bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying consistent allele frequency differences in studies of stratified populations
Authors: Wiberg R. Axel W. , Gaggiotti Oscar E. , Morrissey Michael B. , Ritchie Michael G.
Published: May 2017

With increasing application of pooled‐sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used, which means that underlying assumptions about the data are frequently violated.

These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including Generalised Linear Models [GLMs] with quasibinomial error structure) with attractive properties for the analysis of allele frequency differences and re‐analyse a published dataset.

The simulations show that common statistical tests for consistent allele frequency differences perform poorly, with high false positive rates. Applying tests that do not confound heterogeneity and main effects significantly improves inference. Variation in sequencing coverage likely produces many false positives and re‐scaling allele frequencies to counts out of a common value or an effective sample size reduces this effect.

Many researchers are interested in identifying allele frequencies that vary consistently across replicates to identify loci underlying phenotypic responses to selection or natural variation in phenotypes. Popular methods that have been suggested for this task perform poorly in simulations. Overall, quasibinomial GLMs perform better and also have the attractive feature of allowing correction for multiple testing by standard procedures and are easily extended to other designs.
Attributing changes in the distribution of species abundance to weather variables using the example of British breeding birds
Authors: Oedekoven Cornelia S. , Elston David A. , Harrison Philip J. , Brewer Mark J. , Buckland Stephen T. , Johnston Alison , Foster Simon , Pearce‐Higgins James W.
Published: May 2017

Modelling spatio‐temporal changes in species abundance and attributing those changes to potential drivers such as climate, is an important but difficult problem. The standard approach for incorporating climatic variables into such models is to include each weather variable as a single covariate, whose effect is expressed through a low‐order polynomial or smoother in an additive model. This, however, confounds the spatial and temporal effects of the covariates.

We developed a novel approach to distinguish between three types of change in any particular weather covariate. We decomposed the weather covariate into three new covariates by separating out temporal variation in weather (averaging over space), spatial variation in weather (averaging over years) and a space–time anomaly term (residual variation). These three covariates were each fitted separately in the models. We illustrate the approach using generalized additive models applied to count data for a selection of species from the UK's Breeding Bird Survey, 1994–2013. The weather covariates considered were the mean temperatures during the preceding winter and temperatures and rainfall during the preceding breeding season. We compare models that include these covariates directly with models including decomposed components of the same covariates, considering both linear and smooth relationships.

The lowest QAIC values were always associated with a decomposed weather covariate model. Different relationships between counts and the three new covariates provided strong evidence that the effects of changes in covariate values depended on whether changes took place in space, in time, or in the space–time anomaly. These results promote caution in predicting species distribution and abundance in future climate, based on relationships that are largely determined by environmental variation over space.

Our methods estimate the effect of temporal changes in weather, while accounting for spatial effects of long‐term climate, improving inference on overall and/or localized effects of climate change. With increasing availability of large‐scale datasets, need is growing for appropriate analytical tools. The proposed decomposition of the weather variables represents an important advance by eliminating the confounding issue often inherent in analyses of large‐scale datasets.
International trends in clozapine use: a study in 17 countries
Authors: Bachmann C. J. , Aagaard L. , Bernardo M. , Brandt L. , Cartabia M. , Clavenna A. , Coma Fusté A. , Furu K. , Garuoliené K. , Hoffmann F. , Hollingworth S. , Huybrechts K. F. , Kalverdijk L. J. , Kawakami K. , Kieler H. , Kinoshita T. , López S. C. , Machado‐Alba J. E. , Machado‐Duque M. E. , Mahesri M. , Nishtala P. S. , Piovani D. , Reutfors J. , Saastamoinen L. K. , Sato I. , Schuiling‐Veninga C. C. M. , Shyu Y.‐C. , Siskind D. , Skurtveit S. , Verdoux H. , Wang L.‐J. , Zara Yahni C. , Zoëga H. , Taylor D.
Published: May 2017

Objective

There is some evidence that clozapine is significantly underutilised. Also, clozapine use is thought to vary by country, but so far no international study has assessed trends in clozapine prescribing. Therefore, this study aimed to assess clozapine use trends on an international scale, using standardised criteria for data analysis.

Method

A repeated cross‐sectional design was applied to data extracts (2005–2014) from 17 countries worldwide.

Results

In 2014, overall clozapine use prevalence was greatest in Finland (189.2/100 000 persons) and in New Zealand (116.3/100 000), and lowest in the Japanese cohort (0.6/100 000), and in the privately insured US cohort (14.0/100 000). From 2005 to 2014, clozapine use increased in almost all studied countries (relative increase: 7.8–197.2%). In most countries, clozapine use was highest in 40–59‐year‐olds (range: 0.6/100 000 (Japan) to 344.8/100 000 (Finland)). In youths (10–19 years), clozapine use was highest in Finland (24.7/100 000) and in the publicly insured US cohort (15.5/100 000).

Conclusion

While clozapine use has increased in most studied countries over recent years, clozapine is still underutilised in many countries, with clozapine utilisation patterns differing significantly between countries. Future research should address the implementation of interventions designed to facilitate increased clozapine utilisation.
Contemporary role of ureterolysis in retroperitoneal fibrosis: treatment of last resort or first intent? An analysis of 50 cases
Authors: O'Brien Tim , Fernando Archie
Published: May 2017

Objective

To determine the outcomes of open ureterolysis in a contemporary cohort of patients presenting with ureteric obstruction secondary to retroperitoneal fibrosis (RPF).

