bluuebunny/crossref_metadata_2025 huggingface dataset:
YeATSAM analysis of the chloroplast genome of walnut reveals several putative un-annotated genes and mis-annotation of the trans-spliced rps12 gene in other organisms
Authors: Chakraborty Sandeep
Published: December 2016

An open reading frame (ORF) is genomic sequence that can be translated into amino acids, and does not contain any stop codon. Previously, YeATSAM analyzed ORFs from the RNA-seq derived transcriptome of walnut, and revealed several genes that were not annotated by widely-used methods. Here, a similar ORF-based method is applied to the chloroplast genome from walnut (Accid:KT963008). This revealed, in addition to the ~84 protein coding genes, ~100 additional putative protein coding genes with homology to RefSeq proteins. Some of these genes have corresponding transcripts in the previously derived transcriptome from twenty different tissues, establishing these as bona fide genes. Other genes have introns, and need to be manually annotated. Importantly, this analysis revealed the mis-annotation of the rps12 gene in several organisms which have used an automated annotation flow. This gene has three exons - exon1 is ~28kbp away from exon2 and exon3 - and is assembled by trans-splicing. Automated annotation tools are more likely to select an ORF closer to exon2 to complete a possible protein, and are unlikely to properly annotate trans-spliced genes. A database of trans-spliced genes would greatly benefit annotations. Thus, the current work continues previous work establishing the proper identification of ORFs as a simple and important step in many applications, and the requirement of validation of annotations.
Accuracy in wrist-worn, sensor-based measurements of heart rate and energy expenditure in a diverse cohort
Authors: Shcherbina Anna , Mattsson C. Mikael , Waggott Daryl , Salisbury Heidi , Christle Jeffrey W. , Hastie Trevor , Wheeler Matthew T. , Ashley Euan A.
Published: December 2016

Background

The ability to measure activity and physiology through wrist-worn devices provides an opportunity for cardiovascular medicine. However, the accuracy of commercial devices is largely unknown.

Objective

To assess the accuracy of seven commercially available wrist-worn devices in estimating heart rate (HR) and energy expenditure (EE) and to propose a wearable sensor evaluation framework.

Methods

We evaluated the Apple Watch, Basis Peak, Fitbit Surge, Microsoft Band, Mio Alpha 2, PulseOn, and Samsung Gear S2. Participants wore devices while being simultaneously assessed with continuous telemetry and indirect calorimetry while sitting, walking, running, and cycling. Sixty volunteers (29 male, 31 female, age 38 ± 11 years) of diverse age, height, weight, skin tone, and fitness level were selected. Error in HR and EE was computed for each subject/device/activity combination.

Results

Devices reported the lowest error for cycling and the highest for walking. Device error was higher for males,greater body mass index, darker skin tone, and walking. Six of the devices achieved a median error for HR below 5% during cycling. No device achieved an error in EE below 20 percent. The Apple Watch achieved the lowest overall error in both HR and EE, while the Samsung Gear S2 reported the highest.

Conclusions

Most wrist-worn devices adequately measure HR in laboratory-based activities, but poorly estimate EE, suggesting caution in the use of EE measurements as part of health improvement programs. We propose reference standards for the validation of consumer health devices (http://precision.stanford.edu/).

Abbreviations

(EE)

Energy expenditure

(HR)

Heart rate

(GEE)

General estimating equation
Familial Mutations and Post-translational Modifications of UCH-L1 in Parkinson’s Disease and Neurodegenerative Disorders
Authors: Lee Yun-Tzai Cloud , Hsu Shang-Te Danny
Published: December 2016

Parkinson’s disease (PD) is one of the most common progressive neurodegenerative disorders in modern society. The disease involves many genetic risk factors as well as a sporadic pathogenesis that is age- and environment-dependent. Of particular interest is the formation of intra-neural fibrillar aggregates, namely Lewy bodies (LBs), the histological hallmark of PD, which results from aberrant protein homeostasis or misfolding that results in neurotoxicity. A better understanding of the molecular mechanism and composition of these cellular inclusions will help shed light on the progression of misfolding-associated neurodegenerative disorders. Ubiquitin carbonyl-terminal hydrolase L1 (UCH-L1) is found to co-aggregate with α-synuclein (αS), the major component of LBs. Several familial mutations of UCH-L1, namely p.Ile93Met (p.I93M), p.Glu7Ala (p.E7A), and p.Ser18Tyr (p.S18Y), are associated with PD and other neurodegenerative disorders. Here, we review recent progress and recapitulate the impact of PD-associated mutations of UCH-L1 in the context of their biological functions gleaned from biochemical and biophysical studies. Finally, we summarize the effect of these genetic mutations and post-translational modifications on the association of UCH-L1 and PD in terms of loss of cellular functions or gain of cellular toxicity.
In silicoepitope prediction and 3D model analysis of Peste des petits ruminants virus nucleoprotein (PPRV N)
Authors: Baloi Bakang
Published: December 2016

Peste des petits ruminants virus (PPRV) is an acute, highly contagious viral disease of small ruminants. It is endemic to sub-Saharan Africa, Asia and the Arabian Peninsula. The disease is a major constraint to food security, causing significant economic losses to subsistence farmers in affected areas.

