bluuebunny/crossref_metadata_2025 huggingface dataset:
Geogenic CO2 affects inorganic soil properties and the composition of soil organic matter in physical fractions
Authors: Rennert Thilo
Published: March 2018

The presence of geogenic CO2 has been recently identified as a soil-forming factor in soil on mofette sites. Topsoil samples (with a maximum CO2 concentration of 52% at 10 cm depth) were studied along a transect on a mofette site in the NW Czech Republic to further understand the processes within soil and the soil properties induced by CO2 in the soil atmosphere. Geogenic CO2 negatively affected the cation exchange capacity, the ratio of exchangeable Ca and Mg, and the total contents of Al, Mg and Mn. No effect was detected on a chemical index of weathering and the mineralogical composition of the clay fractions, which might be explained by the acidic parent material and the progress of soil development. Diffuse reflectance infrared spectroscopy indicated that the composition of particulate soil organic matter was partially affected by CO2 concentrations: the higher the CO2 concentrations, the smaller the extent of oxidative transformation and the smaller the abundance of carboxyl groups. In the clay fractions, stabilisation of transformed soil organic matter (SOM) was promoted by exchangeable Al. This study quantifies, for the first time, the correlation between geogenic CO2 and several inorganic soil properties and the composition of SOM in physical fractions.
Are any populations 'safe'? Unexpected reproductive decline in a population of Tasmanian devils free of devil facial tumour disease
Authors: Farquharson K. A. , Gooley R. M. , Fox S. , Huxtable S. J. , Belov K. , Pemberton D. , Hogg C. J. , Grueber C. E.
Published: March 2018

Context
Conservation management relies on baseline demographic data of natural populations. For Tasmanian devils (Sarcophilus harrisii), threatened in the wild by two fatal and transmissible cancers (devil facial tumour disease DFTD: DFT1 and DFT2), understanding the characteristics of healthy populations is crucial for developing adaptive management strategies to bolster populations in the wild.

Aims
Our analysis aims to evaluate contemporary reproductive rates for wild, DFTD-free Tasmanian devil populations, and to provide a baseline with which to compare the outcome of current translocation activities.

Methods
We analysed 8 years of field-trapping data, including demographics and reproductive rates, across 2004–16, from the largest known DFTD-free remnant population at Woolnorth, Tasmania.

Key results
Surprisingly, we found a dramatic and statistically significant decline in female breeding rate when comparing data collected from 2004–2009 with data from 2014–2016. Unfortunately we do not have any data from the intermediate years. This decline in breeding rate was accompanied by a subtle but statistically significant decline in litter sizes. These changes were not associated with a change in body condition over the same period. Furthermore, we could not attribute the decline in breeding to a change in population size or sex ratio. Preliminary analysis suggested a possible association between annual breeding rate and coarse measures of environmental variation (Southern Oscillation Index), but any mechanistic associations are yet to be determined.

Conclusions
The decline in breeding rates was unexpected, so further monitoring and investigation into potential environmental and/or biological reasons for the decline in breeding rate are recommended before the arrival of DFTD at Woolnorth.

Implications
Our results provide valuable data to support the conservation management of Tasmanian devils in their native range. They also highlight the importance of continued monitoring of ‘safe’ populations, in the face of significant threats elsewhere.
Classification ofBrachyspiraspp. isolated from Swedish dogs
Authors: Fellström Claes , Pettersson Bertil , Zimmerman Ulla , Gunnarsson Anders , Feinstein Ricardo
Published: March 2018

Brachyspira spp.were isolated from 21 of 32 sampled dogs (66%) in a colony of Swedish beagle dogs with a history of diarrhea and from 3 of 17 Swedish pet dogs (17%) with diarrhea. All Swedish isolates were weakly β-hemolytic and gave a negative indole reaction. Eighty-eight percent showed negative α-galactosidase and hippurate reactions, but a positive β-glucosidase reaction. Two isolates were hippurate positive with a negative β-glucosidase reaction. One additional German isolate diverged by showing a positive indole reaction in combination with a positive hippurate reaction. Sequencing of 16S rDNA indicated that the hippurate-positive isolates belonged to the speciesBrachyspira pilosicoli. Four representative isolates were examined using pulsed-field gel electrophoresis (PFGE) and compared with six reference strains and five porcine isolates ofBrachyspiraspp. The canine isolates clustered together in the PFGE analysis. Necropsy examination of a culture-positiveB. pilosicolicolony-raised beagle dog revealed macro- and microscopical lesions of colitis with numerous spiral-shaped bacteria in the lumens of the crypts, in goblet cells and within the colonic epithelium.
Integration of a Clinical Pharmacy Specialist into a Substance use Disorder Intensive Outpatient Treatment Program to Improve Prescribing Rates of Alcohol use Disorder Pharmacotherapy
Authors: Dimitropoulos Erica , Bertucci Stephanie , Wong Kara
Published: March 2018