Patients and methods

We conducted a prospective analysis of 50 patients undergoing open ureterolysis and omental wrap between January 2012 and January 2016 in a single centre, managed by a multi‐disciplinary RPF team. Patients had a minimum follow‐up of 1 year. Indications were: nephrostomy‐dependent drainage (n = 5); stent failure as evidenced by persistent hydronephrosis (n = 20); severe stent symptoms (n = 22); and patient choice/pre‐emptive (n = 3). Outcome measures were stent‐free rate; change in renal function post‐ureterolysis; operating variables (operating time, blood loss, complications, length of hospital stay); and need for further intervention.

Results

Of the 50 patients, 48 (96%) were stent‐free at 3 months and 47/50 (94%) were stent‐free at 12 months. The median (interquartile range [IQR]) changes in glomerular filtration rate, according to these indication groups, at 1 year were: overall +6 (−4 to +22)% (P < 0.05); stent failure +25 (+5 to +27)% (P < 0.001); stent symptoms +0 (−17 to +6)% (P = 0.834); nephrostomy‐dependent drainage −10 (−19 to −2)% (P = 0.731); and pre‐emptive 0 (0 to +8)% (P = 0.5). A total of 11/50 patients (22%) underwent additional procedures: nephrectomy, n = 7; uretero‐ureterostomy, n = 1; aneurysm repair, n = 1; 1 Boari flap, n = 1; and ureteric re‐implant, n = 1. Serious complications (Clavien III or IV) occurred in 12% of patients. The median (IQR) blood loss was 390 (20–1,200) mL and the median (IQR) length of hospital stay was 8 (3–21) days.

Conclusions

This study suggests that for patients with ureteric obstruction caused by RPF, contemporary ureterolysis performed by a high‐volume specialist team can successfully render patients stent‐ or nephrostomy‐free without compromising renal function. The results suggest that ureterolysis should be considered in all patients who present with ureteric obstruction caused by RPF that does not respond quickly to standard treatment.
Dual‐specificity tyrosine‐regulated kinase 2 is a suppressor and potential prognostic marker for liver metastasis of colorectal cancer
Authors: Ito Daisuke , Yogosawa Satomi , Mimoto Rei , Hirooka Shinichi , Horiuchi Takashi , Eto Ken , Yanaga Katsuhiko , Yoshida Kiyotsugu
Published: May 2017

Colorectal cancer is a common cancer and a leading cause of cancer‐related death worldwide. The liver is a dominant metastatic site for patients with colorectal cancer. Molecular mechanisms that allow colorectal cancer cells to form liver metastases are largely unknown. Activation of epithelial–mesenchymal transition is the key step for metastasis of cancer cells. We recently reported that dual‐specificity tyrosine‐regulated kinase 2 (DYRK2) controls epithelial–mesenchymal transition in breast cancer and ovarian serous adenocarcinoma. The aim of this study is to clarify whether DYRK2 regulates liver metastases of colorectal cancer. We show that the ability of cell invasion and migration was abrogated in DYRK2‐overexpressing cells. In an in vivo xenograft model, liver metastatic lesions were markedly diminished by ectopic expression of DYRK2. Furthermore, we found that patients whose liver metastases expressed low DYRK2 levels had significantly worse overall and disease‐free survival. Given the findings that DYRK2 regulates cancer cell metastasis, we concluded that the expression status of DYRK2 could be a predictive marker for liver metastases of colorectal cancer.
Upregulation of ASAP3 contributes to colorectal carcinogenesis and indicates poor survival outcome
Authors: Tian Haiying , Qian Jin , Ai Luoyan , Li Yueyuan , Su Wenyu , Kong Xian‐Ming , Xu Jie , Fang Jing‐Yuan
Published: May 2017

The function and clinical implication of ArfGAP with SH3 domain, ankyrin repeat, and PH domain 3 (ASAP3) in colorectal cancer (CRC) remains undefined. In the present study, we showed that the expression level of ASAP3 was dramatically increased in CRC and its upregulation was associated with American Joint Committee on Cancer stage (P < 0.001) and poor prognosis (P = 0.0022). The combination of stage and ASAP3 expression improved the prediction of survival in CRC patients. Suppression of ASAP3 inhibited cell proliferation by inducing G1 phase arrest without influencing apoptosis. ASAP3 promoted growth of colon tumors in mice with colitis, and accelerated cell invasion and migration in vitro. Increased ASAP3 was associated with activation of the nuclear factor‐κB (NF‐κB) canonical pathway in CRC. Upregulation of ASAP3 increased the phosphorylation and nuclear translocation of the p65 NF‐κB subunit. Mechanistically, ASAP3 interacts with NF‐κB essential modulator (NEMO) and could reduce the polyubiquitinylation of NEMO. Overall, ASAP3 might regulate NF‐κB via binding to NEMO. ASAP3 acts as an oncogene in colonic cancer and could be a potential biomarker of colon carcinogenesis.
Microstructure alterations in the hypothalamus in cranially radiated childhood leukaemia survivors but not in craniopharyngioma patients unaffected by hypothalamic damage
Authors: Follin Cecilia , Fjalldal Sigridur , Svärd Daniel , van Westen Danielle , Gabery Sanaz , Petersén Åsa , Lätt Jimmy , Rylander Lars , Erfurth Eva Marie
Published: May 2017

Objective

Metabolic complications are frequent in childhood leukaemia (ALL) survivors treated with cranial radiotherapy (CRT). These complications are potentially mediated by damage to the hypothalamus (HT), as childhood onset (CO) craniopharyngioma (CP) survivors without HT involvement are spared overt obesity. Diffusion tensor imaging (DTI) shows brain tissue microstructure alterations, by fractional anisotrophy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD). We used DTI to determine the integrity of the microstructure of the HT in ALL survivors.