The nucleoprotein of morbilliviruses is highly immunogenic and produced in large quantities in virus infected cells. This makes it a suitable target for the host’s immune response. In this study, B-cell and T-cell epitopes of PPRV Nig/75/1 nucleoprotein were predicted using a suite ofin silicotools. Forty-six T-cell epitopes were predicted, of which 38 were MHC-I binding while eight were MHC-II binding. Of the 19 B-cell epitopes predicted, 15 were linear epitopes while four were discontinuous epitopes. Homology modelling of PPRV-N was done to elucidate the 3D structure of the protein and conformational epitopes. Conservation analysis of the discontinuous epitopes gave an indication into the similarity of the selected epitopes with other isolates of PPRV.

Predicted epitopes may form an important starting point for serological screening and diagnostic tools against PPRV. Experimental validation of the predicted epitopes will assist in selection of promising candidates for consideration as antigen-based diagnostic tools. Such diagnostic tools would play a role in the global fight and possible eradication of PPR.
Co-estimating Reticulate Phylogenies and Gene Trees from Multi-locus Sequence Data
Authors: Wen Dingqiao , Nakhleh Luay
Published: December 2016

The multispecies network coalescent (MSNC) is a stochastic process that captures how gene trees grow within the branches of a phylogenetic network. Coupling the MSNC with a stochastic mutational process that operates along the branches of the gene trees gives rise to a generative model of how multiple loci from within and across species evolve in the presence of both incomplete lineage sorting (ILS) and reticulation (e.g., hybridization). We report on a Bayesian method for sampling the parameters of this generative model, including the species phylogeny, gene trees, divergence times, and population sizes, from DNA sequences of multiple independent loci. We demonstrate the utility of our method by analyzing simulated data and reanalyzing three biological data sets. Our results demonstrate the significance of not only co-estimating species phylogenies and gene trees, but also accounting for reticulation and ILS simultaneously. In particular, we show that when gene flow occurs, our method accurately estimates the evolutionary histories, coalescence times, and divergence times. Tree inference methods, on the other hand, underestimate divergence times and overestimate coalescence times when the evolutionary history is reticulate. While the MSNC corresponds to an abstract model of “intermixture,” we study the performance of the model and method on simulated data generated under a gene flow model. We show that the method accurately infers the most recent time at which gene flow occurs. Finally, we demonstrate the application of the new method to a 106-locus yeast data set. [Multispecies network coalescent; reticulation; incomplete lineage sorting; phylogenetic network; Bayesian inference; RJMCMC.]
Automatic processing of multimodal tomography datasets
Authors: Parsons Aaron D. , Price Stephen W. T. , Wadeson Nicola , Basham Mark , Beale Andrew M. , Ashton Alun W. , Mosselmans J. Frederick. W. , Quinn Paul. D.
Published: December 2016

With the development of fourth-generation high-brightness synchrotrons on the horizon, the already large volume of data that will be collected on imaging and mapping beamlines is set to increase by orders of magnitude. As such, an easy and accessible way of dealing with such large datasets as quickly as possible is required in order to be able to address the core scientific problems during the experimental data collection. Savu is an accessible and flexible big data processing framework that is able to deal with both the variety and the volume of data of multimodal and multidimensional scientific datasets output such as those from chemical tomography experiments on the I18 microfocus scanning beamline at Diamond Light Source.
Dexmedetomidine preconditioning for myocardial protection in ischaemia‐reperfusion injury in rats by downregulation of the high mobility group box 1‐toll‐like receptor 4‐nuclear factor κB signalling pathway
Authors: Yang Yu‐fan , Peng Ke , Liu Hong , Meng Xiao‐wen , Zhang Jing‐jing , Ji Fu‐hai
Published: December 2016

Pharmacological preconditioning reduces myocardial infarct size in ischaemia‐reperfusion (I‐R) injury. Dexmedetomidine, a selective α2‐adrenoceptor agonist, has a proven cardioprotective effect when administered prior to I‐R, although the underlying mechanisms for this effect are not fully understood. We evaluated whether dexmedetomidine preconditioning could induce a myocardio‐protective effect against I‐R injury by inhibiting associated inflammatory processes through downregulation of the high mobility group box 1 (HMGB1)‐toll‐like receptor 4 (TLR4)‐nuclear factor κB (NF‐κB) signalling pathway. Seventy rats were randomly assigned to seven groups: a control and six test groups, involving I‐R for 30 and 120 minutes, respectively, in isolated rat hearts and different pretreatment protocols with dexmedetomidine (10 nmol/L) as well as yohimbine (1 μmol/L) and recombinant HMGB1 peptide (rHMGB1; 20 μg/L), alone or in combination with dexmedetomidine. Cardiac function was recorded; myocardial HMGB1, TLR4, and NF‐κB activities and levels of tumour necrosis factor‐α (TNF‐α) and interleukin‐6 (IL‐6) were measured as were lactate dehydrogenase (LDH) and creatine kinase (CK) in coronary outflow. Dexmedetomidine preconditioning significantly improved cardiac function (P<.05), downregulated the expression of HMGB1‐TLR4‐NF‐κB, reduced levels of TNF‐α and IL‐6 in isolated ventricles during I‐R injury, and significantly reduced CK and LDH levels in coronary outflow (P<.05). All of these effects were partially reversed by yohimbine (P<.05) or rHMGB1 (P<.05). Dexmedetomidine preconditioning alleviated myocardial I‐R injury in rats through inhibition of inflammatory processes associated with downregulation of the HMGB1‐TLR4‐NF‐κB signalling pathway via activation at α2‐adrenergic receptors.
The Evolving Dynamics of Employer‐Sponsored Health Insurance: Implications for Workers, Employers, and the Affordable Care Act
Authors: GRAVES JOHN A. , MISHRA PRANITA
Published: December 2016

Policy Points:

Increasingly, Americans are relying on coverage through a family member to maintain continuous insurance when their own employer‐sponsored insurance (ESI) ends. Meanwhile, employers have responded by limiting access to and imposing surcharges on dependent coverage elections.