Background

Research has demonstrated that the combination of pharmacotherapy and psychological interventions in alcohol use disorder (AUD) treatment is superior to either alone. Despite this, medications remain highly underutilized in many outpatient treatment facilities. Pharmacists can serve as an excellent resource to aid in improving access to medications.

Methods

This study was a prospective, longitudinal evaluation of a pharmacist's role in a substance use disorder (SUD) clinic, specifically an intensive outpatient program (IOP). The primary objective was to determine if the addition of a clinical pharmacy specialist (CPS) as a bridge until next available provider appointment would improve access to AUD pharmacotherapy for patients in the IOP.

Results

A total of 43 patients were enrolled in the IOP during the study. Of these, 27 patients presented with a primary diagnosis of AUD, and only eight were receiving AUD pharmacotherapy at the start of the program. During this intervention, 11 patients expressed interest in initiating a medication for AUD while in the IOP. The average wait time for a medication evaluation appointment with the CPS was 1.4 days. By comparison, the average wait time for an addiction psychiatrist was approximately 44 days. Each patient was seen for an average of two 30-minute visits, including an initial medication evaluation and one follow-up. Upon completion of CPS services, patients were referred almost equally to an established non-addiction recovery services (ARS) mental health provider (36%), an ARS psychiatrist (36%), or a primary care provider (28%).

Conclusion

Our study highlights the role that pharmacists can play in improving access to evidence-based AUD pharmacotherapy, as well as in providing medication education to patients and providers. Long-term prospective research and pharmacoeconomic analysis are needed to determine the sustainability of this service, both at our facility and in other similar practice settings.
Implementation of a Nationwide Health Economic Consultation Service to Assist Substance use Researchers: Lessons Learned
Authors: Murphy Sean M. , Leff Jared A. , Linas Benjamin P. , Morgan Jake R. , McCollister Kathryn , Schackman Bruce R.
Published: March 2018

Background

Health economic evaluation findings assist stakeholders in improving the quality, availability, scalability, and sustainability of evidence-based services, and in maximizing the efficiency of service delivery. The Center for Health Economics of Treatment Interventions for Substance Use Disorders, HCV, and HIV (CHERISH) is a NIDA-funded multi-institutional center of excellence whose mission is to develop and disseminate health-economic research on healthcare utilization, health outcomes, and health-related behaviors that informs substance use disorder treatment policy, and HCV and HIV care of people who use substances.

Methods

We designed a consultation service that is free to researchers whose work aligns with CHERISH's mission. The service includes up to six hours of consulting time. After prospective consultees submit their request online, they receive a screening call from the consultation service director, who connects them with a consultant with relevant expertise. Consultees and consultants complete web-based evaluations following the consultation; consultees also complete a six-month follow-up. We report on the status of the service from its inception in July 2015 through June 2017.

Results

We have received 28 consultation requests (54% Early Stage Investigators, 57% MD or equivalent, 28% PhD, 61% women) on projects typically related to planning a study or grant application (93%); 71% were HIV/AIDS-related. Leading topics included cost-effectiveness (43%), statistical-analysis/econometrics (36%), cost (32%), cost-benefit (21%), and quality-of-life (18%). All consultees were satisfied with their overall experience, and felt that consultation expectations and objectives were clearly defined and the consultant's expertise was matched appropriately with their needs. Results were similar for consultants, who spent a median of 3 hours on consultations.