Design

Case‐control study.

Patients

Three groups were included: (i) 27 CRT treated ALL survivors on hormone supplementation, (ii) 17 CO‐CP survivors on hormone supplementation but without HT involvement and (iii) 27 matched controls.

Measurements

DTI parameters of the HT were measured and body composition.

Results

Microstructural alterations in the HT were more severe in ALL survivors with a BMI ≥25 than with BMI <25. Compared to controls, ALL survivors had reduced FA (P=.04), increased MD (P<.001), AD (P<.001) and RD (P<.001) in the right and left HT. In the right HT, ALL survivors with a BMI ≥25 showed elevated MD (P=.03) and AD (P=.02) compared to ALL survivors with BMI <25. In contrast, DTI parameters did not differ between CP survivors and controls.

Conclusions

Long‐term follow‐up after CRT for ALL DTI measures were affected in the HT despite complete hormone replacement. The present data suggest that ALL survivors have demyelination and axonal loss in the HT.
Longitudinal changes in serum 25‐hydroxyvitamin D in the Dallas Heart Study
Authors: Mirfakhraee Sasan , Ayers Colby R. , McGuire Darren K. , Maalouf Naim M.
Published: May 2017

Context

While the prevalence of vitamin D deficiency is well described in various populations, limited data are available regarding longitudinal variation in serum 25‐hydroxyvitamin D concentrations.

Objectives

To evaluate the temporal trends in serum 25(OH)D, prevalence of vitamin D deficiency and factors influencing these trends.

Participants, Design and Setting:

Adults enrolled in the Dallas Heart Study, a longitudinal, probability‐based, multiethnic, population study in Dallas, Texas, USA.

Main Outcome Measures

Prevalence of vitamin D deficiency and predictors of change in serum 25(OH)D.

Results

A total of 2045 participants had serum 25(OH)D measured on two occasions (2000‐2002 and 2007‐2009) at a median interval of 7 years. Serum 25(OH)D decreased (42.7‐39.4 nmol/L, P<.001) and the prevalence of vitamin D deficiency [25(OH)D <50 nmol/L] increased significantly (60.6%‐66.4%, P<.0001) despite vitamin D supplementation increasing over the interval (7.2%‐23.0%; P<.0001). In a multivariable model adjusting for sex, race, BMI, age, season of blood draw, smoking and exercise, a greater decline in serum 25(OH)D was noted in men compared with women (−8.0 vs −3.5 nmol/L, P<.0001), in participants of Hispanic ethnicity vs White and Black ethnicity (P<.0001), in nonobese vs obese participants (−7.2 vs −4.0 nmol/L, P=.005) and in nonusers vs users of vitamin D supplements (−5.7 vs −1.7 nmol/L, P=.032).

Conclusions

Despite increased vitamin D supplementation, serum 25(OH)D decreased in an ethnically diverse cohort of Dallas County residents between 2000‐2002 and 2007‐2009. Features most predictive of a decline in serum 25(OH)D include male sex, Hispanic ethnicity and weight gain.
Identification of somatic TERT promoter mutations in familial nonmedullary thyroid carcinomas
Authors: Marques Inês J. , Moura Margarida M. , Cabrera Rafael , Pinto António E. , Simões‐Pereira Joana , Santos Catarina , Menezes Francisco D. , Montezuma Diana , Henrique Rui , Rodrigues Teixeira Manuel , Leite Valeriano , Cavaco Branca M.
Published: May 2017

Objective

The genes causing familial nonmedullary thyroid carcinoma (FNMTC) identified to date are only involved in a small fraction of the families. Recently, somatic mutations in TERT promoter region and in EIF1AX gene were reported in thyroid tumours of undefined familial status. The aim of this study was to investigate the role of TERT and EIF1AX mutations in familial thyroid tumours.

Design

The promoter region of TERT was sequenced in leucocyte DNA of the probands from 75 FNMTC families. In thyroid tumours from 54 familial cases, we assessed somatic TERT promoter, RAS and BRAF hotspot mutations, and the whole EIF1AX gene.

Results

No potentially pathogenic germline variants were identified in TERT in the 75 FNMTC families’ probands. In the 54 carcinomas, we identified five cases (9%) with hotspot somatic TERT promoter mutations. BRAF mutations were found in 41% of the tumours. All TERT‐positive samples were also positive for BRAF p.Val600Glu, and this co‐occurrence was found to be statistically significant (P=.008). RAS mutations were detected in four tumours wild‐type for TERT (7%). Evaluation of tumour mutation data together with the patients’ clinicopathological features revealed a significant correlation between TERT plus BRAF mutations and advanced tumour stage (T4) (P=.020). No mutations were identified in EIF1AX.

Conclusions

The results of this study suggest that TERT promoter and EIF1AX mutations are not frequently involved in FNMTC aetiology. However, we show for the first time that TERT alterations are associated with familial thyroid tumour progression. Our data also suggest that TERT mutations are more often found in concomitance with BRAF mutations in advanced stages of FNMTC.
Oral health‐related quality of life and risk factors associated with traumatic dental injuries in Brazilian children: A multilevel approach
Authors: Bomfim Rafael A. , Herrera Daniel Rodrigo , De‐Carli Alessandro Diogo
Published: May 2017

Background/Aims

Among the diseases related to oral health, such as caries and oral cancer, dental trauma stands out as one of the major public health problems worldwide. The aim of this study was to verify the occurrence of factors associated with traumatic dental injuries (TDIs), including oral health‐related quality of life (OHRQoL), sociodemographic characteristics, untreated caries, occlusal problems and contextual variables in 12‐year‐old Brazilian children.