Between 2005 and 2013, adults who transitioned off ESI became likely to enroll in a non‐group plan and were twice as likely to become uninsured. Special Enrollment Period enrollment figures under the Affordable Care Act (ACA) suggest these dynamics have not meaningfully changed since 2014.

Moving forward, more Americans will rely on alternative sources for affordable health insurance outside the ESI system. New ACA outreach efforts are needed to identify and enroll the large and increasing number of individuals who face the end of ESI benefits throughout the year.

Context

Employer‐sponsored insurance (ESI) is the predominant form of health insurance coverage in the United States, yet little is known about transitions into and out of ESI or whether turnover has increased over time.

Methods

We fit multistate dynamic transition models for adults aged 18‐61 using Survey of Income and Program Participation data from 2005‐2007 to 2010‐2013 and preliminary Medical Expenditure Panel Survey from the period 2012‐2014.

Findings

Over a 2‐year period beginning in 2010, 34.6% of adults with ESI experienced a change, up from 31.7% in 2005‐2007. Transitions occurred most frequently among young adults, Hispanic adults, low‐income adults, those in fair or poor health, and service industry workers. But even the groups with the lowest turnover—older adults, married adults, and those with a college degree—had 2‐year rates of change of up to 30%. The probability that an ESI policyholder regained an employer‐based policy after a job change declined by 15% between 2005 and 2013. Meanwhile, the probability that an ESI policyholder enrolled as a dependent on another family member's plan or became uninsured increased twofold. We found little evidence of changes in these dynamics during the first year (2014) of the Affordable Care Act's (ACA) major coverage reforms.

Conclusions

Increasingly, Americans are relying on dependent ESI coverage through a family member to maintain continuous insurance when their own employer‐based benefits end. Those who transitioned off ESI were also less likely to enroll in a non‐group plan and were twice as likely to become uninsured. The first year of the ACA did not see material changes in the likelihood that an ESI‐insured adult became uninsured or switched to an alternative public or private plan. New ACA outreach efforts are needed to identify and enroll the large and increasing number of individuals who face the end of ESI benefits throughout the year.
Negative symptoms mediate the relationship between neurocognition and function in individuals at ultrahigh risk for psychosis
Authors: Glenthøj L. B. , Jepsen J. R. M. , Hjorthøj C. , Bak N. , Kristensen T. D. , Wenneberg C. , Krakauer K. , Nordentoft M. , Fagerlund B.
Published: December 2016

Objective

Neurocognition is known to impact functioning in individuals at ultrahigh risk (UHR) for psychosis, but studies investigating potential mediators of this relationship are scarce. Building on evidence from schizophrenia spectrum disorders, the study tested whether negative symptoms and social skills act as mediators between neurocognition and functional outcome in UHR individuals.

Methods

Ultrahigh risk participants (N = 84) underwent neurocognitive testing using the Brief Assessment of Cognition in Schizophrenia. Social skills and negative symptoms were assessed using the High‐Risk Social Challenge task and the Scale for the Assessment of Negative Symptoms respectively. Four instruments were used to assess overall functioning, and one instrument assessed quality of life encompassing social functioning.

Results

The cross‐sectional analyses revealed that neurocognition was related to the measures of functioning. Negative symptoms mediated the relationship between neurocognition and four of the five measures of functioning. We did not find social skills to mediate between neurocognition and functioning.

Conclusion

Negative symptoms appear to mediate the relationship between neurocognition and functional outcome in UHR individuals, but the finding needs to be confirmed and extended to longitudinal studies. This underscores the importance of focusing on both neurocognition and negative symptoms when aiming at improving the functional outcome of UHR individuals.
Oral health interventions in Australian Aboriginal communities: a review of the literature
Authors: Patel J , Durey A , Hearn L , Slack‐Smith LM
Published: December 2016

Aboriginal Australians experience significant disparities in oral health with even poorer outcomes reported in rural and remote areas. The high rates of preventable dental disease in Aboriginal communities are a serious concern from a social standpoint and in terms of service provision and health care expenditure. In this review, primary research literature was comprehensively reviewed. Papers were selected if they reported designing or implementing an intervention or oral health programme specific to the needs of Aboriginal communities. Twenty‐one publications fulfilled the inclusion criteria with 19 different interventions being described. Interventions were categorized using a classification adapted from the work of Whitehead (2002). The review identified interventions that aimed to reduce early childhood caries, increase services to remote communities, develop the role of Aboriginal health workers, improve oral health literacy, establish water fluoridation and provide periodontal therapy. Implementing successful oral health interventions in Aboriginal communities is a challenge that is compounded by the complex interplay between psychosocial and cultural determinants. Even interventions that follow a rigorous and consultative design have a high failure rate in Aboriginal communities if upstream determinants of health are not adequately understood and addressed.
In‐training assessments: ‘The difficulty is trying to balance reality and really tell the truth’
Authors: Scarff Catherine E , Corderoy Robert M , Bearman Margaret
Published: December 2016

Background

In‐training assessments (ITA) aim to evaluate trainees’ progress and give valuable feedback on their performance. Many factors can affect supervisors during their completion of assessments and these can influence the final results recorded.

