ACC oxidase, AOC, MAPK) and a Myb transcription factor were compared in two Hevea brasiliensis budded clones (RRIM612 and PR107) 5 weeks after wounding and artificial inoculation with the white rot fungus, Rigidoporus microporus. PR3 class I chitinase was upregulated in RRIM612 in response to the pathogen when compared with the wounded control. PR9 class IV peroxidase was highly upregulated in PR107. PR1 and PR8 were expressed more in wounded than in inoculated clones. Genes involved in ethylene and jasmonic acid signalling pathways and phenylalanine ammonia‐lyase (PAL) were upregulated almost equally in both clones. The Myb transcription factor was upregulated in RRIM612, while MAPK was upregulated in PR107 when compared to the wounded control. The predicted expansin‐like protein was upregulated 40‐fold in RRIM612 when compared to the wounded control. The results demonstrate the variability in defence responses in different clones and provide the first set of defence genes expression profiles in the host–pathogen interaction of the white rot disease of rubber trees.
What factors contribute to the risk of depression in epilepsy?—Tasmanian Epilepsy Register Mood Study (TERMS)
Authors: Lacey Cameron J. , Salzberg Michael R. , D'Souza Wendyl J.
Published: January 2016

Objective

To model the factors associated with depression in a community sample of people with epilepsy. The factors investigated were derived from proposed risk factors for depression from patients with epilepsy, other chronic illness, and the general population.

Methods

Multivariate analysis using general linear regression models of factors associated with depression in the Tasmanian Epilepsy Register Mood Study (TERMS), a cross‐sectional community sample of 440 patients with epilepsy.

Results

A model with acceptable fit was created that explained 66% of the variance of depression. Associated factors included in this model were neuroticism, physical functioning, social support, past history of depression, and stressful life events.

Significance

In this cross‐sectional study designed specifically to investigate depression in epilepsy, we showed that general risk factors for depression in other illness and in the general population are also important in patients with epilepsy, with little support for disease‐related risk factors.