Methods

This study assessed a complex sample of the National Research in Oral Health (SBBrasil 2010) data on 7240 12‐year‐old children and contextual features of the municipalities where they lived.

Results

TDI prevalence in 12‐year‐old schoolchildren was 23.96%. Being female was a protective factor for all trauma outcome variables. Non‐white children were at risk of maxillary tooth fractures. Maxillary overjet greater than 3 mm was associated with all trauma outcomes. Crowding and spacing were risk factors for enamel trauma. TDI has a negative impact on OHRQoL. None of the contextual variables analysed (Gini coefficient, MHDI, family health strategy and water fluoridation) were associated with TDI in the multilevel approach.

Conclusions

TDI was better explained by individual factors, related to sociodemographic conditions and occlusal problems, with a negative impact on OHRQoL, adjusted for untreated caries. Contextual variables were not associated with TDI in 12‐year‐old Brazilian schoolchildren. Interdisciplinary actions for preventing dental trauma, such as stimulating the use of mouthguards, have to be encouraged by the family health strategy (FHS) and school health programme (SHP).
Successful use of lipid emulsion to resuscitate a foal after intravenous lidocaine induced cardiovascular collapse
Authors: Vieitez V. , Gómez de Segura I. Á. , Martin‐Cuervo M. , Gracia L. A. , Ezquerra L. J.
Published: May 2017

Background

Lipid emulsion has been reported to be effective for the treatment of local anaesthetic overdoses in rats, dogs and man.

Objectives

To describe the successful treatment of cardiovascular lidocaine toxicity in a foal with intravenous lipid administration.

Study design

Observational study: case report.

Methods

An 8‐month‐old Arabian cross foal was anaesthetised for removal of the right alar fold and nasal plate. Anaesthesia was maintained with isoflurane in oxygen and lidocaine administered with a loading dose followed by a continuous rate infusion (CRI). The anaesthetic period was uneventful and 30 min before expected termination of the procedure lidocaine infusion was stopped. A sudden drop in mean arterial blood pressure was then observed. The ECG signal was lost, the end tidal CO2 tension dropped from 40 to 10 mmHg, corneal reflex was absent and asystole diagnosed. Cardiopulmonary resuscitation manoeuvres were immediately initiated, but epinephrine and atropine were unsuccessfully administered. Lipid emulsion was administered and the heart rate and arterial blood pressure gradually returned to normal.

Results

The foal recovered consciousness 3 h later, regained its sternal position, was responsive and 20 h later was able to stand up alone.

Main limitations

It will be necessary to evaluate a greater number of cases to determine the effectiveness of lipids in foals intoxicated with lidocaine.

Conclusion

Intravenous lipid emulsion may be helpful in the treatment of potentially lethal cardiotoxicity attributable to lidocaine overdose in the foal.
HER2FISHresults in breast cancers with increasedCEN17 signals using alternative chromosome 17 probes – reclassifying cases in the equivocal category
Authors: Holzschuh Maria‐Anna , Czyz Zbigniew , Hauke Sven , Inwald Elisabeth C , Polzer Bernhard , Brockhoff Gero
Published: May 2017

Aims

HER2testing of invasive breast cancer byin‐situhybridization guides therapy decisions. ProbingHER2and centromere of chromosome 17 (cen17) simultaneously is supposed to reveal both a potentialHER2gene amplification and polysomy 17. However, a considerable number of breast cancer patients with quasi polysomy 17 are considered ‘equivocal’, which is diagnostically meaningless. Moreover, patients with equivocal/false polysomic tumours are prevented from a potentially beneficial anti‐HER2treatment. Here we evaluated theRAI1,D17S122andTP53hybridization markers to indicate true polysomy reliably and to reclassify equivocal samples accurately asHER2‐positive.

Methods and results

Samples with (n= 82) and without (n= 52) increased cen17 copy numbers and 78 evidentlyHER2‐amplified specimens were analysed using dual and triple marker hybridization probes. Selected putative polysomic samples were subjected to array‐based comparative genomic hybridization (aCGH). We found that 37.8% samples with putative polysomy 17 did not show any gain inRAI1,D17S122orTP53. Accordingly, aCGH revealed evidence for the presence ofHER2/cen17 co‐amplification rather than for true polysomy in those cases. Reflex testing using alternate 17p markers reclassified up to 56.3% equivocal cases asHER2‐positive and the combined assessment of a 17p and 17q locus allows the differentiation of true versus false polysomy.

Conclusions

An increased cen17 copy number does not necessarily reflect polysomy, and reflex testing facilitates the reclassification of ‘equivocals’. Nevertheless, the prognostic and predictive value of aHER2/cen17 co‐amplification versusHER2gene amplification alone must still be evaluated prospectively.
PD‐L1 overexpression in ampulla of Vater carcinoma and its pre‐invasive lesions
Authors: Saraggi Deborah , Galuppini Francesca , Remo Andrea , Urso Emanuele D L , Bacchin Deborah , Salmaso Roberta , Lanza Cristiano , Bao Riccardo Q , Fanelli Giuseppe N , Guzzardo Vincenza , Luchini Claudio , Scarpa Marco , Farinati Fabio , Fassan Matteo , Rugge Massimo
Published: May 2017

Aims

PD‐1/PD‐L1 checkpoint immunotherapy has been proposed recently as a promising treatment in relapsed/refractory disease, used eventually in combination with traditional chemotherapy in different cancer settings. To date, no data are available concerning PD‐L1 expression in ampulla of Vater carcinoma and its pre‐invasive lesions.