Methods

This is the second part of a study of supervisors of the Australasian College of Dermatologists (ACD) and presents the qualitative data on their opinions of the ACD ITA process and the influences on their ITA ratings.

Results

Supervisors noted the benefits of this assessment tool, together with many limitations. Potential influences upon supervisor ratings included the relationship between the supervisor and trainee and the level of honesty in completing and delivery of the assessment.

Conclusions

Many factors influence supervisors in the completion of the ITA. These include the impact of interpersonal relationships and concerns about the consequences of delivering a negative assessment, which sometimes lead supervisors to modify the assessment they deliver to the trainee. Further research is needed into honesty in assessment judgements.
Evidence for non‐random sampling in randomised, controlled trials by Yuhji Saitoh
Authors: Carlisle J. B. , Loadsman J. A.
Published: December 2016

A large number of randomised trials authored by Yoshitaka Fujii have been retracted, in part as a consequence of a previous analysis finding a very low probability of random sampling. Dr Yuhji Saitoh co‐authored 34 of those trials and he was corresponding author for eight of them. We found a number of additional randomised, controlled trials that included baseline data, with Saitoh as corresponding author, that Fujii did not co‐author. We used Monte Carlo simulations to analyse the baseline data from 32 relevant trials in total as well as an outcome (muscle twitch recovery ratios) reported in several. We also compared a series of muscle twitch recovery graphs appearing in a number of Saitoh's publications. The baseline data in 14/32 randomised, controlled trials had p < 0.01, of which seven p values were < 0.001. Eight trials reported four ratios of the time for the return of muscle activity after neuromuscular blockade, the distributions of which were homogeneous: the p values for the observed Q statistics were 0.0055, 0.031, 0.016 and 0.0071. Comparison of graphs revealed multiple coincident or near‐coincident curves across a large number of publications, a finding also inconsistent with random sampling. Combining the continuous and categorical probabilities of the 32 included trials, we found a very low likelihood of random sampling: p = 1.27 × 10−8 (1 in 100,000,000). The high probability of non‐random sampling and the repetition of lines in multiple graphs suggest that further scrutiny of Saitoh's work is warranted.
Long‐term evolution of superficial optic disc drusen
Authors: Malmqvist Lasse , Lund‐Andersen Henrik , Hamann Steffen
Published: December 2016

Purpose

Optic disc drusen (ODD) is hyaline deposits in the optic nerve head seen in 1–2% of the population. Long‐term evolution of ODD anatomy and visual field defects in ODD patients is a key factor for learning more about pathophysiology and prognosis of the condition. With a median follow‐up period of 56 years, this is the first study that evaluates superficial optic disc anatomy and visual fields in patients with ODD over a life span.

Methods

Observational case series investigating progression of superficial optic disc anatomy and visual fields in ODD patients. Eight patients with hereditary ODD were included.

Results

Mean age at initial and follow‐up examination was, respectively, 16.8 and 73.3 years. The median follow‐up time was 56 years. A minimal or non‐existing change in superficial ODD anatomy (size and number) was seen in 10 of 12 eyes. There was a tendency towards more anatomical change in subjects younger at first examination. A 27% decrease in Goldmann perimetric visual field area (cm2) was found between initial and follow‐up examinations.

Conclusion

Minimal or no change in superficial optic disc anatomy and visual fields in ODD patients oldest at the initial examination suggests that anatomical progression of ODD in patients with hereditary ODD happens primarily before adulthood.
Effect of different lubricant eye gels on tear film thickness as measured with ultrahigh‐resolution optical coherence tomography
Authors: Wozniak Piotr A. , Schmidl Doreen , Bata Ahmed M. , Fondi Klemens , Witkowska Katarzyna J. , Aranha dos Santos Valentin , Baar Carina , Room Kim I. , Nepp Johannes , Baumgartner Isabella , Popa‐Cherecheanu Alina , Garhöfer Gerhard , Werkmeister René M. , Schmetterer Leopold
Published: December 2016

Purpose

To compare the effect of a single drop of different lubricant eye gels on tear film thickness (TFT) as measured with ultrahigh‐resolution optical coherence tomography (UHR‐OCT) in patients with mild‐to‐moderate dry eye disease (DED).

Methods

The study followed a randomized, single‐masked, observer‐blinded parallel group design. Patients received a single dose of either unpreserved trehalose 3% + hyaluronic acid 0.15% (TH), hyaluronic acid 0.2% (HA) or polyethylene glycol 0.4% + propylene glycol 0.3% (PP) eye drops. In total, 60 patients were included and TFT was measured using a custom‐built UHR‐OCT system.