Conclusions

There is a need for health-economic methodological guidance among substance use, HCV, and HIV researchers. Lessons learned pertain to the feasibility of service provision, the need to implement systems to measure and improve service value, and strategies for service promotion.
Oral supplementation ofBifidobacterium longumstrain BR-108 alters cecal microbiota by stimulating gut immune system in mice irrespectively of viability
Authors: Makioka Yuko , Tsukahara Takamitsu , Ijichi Tetsuo , Inoue Ryo
Published: March 2018

Effect on cecal microbiota and gene expression of various cytokines in ileal Peyer’s patches and cecal tissues were compared between viable and heat-killed Bifidobacterium longum strain BR-108 (BR-108) using a mouse model. Irrespectively of viability, oral supplementation of BR-108 altered the cecal microbiota and stimulated gene expression of cytokines such as IL-6 and IL-10 in ileal Peyer’s patches and cecal tissue of mice. In addition, BR-108 supplementation significantly affected the relative abundance of bacterial genera and family, Oscillospira, Bacteroides and S24-7. The abundance of these bacterial genera and family strongly correlated with gene expression induced by BR-108. This study demonstrated that the effect of heat-killed BR-108 on the mouse cecal microbiota is similar to that of viable BR-108, most likely due to stimulation of the gut immune system by both heat-killed and viable BR-108 is also similar.
Predestination and Toleration: The Dutch Republic’s Single Judicial Persecution of Jews in Theological Context
Authors: van der Haven Alexander
Published: March 2018

The toleration of Jews in early modern Dutch society is commonly seen as predicated on the maintenance of a clear social and religious separation between Jews and Christians. I argue that this view is incomplete and misleading. Close analysis of the only judicial persecution of Jews in the Dutch Republic’s history, the trial of three Jewish proselytes in the anti-Calvinist city of Hoorn in 1614–15, yields a more complex picture. Comparison of the Hoorn trial with cases of apostasy to Judaism in orthodox Calvinist Amsterdam during the same period suggests that the theological commitments of orthodox Calvinism played an important and hitherto unrecognized role in Dutch toleration.
Aid, Protection, and Social Alliance: The Role of Jewelry in the Margins of theHours of Catherine of Cleves
Authors: Decker John R.
Published: March 2018

This article examines five miniatures in the “Hours of Catherine of Cleves” (completed 1442), each containing representations of jewelry in the margins, which operate on two different levels. First, they demonstrate Catherine of Cleves’s adoration of five female saints. I argue that the fictive jewelry may be understood as simulated ex-votos designed to secure the aid and protection of the saints. Second, the images establish strategic alliances with each saint. As a final dimension, I explore how the vitae of these saints may have had resonances for the duchess that help explain the focus placed on them in the manuscript.
‘Wage’, ‘Salary’ and ‘Remuneration’: A Genealogical Exploration of Juridical Terms and their Significance for the Employer’s Power to Make Deductions from Wages
Authors: Adams Zoe
Published: March 2018

The Supreme Court in Hartley v King Edwards VI College (2017) has confirmed that an employee who refuses to work in accordance with his contract forfeits his right to be paid for the duration of the breach. The decision extends to professional employees paid a periodical salary the principle established in Miles v Wakefield MDC (1987). The present article sheds new light on these decisions by situating them within a broader debate concerning the function of the wage and the proper relationship between work and payment. Drawing on insights from economic theory, and engaging in a genealogical analysis of legal concepts, the article shows how this debate has, over time, conditioned the use of concepts such as the ‘wage’, ‘the salary’ and ‘remuneration’ in legislation and case law concerning deductions. It shows that the legal concept of the ‘wage’ is closely related to the economic idea of the wage as the price of a commodity, while the legal concepts of ‘salary’ and ‘remuneration’ are more closely analogous to the economic idea of the wage as the cost of subsistence. The courts’ tendency to confuse these concepts, and to analyse the employer’s power to deduct as a right to withhold wages for non-performance of the contract, tells us much about the implicit assumptions underpinning cases, such as Miles and Hartley, and how they have shaped the path of the law.
Improving dermatological screening in primary care
Authors: Wheatley Brittany
Published: March 2018

Skin cancer is treatable and curable. Primary care providers should perform skin assessments for detection of skin cancer, however, due to conflicting guidelines and time constraints, many providers do not conduct adequate skin inspections. This quality improvement project aimed to improve skin inspection, documentation, and skin cancer detection through increased patient gowning.
Validation of Patient Reported Outcomes Measurement Information System (PROMIS) Computer Adaptive Tests (CATs) in the Surgical Treatment of Lumbar Spinal Stenosis
Authors: Patel Alpesh A. , Dodwad Shah-Nawaz M. , Boody Barrett S. , Bhatt Surabhi , Savage Jason W. , Hsu Wellington K. , Rothrock Nan E.
Published: March 2018

Study Design.

Prospective, cohort study.

Objective.

Demonstrate validity of Patient reported outcomes measurement information system (PROMIS) physical function, pain interference, and pain behavior computer adaptive tests (CATs) in surgically treated lumbar stenosis patients.