Methods and results

We assessed the immunohistochemical expression of PD‐L1 in a series of 26 ampullary adenocarcinomas, 50 ampullary dysplastic lesions and 10 normal duodenal mucosa samples. Moreover, in all cases DNA mismatch repair proteins status was investigated. PD‐L1 was expressed in seven of 26 (26.9%) invasive carcinomas and three of 50 (6.0%) dysplastic samples. Most of the PD‐L1‐positive tumours (seven of 10) were intestinal‐type and poorly differentiated (G3). The number of PD‐L1‐positive stromal lymphoid cells was significantly higher in dysplastic and invasive lesions than in the normal samples (P = 0.011). Nineteen dysplastic lesions and eight invasive carcinomas did not show any evident epithelial or stromal PD‐L1 expression. Four of the carcinomas were mismatch repair‐deficient and two of these were PD‐L1‐positive. Furthermore, mismatch repair‐deficient lesions showed a significantly higher average of PD‐L1‐positive stromal lymphoid cells than those of neoplastic PD‐L1‐negative samples (62.8 versus 21.6; P < 0.001).

Conclusions

The present results suggest a role of the PD‐1/PD‐L1 axis in ampullary adenocarcinomas, and therefore this may also prompt consideration of checkpoint immunotherapy as a novel promising treatment for these tumours.
The TLR4–TRIF pathway can protect against the development of experimental allergic asthma
Authors: Shalaby Karim H. , Al Heialy Saba , Tsuchiya Kimitake , Farahnak Soroor , McGovern Toby K. , Risse Paul‐Andre , Suh Woong‐Kyung , Qureshi Salman T. , Martin James G.
Published: May 2017

The Toll‐like receptor (TLR) adaptor proteins myeloid differentiating factor 88 (MyD88) and Toll, interleukin‐1 receptor and resistance protein (TIR) domain‐containing adaptor inducing interferon‐β (TRIF) comprise the two principal limbs of the TLR signalling network. We studied the role of these adaptors in the TLR4‐dependent inhibition of allergic airway disease and induction of CD4+ ICOS+ T cells by nasal application of Protollin™, a mucosal adjuvant composed of TLR2 and TLR4 agonists. Wild‐type (WT), Trif−/− or Myd88−/− mice were sensitized to birch pollen extract (BPEx), then received intranasal Protollin followed by consecutive BPEx challenges. Protollin's protection against allergic airway disease was TRIF‐dependent and MyD88‐independent. TRIF deficiency diminished the CD4+ ICOS+ T‐cell subsets in the lymph nodes draining the nasal mucosa, as well as their recruitment to the lungs. Overall, TRIF deficiency reduced the proportion of cervical lymph node and lung CD4+ ICOS+ Foxp3− cells, in particular. Adoptive transfer of cervical lymph node cells supported a role for Protollin‐induced CD4+ ICOS+ cells in the TRIF‐dependent inhibition of airway hyper‐responsiveness. Hence, our data demonstrate that stimulation of the TLR4‐TRIF pathway can protect against the development of allergic airway disease and that a TRIF‐dependent adjuvant effect on CD4+ ICOS+ T‐cell responses may be a contributing mechanism.
Association between cytokine profile and transcription factors produced by T‐cell subsets in early‐ and late‐onset pre‐eclampsia
Authors: Ribeiro Vanessa R. , Romao‐Veiga Mariana , Romagnoli Graziela G. , Matias Mariana L. , Nunes Priscila R. , Borges Vera Therezinha M. , Peracoli Jose C. , Peracoli Maria Terezinha S.
Published: May 2017

Pre‐eclampsia (PE) is an obstetric pathology characterized by abnormal activation of the innate and adaptive immune systems dependent on the imbalance of T helper subsets. The present study aimed to evaluate the gene and protein expression of T helper type 1 (Th1)/Th2/Th17/regulatory T (Treg) cell transcription factors in peripheral blood lymphocytes from pregnant women with PE employing quantitative RT‐PCR and flow cytometry techniques, as well as the cytokine profile produced by these CD4+ T‐cell subsets in the plasma of pregnant women with PE, classified as early‐onset PE (n = 20), late‐onset PE (n = 20) and normotensive pregnant women (n = 20). Results showed a higher percentage of CD4+ T cells expressing the RORc transcription factor (Th17) and a lower percentage of cells expressing FoxP3 (Treg) in women with early‐onset PE compared with late‐onset PE and normotensive groups. A lower gene expression of GATA‐3 transcription factor was detected in cells of women with early‐onset PE compared with the late‐onset PE group. Endogenous plasma levels of interleukin‐6 (IL‐6), IL‐17 and tumour necrosis factor‐α were significantly higher in the early‐onset PE group than in the late‐onset PE and normotensive groups, whereas IL‐4 (Th2 profile) and IL‐22 (Th17 profile), were not significantly different between the studied groups. The endogenous levels of transforming growth factor‐β and IL‐10 were significantly lower in the pre‐eclamptic than in the normotensive groups of the same gestational age, with a significant difference between early‐ and late‐onset PE. The results show that in women with PE there is an imbalance between inflammatory and anti‐inflammatory profiles in CD4+ T‐cell subsets, with polarization to Th17 profiles in the early‐onset PE, considered as the severe form of PE.
Epigenetic modifications of the VH region after DJH recombination in Pro‐B cells
Authors: Dong Yanying , Wu Caijun , Zhao Xiaohui , Zhang Ping , Zhang Hua , Zheng Mingzhe , Li Shichang , Jiao Junna , Yu Xiaozhuo , Lv Zhuangwei , Ji Yanhong
Published: May 2017