Results

The mean TFT at baseline was 3.5 ± 0.7 μm. There was a significant difference in the time–course of TFT between the three groups (p = 0.001 between groups). Ten minutes after instillation, TFT increased by 155.8 ± 86.6%, 65.7 ± 71.5% and 33.4 ± 19.6% in the PP, TH and HA group, respectively (p < 0.001 between groups). Thirty minutes after instillation, the effect of all three different agents on TFT was comparable. Sixty and 120 min after administration, a significant increase in TFT was only seen for the TH group, but not for the other products (60 min: p < 0.021 between groups; 120 min: p < 0.037 between groups).

Conclusion

In conclusion, we observed differences in TFT after administration of the lubricant gels. Ten minutes after instillation, a pronounced increase in TFT was observed in all groups. As compared to the other products, the combination of trehalose 3% + hyaluronic acid 0.15% offers a significantly longer increase in TFT indicating for a longer residence time.
Compositional changes in thermophilous oak forests in Poland over time: do they correspond to European trends?
Authors: Reczyńska Kamila , Świerkosz Krzysztof
Published: December 2016

Questions

Have compositional changes occurred in thermophilous oak forests in Poland during the past two decades? What kinds of drivers might be responsible for these changes? Are the thermophilous oak woods still rich in species or have they rather lost their diversity?

Location

Sudetes Mts., SW Poland.

Methods

The vegetation of thermophilous oak forests within four distinct areas was surveyed on 92 semi‐permanent plots in the time periods from 1992 to 1994 and from 2010 to 2014. The overall pattern in vegetation changes, trends in species composition and site parameters, as well as the diversity of studied communities were analysed using ordination and permutation techniques.

Results

The species composition of thermophilous oak forests has changed significantly. We recorded a decrease in the share of oligotrophic light‐demanding species, whereas mesotrophic light‐demanding and nitrophilous species showed an upward trend. Regarding the fourth group of shade‐tolerant species, their share varied depending on the site. The analysis of habitat parameters revealed that the studied oak forest communities generally shifted from communities of moderately oligotrophic and mesic character towards forests growing on nutrient‐richer but drier habitats. Interestingly, the observed change in species composition was not accompanied by the loss of biodiversity that has generally been reported in other types of thermophilous forests in Europe.

Conclusions

Changes observed within thermophilous and previously coppiced oak forests of southwest Poland are going in a direction which has not been recognized so far in analogous communities. The transition of studied communities is probably a result of the cumulative influence of several drivers, the most crucial of which seem to be soil regeneration, after the period of intensive acidity caused by sulphur emission between 1960 and 2000, and decreasing moisture. The observed changes are independent of the type of forest management (or the lack thereof) within the study sites.
Safety and early effectiveness of robot‐assisted partial nephrectomy for large angiomyolipomas
Authors: Golan Shay , Johnson Scott C. , Maurice Matthew J. , Kaouk Jihad H. , Lai Weil R. , Lee Benjamin R. , Kheyfets Steven V. , Sundaram Chandru P. , Cahn David B. , Uzzo Robert G. , Shalhav Arieh L.
Published: December 2016

Objective

To evaluate a multicentre series of robot‐assisted partial nephrectomy (RAPN) performed for the treatment of large angiomyolipomas (AMLs).

Patients and Methods

Between 2005 and 2016, 40 patients with large or symptomatic AMLs underwent RAPN at five academic centres in the USA. Patient demographics, AML characteristics, operative and postoperative clinical outcomes were recorded and analysed. Surgical outcomes were compared between patients who underwent selective arterial embolisation (SAE) before RAPN and patients who did not undergo pre‐RAPN SAE.

Results

The median (interquartile range [IQR]) tumour diameter was 7.2 (5–8.5) cm, and the median (IQR) nephrometry score was 9 (7–10). Six patients (15%) had a history of tuberous sclerosis and 11 (28%) had previously undergone SAE. The median (IQR) operative time and warm ischaemia time was 207 (180–231) and 22.5 (16–28) min, respectively. A non‐clamping technique was used in eight (20%) patients. The median (IQR) estimated blood loss was 200 (100–245) mL, and four patients (10%) received blood transfusion postoperatively. One intraoperative complication occurred (2.5%), and seven postoperative complications occurred in six patients (15%). During a median (IQR) follow‐up of 8 (1–15) months, none of the patients developed AML‐related symptoms. The median estimated glomerular filtration rate preservation rate was 95%. There were no differences in operative or perioperative outcomes between patients who underwent SAE before RAPN and those who did not.