Summary of Background Data.

There has been increasing attention given to patient reported outcomes associated with spinal interventions. Historical patient outcome measures have inadequate validation, demonstrate floor/ceiling effects, and infrequently used due to time constraints. PROMIS is an adaptive, responsive National Institutes of Health (NIH) assessment tool that measures patient-reported health status.

Methods.

Ninety-eight consecutive patients were surgically treated for lumbar spinal stenosis and were assessed using PROMIS CATs, Oswestry disability index (ODI), Zurich Claudication Questionnaire (ZCQ), and Short-Form 12 (SF-12). Prior lumbar surgery, history of scoliosis, cancer, trauma, or infection were excluded. Completion time, preoperative assessment, 6 weeks and 3 months postoperative scores were collected.

Results.

At baseline, 49%, 79%, and 81% of patients had PROMIS pain behavior (PB), pain interference (PI), and physical function (PF) scores greater than 1 standard deviation (SD) worse than the general population. 50.6% were categorized as severely disabled, crippled, or bed bound by ODI. PROMIS CATs demonstrated convergent validity through moderate to high correlations with legacy measures (r = 0.35–0.73). PROMIS CATs demonstrated known groups validity when stratified by ODI levels of disability. ODI improvements of at least 10 points on average had changes in PROMIS scores in the expected direction (PI = −12.98, PB = −9.74, PF = 7.53). PROMIS CATs demonstrated comparable responsiveness to change when evaluated against legacy measures. PROMIS PB and PI decreased 6.66 and 9.62 and PROMIS PF increased 6.8 points between baseline and 3-months post-op (P < 0.001). Completion time for the PROMIS CATs (2.6 min) compares favorably to ODI, ZCQ, and SF-12 scores (3.1, 3.6, and 3.0 min).

Conclusion.

PROMIS CATs demonstrate convergent validity, known groups validity, and responsiveness for surgically treated patients with lumbar stenosis to detect change over time and are more efficient than legacy instruments.

Level of Evidence: 2
Assessment of Functional Rhinoplasty with Spreader Grafting Using Acoustic Rhinomanometry and Validated Outcome Measurements
Authors: Paul Marek A. , Kamali Parisa , Chen Austin D. , Ibrahim Ahmed M. S. , Wu Winona , Becherer Babette E. , Medin Caroline , Lin Samuel J.
Published: March 2018

Background:

Rhinoplasty is 1 of the most common aesthetic and reconstructive plastic surgical procedures performed within the United States. Yet, data on functional reconstructive open and closed rhinoplasty procedures with or without spreader graft placement are not definitive as only a few studies have examined both validated measurable objective and subjective outcomes of spreader grafting during rhinoplasty. The aim of this study was to utilize previously validated measures to assess objective, functional outcomes in patients who underwent open and closed rhinoplasty with spreader grafting.

Methods:

We performed a retrospective review of consecutive rhinoplasty patients. Patients with internal nasal valve insufficiency who underwent an open and closed approach rhinoplasty between 2007 and 2016 were studied. The Cottle test and Nasal Obstruction Symptom Evaluation survey was used to assess nasal obstruction. Patient-reported symptoms were recorded. Acoustic rhinometry was performed pre- and postoperatively. Average minimal cross-sectional area of the nose was measured.

Results:

One hundred seventy-eight patients were reviewed over a period of 8 years. Thirty-eight patients were included in this study. Of those, 30 patients underwent closed rhinoplasty and 8 open rhinoplasty. Mean age was 36.9 ± 18.4 years. The average cross-sectional area in closed and open rhinoplasty patients increased significantly (P= 0.019). There was a functional improvement in all presented cases using the Nasal Obstruction Symptom Evaluation scale evaluation.

Conclusions:

Closed rhinoplasty with spreader grafting may play a significant role in the treatment of nasal valve collapse. A closed approach rhinoplasty including spreader grafting is a viable option in select cases with objective and validated functional improvement.
An Exploratory Study of Sevoflurane as an Alternative for Difficult Sedation in Critically Ill Children*
Authors: Mencía Santiago , Palacios Alba , García Miriam , Llorente Ana M. , Ordóñez Olga , Toledo Blanca , López-Herce Jesús
Published: March 2018

Objectives:

To analyze the effectiveness of inhaled sevoflurane in critically ill children with challenging sedation.

Design:

Prospective case series.