The variable region of murine immunoglobulin heavy chain (Igh) is assembled by sequential DH–JH and VH–DJH recombination. The accessibility of the Igh locus determines the order of rearrangement. Because of the large number of VH genes and the lack of a suitable model, the epigenetic modifications of VH genes after DJH recombination have not previously been characterized. Here, we employed two v‐Abl pro‐B cell lines, in which the Igh locus is in germline and DJH‐recombined configurations, respectively. The DJH junction displays the characteristics of a recombination centre, such as high levels of activation‐associated histone modifications and recombination‐activating gene protein (RAG) binding in DJH‐rearranged pro‐B cells, which extend the recombination centre model proposed for the germline Igh locus. The different domains of the VH region have distinct epigenetic characteristics after DJH recombination. Distal VH genes have higher levels of active histone modifications, germline transcription and Pax5 binding, and good quality recombination signal sequences. Proximal VH genes are relatively close to the DJH recombination centre, which partially compensates for the low levels of the above active epigenetic modifications. DJH recombination centre might serve as a cis‐acting element to regulate the accessibility of the VH region. Furthermore, we demonstrate that RAG weakly binds to functional VH genes, which is the first detailed assessment of RAG dynamic binding to VH genes. We provide a way for VH–DJH recombination in which the VH gene is brought into close proximity with the DJH recombination centre for RAG binding by a Pax5‐dependent chromosomal compaction event, and held in this position for subsequent cleavage and VH–DJH joining.
Functional analysis by minigene assay of putative splicing variants found in Bardet–Biedl syndrome patients
Authors: Álvarez‐Satta María , Castro‐Sánchez Sheila , Pousada Guillermo , Valverde Diana
Published: May 2017

Bardet–Biedl syndrome (BBS) and Alström syndrome (ALMS) are rare diseases belonging to the group of ciliopathies. Although mutational screening studies of BBS/ALMS cohorts have been extensively reported, little is known about the functional effect of those changes. Thus, splicing variants are estimated to represent 15% of disease‐causing mutations, and there is growing evidence that many exonic changes are really splicing variants misclassified. In this study, we aimed to analyse for the first time several variants in BBS2, ARL6/BBS3, BBS4 and ALMS1 genes predicted to produce aberrant splicing by minigene assay. We found discordance between bioinformatics analysis and experimental data when comparing wild‐type and mutant constructs. Remarkably, we identified nonsense variants presumably resistant to nonsense‐mediated decay, even when a premature termination codon would be introduced in the second amino acid (p.(G2*) mutation in ARL6/BBS3 gene). As a whole, we report one of the first functional studies of BBS/ALMS1 variants using minigene assay, trying to elucidate their role in disease. Functional studies of variants identified in BBS and ALMS patients are essential for their proper classification and subsequent genetic counselling and could also be the start point for new therapeutic approaches, currently based only on symptomatic treatment.
Sodium‐glucose cotransporter‐2 inhibitor luseogliflozin added to glucagon‐like peptide 1 receptor agonist liraglutide improves glycemic control with bodyweight and fat mass reductions in Japanese patients with type 2 diabetes: A 52‐week, open‐label, single‐arm study
Authors: Seino Yutaka , Yabe Daisuke , Sasaki Takashi , Fukatsu Atsushi , Imazeki Hisae , Ochiai Hidekazu , Sakai Soichi
Published: May 2017

Aims/Introduction

The aim of the present study was to evaluate the safety and efficacy of luseogliflozin added to liraglutide monotherapy in Japanese individuals with type 2 diabetes.

Materials and Methods

This 52‐week, multicenter, open‐label, single‐arm clinical study enrolled Japanese patients who had inadequate glycemic control with diet/exercise and liraglutide monotherapy. Major efficacy end‐points included the changes from baseline in glycated hemoglobin, fasting plasma glucose and bodyweight. Body composition was also assessed in individuals who had access to bioelectrical impedance analysis. Safety assessments included adverse events, clinical laboratory tests, vital signs and 12‐lead electrocardiograms.

Results

Of 76 patients who received luseogliflozin, 62 completed the study. The changes from baseline in glycated hemoglobin, fasting plasma glucose, and bodyweight (mean ± SE) were −0.68 ± 0.10%, −32.1 ± 3.6 mg/dL and −2.71 ± 0.24 kg at week 52, respectively (all, P < 0.001 vs baseline). Luseogliflozin was associated with greater reductions in fat mass than lean mass at all measuring points (n = 22): fat vs lean mass changes (mean ± SE) at week 52 were −2.49 ± 0.45 kg (P < 0.001 vs baseline) and −0.44 ± 0.26 kg (P = 0.107 vs baseline), respectively. Insulin secretion and Matsuda Index were also improved at weeks 12 and 52 compared with baseline. Adverse events and adverse drug reactions occurred in 65.8 and 27.6% of patients, respectively. The overall safety profile, including frequency of hypoglycemia, was found to be consistent with those of previous studies and there were no new safety concerns.

Conclusions

Luseogliflozin added to liraglutide was well tolerated, and improved glycemic control with bodyweight and fat mass reductions in Japanese type 2 diabetes patients.
In vivo microvascular imaging of cutaneous actinic keratosis, Bowen's disease and squamous cell carcinoma using dynamic optical coherence tomography
Authors: Themstrup L. , Pellacani G. , Welzel J. , Holmes J. , Jemec G.B.E. , Ulrich M.
Published: May 2017

Background

A clear distinction between actinic keratosis (AK), Bowen's disease (BD) and squamous cell carcinoma (SCC) cannot reliably be made by clinical and dermoscopic evaluation alone. Dynamic optical coherence tomography (D‐OCT) is a novel angiographic variant of OCT that allows for non‐invasive, in vivo evaluation of the cutaneous microvascular morphology.