Conclusions

Robot‐assisted partial nephrectomy appears to be a safe primary or secondary (post‐SAE) treatment for large AMLs, with a favourable perioperative morbidity profile and excellent functional preservation. Longer follow‐up is required to fully evaluate therapeutic efficacy.
A brain in flame; do inflammasomes and pyroptosis influence stroke pathology?
Authors: Barrington Jack , Lemarchand Eloise , Allan Stuart M.
Published: December 2016

Stroke is one of the leading causes of death and disability worldwide. Inflammation plays a key role across the time course of stroke, from onset to the post‐injury reparative phase days to months later. Several regulatory molecules are implicated in inflammation, but the most established inflammatory mediator of acute brain injury is the cytokine interleukin‐1. Interleukin‐1 is regulated by large, macromolecular complexes called inflammasomes, which play a central role in cytokine release and cell death. In this review we highlight recent advances in inflammasome research and propose key roles for inflammasome components in the progression of stroke damage.
MR‐FLIP: a new method that combines a functional lumen imaging probe with anatomical information for spatial compliance assessment of the anal sphincter muscles
Authors: Brusa T. , Abler D. , Tutuian R. , Studer P. , Fattorini E. , Gingert C. , Heverhagen J. T. , Brügger L. E. , Büchler P.
Published: December 2016

Aim

Continence results from a complex interplay between anal canal (AC) muscles and sensorimotor feedback mechanisms. The passive ability of the AC to withstand opening pressure – its compliance – has recently been shown to correlate with continence. A functional lumen imaging probe (FLIP) is used to assess AC compliance, although it provides no anatomical information. Therefore, assessment of the compliance specific anatomical structures has not been possible, and the anatomical position of critical functional zones remains unknown. In addition, the FLIP technique assumes a circular orifice cross‐section, which has not been shown for the AC. To address these shortcomings, a technique combining FLIP with a medical imaging modality is needed.

Method

We implemented a new research method (MR‐FLIP) that combines FLIP with MR imaging. Twenty healthy volunteers underwent MR‐FLIP and conventional FLIP assessment. MR‐FLIP was validated by comparison with FLIP results. Anatomical markers were identified, and the cross‐sectional shape of the orifice was investigated.

Results

MR‐FLIP provides compliance measurements identical to those obtained by conventional FLIP. Anatomical analysis revealed that the least compliant AC zone was located at the proximal end of the external anal sphincter (EAS). The cross‐sectional shape of the AC was found to deviate only slightly from circularity in healthy volunteers.

Conclusion

The proposed method is equivalent to classical FLIP. It establishes for the first time direct mapping between local tissue compliance and anatomical structure, which is key to gaining novel insights into (in)continence. In addition, MR‐FLIP provides a tool for better understanding conventional FLIP measurements in the AC by quantifying its limitations and assumptions.
Planning Beyond the Next Trial in Adaptive Experiments: A Dynamic Programming Approach
Authors: Kim Woojae , Pitt Mark A. , Lu Zhong‐Lin , Myung Jay I.
Published: December 2016

Experimentation is at the heart of scientific inquiry. In the behavioral and neural sciences, where only a limited number of observations can often be made, it is ideal to design an experiment that leads to the rapid accumulation of information about the phenomenon under study. Adaptive experimentation has the potential to accelerate scientific progress by maximizing inferential gain in such research settings. To date, most adaptive experiments have relied on myopic, one‐step‐ahead strategies in which the stimulus on each trial is selected to maximize inference on the next trial only. A lingering question in the field has been how much additional benefit would be gained by optimizing beyond the next trial. A range of technical challenges has prevented this important question from being addressed adequately. This study applies dynamic programming (DP), a technique applicable for such full‐horizon, “global” optimization, to model‐based perceptual threshold estimation, a domain that has been a major beneficiary of adaptive methods. The results provide insight into conditions that will benefit from optimizing beyond the next trial. Implications for the use of adaptive methods in cognitive science are discussed.
Second Language Experience Facilitates Statistical Learning of Novel Linguistic Materials
Authors: Potter Christine E. , Wang Tianlin , Saffran Jenny R.
Published: December 2016

Recent research has begun to explore individual differences in statistical learning, and how those differences may be related to other cognitive abilities, particularly their effects on language learning. In this research, we explored a different type of relationship between language learning and statistical learning: the possibility that learning a new language may also influence statistical learning by changing the regularities to which learners are sensitive. We tested two groups of participants, Mandarin Learners and Naïve Controls, at two time points, 6 months apart. At each time point, participants performed two different statistical learning tasks: an artificial tonal language statistical learning task and a visual statistical learning task. Only the Mandarin‐learning group showed significant improvement on the linguistic task, whereas both groups improved equally on the visual task. These results support the view that there are multiple influences on statistical learning. Domain‐relevant experiences may affect the regularities that learners can discover when presented with novel stimuli.
Advances in pleuroscopy
Authors: Anevlavis Stavros , Froudarakis Marios E.
Published: December 2016

Objectives

To describe the technique of pleuroscopy, its clinical uses such as diagnosis of exudative pleural effusion, treatment of pleural infection, treatment of pneumothorax, and diagnosis and pleurodesis of malignant pleural mesothelioma. Also to describe the newer techniques developed such as minothoracoscopy, semirigid thoracoscopy, narrow band imaging pleuroscopy, infrared pleuroscopy, autofluorescence pleuroscopy.

Data source

We searched the pubmed the last decade for publications with the key words pleuroscopy, medical thoracoscopy, pneumothorax and pleuroscopy, malignant pleural mesothelioma, minothoracoscopy, semirigid thoracoscopy, autofluorescence pleuroscopy.