Objective

To investigate the microvascular structures of AK, BD and invasive SCC using D‐OCT in order to gain insights into the microvascular morphology of lesions in the spectrum of keratinocyte skin cancers.

Methods

Forty‐seven patients with a total of 54 lesions (18 AK, 12 BD and 24 SCC) were included in the study. D‐OCT still images of AK, BD and SCC at three predefined skin depths were prepared and randomized, creating a study set of 162 D‐OCT images. Three observers performed blinded evaluations of the randomized study set assessing multiple parameters including the different types of vascular morphology. Non‐blinded quantitative measurements of vascular diameter were also performed.

Results

The blinded observer analysis suggests that D‐OCT evaluation of the vascular morphology may aid in distinguishing AK, BD and SCC lesions. We identified two vascular shapes that presented significantly differently across the lesion types, namely ‘blobs’ and ‘curves’. A strong presence of blobs at 300 μm skin depth was characteristically seen in a third of BD cases, while not or only slightly present in AK and SCC lesions. Vascular curves were predominantly present in AK lesions.

Conclusion

We identified various vascular D‐OCT features that may aid in non‐invasively differentiating subtypes within the keratinocyte skin cancer spectrum.
Limited impact of awareness‐raising campaigns on hepatitis C testing practices among general practitioners
Authors: McLeod A. , Cullen B. L. , Hutchinson S. J. , Roy K. M. , Dillon J. F. , Stewart E. A. , Goldberg D. J.
Published: May 2017

The global hepatitis strategy calls for increased effort to diagnose those infected, with a target of 90% diagnosed by 2030. Scotland's Action Plan on Hepatitis C included awareness‐raising campaigns, undertaken during 2008‐2011, to promote testing by general practitioners. We examined hepatitis C virus (HCV) testing practice among general practitioners before and following these campaigns. Scottish general practitioners were surveyed, using Dillman's method, in 2007 and 2013; response rates were 69% and 60%, respectively. Most respondents offer testing when presented with a risk history (86% in 2007, 88% in 2013) but only one‐fifth actively sought out risk factors (19% in 2007, 21% in 2013). Testing was reportedly always/almost always/usually offered to people who inject drugs (84% in 2007, 87% in 2013). Significant improvements in the offer of testing were reported in patients with abnormal LFTs (41% in 2007, 65% in 2013, P<.001) and who had received medical/dental treatment in high prevalence countries (14% in 2007, 24% in 2013, P=.001). In 2013, 25% of respondents had undertaken HCV‐related continued professional development. This group was significantly more likely to actively seek out risk factors (P=.009) but only significantly more likely to offer a test to patients who had received medical/dental treatment in high prevalence countries (P=.001). Our findings suggest that government‐led awareness raising campaigns have limited impact on general practitioners’ testing practices. If the majority of the HCV‐infected population are to be diagnosed, practitioner‐based or physician‐centred interventions should be considered alongside educational initiatives targeted at professionals.
HIV/HCV coinfection and the risk of cardiovascular disease: A meta‐analysis
Authors: Osibogun O. , Ogunmoroti O. , Michos E. D. , Spatz E. S. , Olubajo B. , Nasir K. , Madhivanan P. , Maziak W.
Published: May 2017

The emergence of improved antiretroviral therapy has increased the life expectancy of human immunodeficiency virus (HIV)‐infected individuals, although there is an increased susceptibility to developing cardiovascular diseases (CVD). The risk for CVD is purported to be even higher among people with HIV and hepatitis C virus (HCV) coinfection because of the increased inflammatory response, which may synergistically impact CVD risk. However, studies comparing CVD outcomes between HIV alone and HIV/HCV individuals have been discordant. Accordingly, we conducted a meta‐analysis to clarify and quantify the association between HIV/HCV coinfection and the risk for CVD. We searched EMBASE, CINAHL, Google Scholar, PubMed, and Web of Science from inception to December 2016 to identify studies that provided information on HIV/HCV coinfection and CVD, defined as coronary artery disease, congestive heart failure and stroke. We used a random‐effects model to abstract and pool data on the hazard ratios (HRs) for CVD. HRs were adjusted for traditional CVD risk factors including age, sex, smoking, hypertension, diabetes and LDL cholesterol. Among the 283 articles reviewed, four cohort studies met inclusion criteria with a total of 33 723 participants. The pooled adjusted HRs for the association between HIV/HCV coinfection and CVD were 1.24 (95% CI: 1.07‐1.40) compared to HIV monoinfection. The test for heterogeneity was not statistically significant (I2=0.0%, P=.397). In conclusion, individuals with HIV/HCV coinfection had an increased CVD risk compared to those with HIV monoinfection. More research is needed to further examine the nature of this association, and response to traditional risk‐reduction therapies.
Protection of traditional knowledge: A perspective on Intellectual Property Law in Indonesia
Authors: Irawan Candra
Published: May 2017