Conclusion

Medical thoracoscopy is the method of choice for investigation of the undiagnosed exudative pleural effusions. Newer techniques, such as narrow band imaging thoracoscopy, infrared thoracoscopy, autofluorescence thoracoscopy are offering a promising future for medical thoracoscopy.
Calcification score evaluation in patients listed for renal transplantation
Authors: Kahn Judith , Ram Leona Marleen , Eberhard Katharina , Groselj‐Strele Andrea , Obermayer‐Pietsch Barbara , Müller Helmut
Published: December 2016

Based on native CT scans of the pelvic region using a standardized calcification score, evaluation of iliac vascular calcification was performed between 2008 and 2012 prior to listing for renal transplantation in 205 patients with chronic kidney disease. Vascular calcification showed a decrease from proximal to distal. The difference between the degree of calcification in the common iliac artery and in the external iliac artery was significant (P<.001). Risk factors for total iliac vascular calcification were age, smoking, sex, underlying renal disease, and diabetes. Multivariate analysis revealed age to be the most relevant risk factor (P<.001). The duration of hemodialysis correlated significantly with total iliac vascular calcification. As the introduction of the standardized surgical evaluation protocol, no transplantation has had to be broken off and no early graft loss due to calcification has occurred. Thus, careful scoring of vascular calcification prior to transplantation may be a valuable tool to support surgical decisions and to improve patient safety and outcome in increasingly older transplant recipients.
Gender differences in long‐term survival post‐transplant: A single‐institution analysis in the lung allocation score era
Authors: Loor Gabriel , Brown Roland , Kelly Rosemary F. , Rudser Kyle D. , Shumway Sara J. , Cich Irena , Holley Christopher T. , Quinlan Colleen , Hertz Marshall I.
Published: December 2016

The purpose of this study was to clarify the significance of recipient gender status on lung transplant outcomes in a large single‐institution experience spanning three decades, we analyzed data from all lung transplants performed in our institution since 1986. Kaplan‐Meier curves and Cox proportional hazard models were used to evaluate the effect of recipient characteristics on survival and BOS score ≥1‐free survival. Logistic regression analysis was used to explore the association of gender with short‐term graft function. About 876 lung transplants were performed between 1986 and 2016. Kaplan‐Meier survival estimates at 5 years post‐transplant for females vs males in the LAS era were 71% vs 58%. In the LAS era, females showed greater unadjusted BOS≥1‐free survival than males (35% vs 25%, P=.02) over 5 years. Female gender was the only factor in the LAS era significantly associated with improved adjusted 5‐year survival [HR 0.56 (95% CI 0.33, 0.95) P=.03]. Conversely, in the pre‐LAS era female gender was not associated with improved survival. Female recipients showed significantly improved survival over 5 years compared to males in the LAS era. A prospective analysis of biologic and immunologic differences is warranted.
Prediction of nonalcoholic fatty liver in prospective liver donors
Authors: Choudhary Narendra S. , Saraf Neeraj , Saigal Sanjiv , Duseja Ajay , Gautam Dheeraj , Lipi Lipika , Rastogi Amit , Goja Sanjay , Bhangui Prashant , Ramchandra Sumana K. , Babu Yalakanti Raghavendra , Soin Arvinder S.
Published: December 2016

Background

Metabolic risk factors should be important in addition to imaging for prediction of steatosis in prospective liver donors.

Materials and methods

The study group included all prospective liver donors who had a liver biopsy during workup. Risk factors of metabolic syndrome were analyzed, and body mass index (BMI) ≥25 kg/m2 was used in place of waist circumference. Three BMI cutoffs (25, 28, and 30 kg/m2) and two CT‐measured liver attenuation index (LAI) cutoffs (<5 and ≤10) were used for steatosis assessment of ≥5%, ≥10%, and ≥20%.

Results

Of the 573 prospective donors (307 females), 282 (49.2%) donors had nonalcoholic fatty liver (NAFL). When donors with NAFL were compared with donors having normal histology, multivariate analysis showed BMI, ALT, triglycerides, and LAI as significant predictors of NAFL. BMI ≥25 kg/m2 and LAI <10 were better cutoffs. The presence of ≥2 metabolic risk factors had better sensitivity than CT‐LAI for the presence of NAFL and ≥20% steatosis (58% and 54% vs 47% and 22%, respectively, for CT‐LAI ≤10). The presence of LAI >10 and <2 metabolic risk factors predicted <10% steatosis with 96% specificity and 92% positive predictive value.

Conclusion

The presence of ≥2 metabolic risk factors improves sensitivity of CT‐LAI for prediction of donor steatosis.
Cervical human papillomavirus infection in the early postoperative period after liver transplantation: Prevalence, risk factors, and concordance with anal infections
Authors: Grąt Karolina , Grąt Michał , Wronka Karolina M. , Pietrzak Bronisława , Suchońska Barbara , Walter de Walthoffen Szymon , Młynarczyk Grażyna , Krawczyk Marek , Wielgoś Mirosław
Published: December 2016

Solid organ transplant recipients are at increased risk of developing several human papillomavirus (HPV)‐related malignancies, including cervical and anal cancers. The purpose of this prospective study was to assess the initial prevalence and risk factors for high‐risk HPV (HR‐HPV) cervical infections in liver transplant recipients, as well as their concordance with anal infections. A total of 50 female patients were enrolled in the Department of General, Transplant and Liver Surgery at the Medical University of Warsaw (center with >1600 liver transplantations). The initial prevalence of cervical HR‐HPV infection was 10.0% (5/50). The only significant risk factor for cervical HR‐HPV infection was ≥4 lifetime sexual partners (P=.037). Statistical tendencies toward higher prevalence of cervical HR‐HPV infections were found for patients with hepatitis B virus (HBV, P=.082) and with model for end‐stage liver disease (MELD) score ≤8 (P=.064). Cervical cytology was abnormal in 10 patients, including three with HR‐HPV. Out of 12 patients with available data on anal HR‐HPV, one had concordant HPV 16 infection. In conclusion, the initial prevalence of high‐risk HPV infection is relatively low, except for patients with ≥4 previous sexual partners and potentially in those with HBV and/or low MELD score.
Outcomes in the highest panel reactive antibody recipients of deceased donor kidneys under the new kidney allocation system
Authors: Parajuli Sandesh , Redfield Robert R. , Astor Brad C. , Djamali Arjang , Kaufman Dixon B. , Mandelbrot Didier A.
Published: December 2016

Since the institution of the new kidney allocation system in December 2014, kidney transplant candidates with the highest calculated panel reactive antibodies (cPRA) of 99‐100 have been transplanted at much higher rates. However, concerns have been raised that outcomes in these patients might be impaired due to higher immunological risk and longer cold ischemia times resulting from long‐distance sharing of kidneys. Here, we compare outcomes at the University of Wisconsin between study patients withcPRA99‐100 and all other recipients of deceased donor kidneys transplanted between 12/04/2014 and 12/31/2015. All patients had at least 6 months post‐transplant follow‐up. The mean follow‐up was 13.9±3 months incPRA≥99% and 12.3±3.5 months incPRA≤98%. There was a total of 152 transplants, 25 study patients, and 127 controls. No statistically significant differences were found between the two groups in delayed graft function, rejection, kidney function, graft and patient survival, or infections. We conclude that transplanting the most highly sensitized patients with kidneys shared outside their local donation service areas is associated with excellent short‐term outcomes that are comparable to controls.
Accounting for the UK Productivity Puzzle: A Decomposition and Predictions
Authors: Goodridge Peter , Haskel Jonathan , Wallis Gavin
Published: December 2016

This paper revisits the UK productivity puzzle using new data on outputs and inputs and clarifying the role of output mismeasurement, input growth and industry effects. Our data indicate an implied labour productivity gap of 13 percentage points in 2011 relative to the productivity level on pre‐recession trends. We find that: (a) the labour productivity puzzle is a TFP puzzle, since it is not explained by the contributions of labour or capital services; (b) the reallocation of labour between industries deepens rather than explains the puzzle (i.e. there has been a reallocation of hours away from low‐productivity industries and toward high productivity industries); (c) capitalization of R&D does not explain the productivity puzzle; (d) assuming increased scrapping rates since the recession, a 25% (50%) increase in depreciation rates post‐2009 can potentially explain 15% (31%) of the productivity puzzle; (e) industry data show that 35% of the TFP puzzle can be explained by weak TFP growth in the oil & gas and finance sectors; and (f) cyclical effects via factor utilization could potentially explain 17% of the productivity puzzle. Continued weakness in finance would suggest a future lowering of TFP growth to around 0.8% p.a. from a baseline of 0.9% p.a.
Pyrosequencing of rpoB uncovers a significant biogeographical pattern of rhizobial species in soybean rhizosphere
Authors: Zhang Xing Xing , Guo Hui Juan , Jiao Jian , Zhang Pan , Xiong Hui Yang , Chen Wen Xin , Tian Chang Fu
Published: December 2016

Aim

Most culture‐independent studies of bacterial biogeography have been at genus or higher taxonomic levels, although many important processes mediated by bacteria are at the strain or species level, such as the competitive nodulation of rhizobia on legumes. Here, at the intra‐species level, we characterized the structural variation in rhizobial populations in soybean rhizosphere under field conditions across 32 sampling sites in three eco‐regions.

Location

North‐east (Heilongjiang), north (Hebei–Shandong) and south (Jiangxi) China.

Methods

The intra‐species diversity of rhizobia in soybean rhizospheres was investigated by rpoB pyrosequencing. Soybean nodule isolates were characterized using repetitive extragenic palindromic PCR, restriction fragment length polymorphism of 16S‐23S intergenic sequences and rpoB PCR sequencing. Patterns and processes of biogeography of identified rhizobia were studied.

Results

Significant biogeographical patterns of rhizosphere rhizobia at the species level were found, and the abundant species in the rhizosphere were generally the dominant microsymbionts in soybean nodules. The distribution of rhizobial species in the rhizosphere across eco‐regions correlated with combined effects of spatial, vegetative, edaphic and climatic variables. Gene flow and genetic differentiation analyses revealed that there was no dispersal limitation among geographical populations of the same rhizobial species, and drift or subsequent diversification might be involved in shaping the biogeographical pattern in addition to environmental factors.

Main conclusions

These results constitute the first report of the existence of rhizobial biogeography in legume rhizospheres at the species level, contrasting with most studies, which focused on nodule isolates. The method developed in this study could be used to uncover, at high resolution, the diversity of local rhizobial populations in soils. This information is crucial for choosing suitable strains or species as inoculants for a specific legume host under local field conditions. Moreover, a similar strategy could be used to study other bacteria with important ecological functions.