Traditional knowledge (TK) has historical, cultural, scientific and economic value. Its community ownership characteristics differ from law dealing with traditional intellectual property (e.g. the TRIPS Agreement), which is characterized as individualistic, materialistic and exploitative. Such differences leave the TK possessed by developing countries, including Indonesia, unprotected. TK is often exploited by companies in developed countries to obtain an economic benefit and recognition of the knowledge as an intellectual property right (IPR) (in particular, through patents and copyright), without respect for the original community owner or considering it as within the public domain. Indonesia must protect its wealth of TK in two ways, namely: (i) starting with non‐legal protection through activities tracking, preserving, promoting, documenting and digitizing TK in a manner that is easily accessible, both nationally and internationally, and establishing cooperation with the intellectual property offices of developed countries so that the documentation and digitization of Indonesian TK can become one of the comparators in examining patent and other intellectual property petitions and (ii) legal protection of such intellectual property through new sui generis regulations (currently being discussed in the draft law on Traditional Knowledge and Traditional Cultural Expressions).
“Fix Me Another Marguerite!”: Species delimitation in a group of intensively hybridizing lineages of ox‐eye daisies (Leucanthemum Mill., Compositae‐Anthemideae)
Authors: Wagner Florian , Härtl Sabine , Vogt Robert , Oberprieler Christoph
Published: May 2017

Delineating species boundaries in the framework of the multi‐species coalescent (MSC) proves to be a reliable, objective, and reproducible method in an increasing number of studies. However, the underlying model assumes the lack of gene flow after speciation; an assumption which may be frequently violated in plant evolution. This study evaluates the robustness of currently available species delimitation methods implemented in beast (BFD, BFD*, and dissect) in the closely‐knit ox‐eye daisy group around Leucanthemum ageratifolium Pau. Comprising five taxa being allopatrically distributed between northern Spain and southern Italy this study group shows signs of hybridization with the widespread and codistributed species Leucanthemum vulgare (Vaill.) Lam. to various extent. As expected, our empirical analyses based on both AFLP fingerprinting and sequence data demonstrate that the robustness of species delimitation results is considerably influenced by the intensity of hybridization among species and the number of hybrid individuals included. Therefore, we set up a methodological pipeline with a first step of identification and subsequent removal of individuals showing admixed genetic patterns caused by actual interbreeding using AFLP‐fingerprint and morphometric data, followed by application of different Bayesian MSC species delimitation methods based on the remnant individuals using both AFLP‐fingerprint and sequence data (four nuclear markers, five concatenated intergenic spacer regions of the plastid genome). The results argue for acknowledgement of Leucanthemum laciniatum, L. legraeanum, and L. ligusticum as independent species, show the close relationship of L. ageratifolium, L. monspeliense, and L. vulgare, and give rise to the description of three nothospecies new to science.
Unravelling seed dispersal through fragmented landscapes: Frugivore species operate unevenly as mobile links
Authors: González‐Varo Juan P. , Carvalho Carolina S. , Arroyo Juan M. , Jordano Pedro
Published: May 2017

Seed dispersal constitutes a pivotal process in an increasingly fragmented world, promoting population connectivity, colonization and range shifts in plants. Unveiling how multiple frugivore species disperse seeds through fragmented landscapes, operating as mobile links, has remained elusive owing to methodological constraints for monitoring seed dispersal events. We combine for the first time DNA barcoding and DNA microsatellites to identify, respectively, the frugivore species and the source trees of animal‐dispersed seeds in forest and matrix of a fragmented landscape. We found a high functional complementarity among frugivores in terms of seed deposition at different habitats (forest vs. matrix), perches (isolated trees vs. electricity pylons) and matrix sectors (close vs. far from the forest edge), cross‐habitat seed fluxes, dispersal distances and canopy‐cover dependency. Seed rain at the landscape‐scale, from forest to distant matrix sectors, was characterized by turnovers in the contribution of frugivores and source‐tree habitats: open‐habitat frugivores replaced forest‐dependent frugivores, whereas matrix trees replaced forest trees. As a result of such turnovers, the magnitude of seed rain was evenly distributed between habitats and landscape sectors. We thus uncover key mechanisms behind “biodiversity–ecosystem function” relationships, in this case, the relationship between frugivore diversity and landscape‐scale seed dispersal. Our results reveal the importance of open‐habitat frugivores, isolated fruiting trees and anthropogenic perching sites (infrastructures) in generating seed dispersal events far from the remnant forest, highlighting their potential to drive regeneration dynamics through the matrix. This study helps to broaden the “mobile‐link” concept in seed dispersal studies by providing a comprehensive and integrative view of the way in which multiple frugivore species disseminate seeds through real‐world landscapes.
Novel method for the depletion of cariogenic bacteria using dextranomer microspheres
Authors: Mashburn‐Warren L. , Downey J.S. , Goodman S.D.
Published: May 2017

Streptococcus mutans is recognized as one of the key contributors to the dysbiotic state that results in dental caries. Existing treatment strategies reduce the incidence of tooth decay, but they also eliminate both the cariogenic and beneficial microbes. Here we introduce a novel treatment alternative using Sephadex, cross‐linked dextranomer microspheres (DMs), typically used for gel filtration chromatography. In addition DM beads can be used for affinity purification of glucosyltransferases (GTFs) from S. mutans. In this study we take advantage of the native pathogenic mechanisms used by S. mutans to adhere, form a biofilm and induce dental caries through the expression of surface‐associated GTFs. We demonstrate that planktonic and biofilm‐grown (adhered to hydroxyapatite‐coated pegs to mimic the tooth surface) S. mutans, specifically and competitively attach to DMs. Further investigation demonstrated that DMs are a specific affinity resin for S. mutans and other cariogenic/pathogenic oral streptococci, whereas other commensal and probiotic strains failed to readily adhere to DMs. Using antimicrobial cargo loaded into the DM lumen, we demonstrate that when in co‐culture with non‐binding to even modestly binding commensal species, S. mutans was selectively killed. This proof of concept study introduces a novel means to safely and effectively reduce the pool of S. mutans and other pathogenic streptococci in the oral cavity with limited disturbance of the necessary commensal (healthy) microbiota when compared with current oral healthcare products.