Setting:

Two PICUs of university hospitals in Spain.

Interventions:

Prospective observational study and exploratory investigation conducted in two PICUs in Madrid, Spain, over a 6-year period. Children treated with inhaled sevoflurane due to difficult sedation were included. Sevoflurane was administered via the anesthetic conserving device (AnaConDa) connected to a Servo-I ventilator (Maquet, Solna, Sweden). A morphine infusion was added to sevoflurane for analgesia. Demographic and clinical data, oral and IV sedatives, Sedation and Analgesic Clinical scores, and Bispectral Index Score monitoring were registered.

Measurements and Main Results:

Twenty-three patients with a median age of 6 months old were included. Fifty percentage of the patients had critical heart diseases. Sedative and analgesic drugs used before starting sevoflurane were mainly midazolam (63%) and fentanyl (53%). Six patients (32%) also received muscle relaxants. Sevoflurane was administered for a median of 5 days (interquartile range, 5.5–8.5 d). Median end-tidal sevoflurane concentration was 0.8% (interquartile range, 0.7–0.85%), achieved with an infusion rate of 7.5 mL/hr (5.7–8.6 mL/hr). After 48 hours of treatment, some sedative drugs could be removed in 18 patients (78%). Median Bispectral Index Score value prior to sevoflurane administration was 61 (interquartile range, 49–62), falling to 42 (interquartile range, 41–47; p < 0.05) after 6 hours of treatment. Six patients (26%) presented withdrawal syndrome after sevoflurane suspension, and all of them had received sevoflurane at least for 6 days. The main side effect was moderate hypotension in seven patients (30%).

Conclusions:

Inhaled sevoflurane appeared to be an effective sedative agent in critically ill children and can be useful in those patients on mechanical ventilation difficult to sedate with conventional drugs. It can be administered easily in the PICU with conventional ventilators using the AnaConDa system. Withdrawal syndrome may occur with prolonged treatment.
Paraneoplastic Pemphigus Associated With Castleman Disease Detected by 18F-FDG PET/CT
Authors: Fu Zhanli , Liu Meng , Chen Xueqi , Yang Xing , Li Qian
Published: March 2018

A 36-year-old woman suffering from oral ulcerations, skin rash, and dyspnea was suspected of having paraneoplastic pemphigus. An 18F-FDG PET/CT was performed to detect the underlying neoplasms and revealed an 18F-FDG–avid mass in the lower right retroperitoneum. The mucocutaneous lesions and dyspnea were relieved after the tumor excision, and the pathology indicated Castleman disease.
Lack of functional caveolae in Cav3 mutated human dystrophic myotubes results in deficient mechanoprotection and IL6/STAT3 mechanosignaling
Authors: Dewulf Melissa , Köster Darius , Sinha Bidisha , Viaris de Lesegno Christine , Chambon Valérie , Bigot Anne , Tardif Nicolas , Johannes Ludger , Nassoy Pierre , Butler-Browne Gillian , Lamaze Christophe , Blouin Cedric M.
Published: March 2018

Caveolin-3 is the major structural protein of caveolae in muscle cells. Mutations in the CAV3 gene cause different type of muscle disorders mostly characterized by defects in membrane integrity and repair, deregulation in the expression of various muscle proteins and deregulation of several muscle associated signaling pathways. We show here that myotubes derived from patients bearing the CAV3 P28L and R26Q mutations present a lack of functional caveolae at the plasma membrane which results in an abnormal mechanoresponse. Mutant myotubes can no longer buffer the increase of membrane tension induced by mechanical stress and present an hyperactivation of the IL6/STAT3 signaling pathway at rest and under mechanical stress. The impaired mechanical regulation of the IL6/STAT3 signaling pathway by caveolae leads to chronic activation and a higher expression of muscle specific genes. These defects could be reversed by reassembling a pool of functional caveolae through expression of wild type Cav3. Our findings bring more mechanistic insight into human Cav3 associated muscle disorders and show a general defect in the mechanoresponse of CAV3 P28L and R26Q myotubes.
Increased H. pylori stool shedding and EPIYA-D cagA alleles are associated with gastric cancer in an East Asian hospital
Authors: Talarico Sarah , Leverich Christina , Wei Bing , Ma Jie , Cao XinGuang , Guo YongJun , Han GuangSen , Yao Lena , Self Steve , Zhao Yuzhou , Salama Nina R.
Published: March 2018

Background

Helicobacter pylori infection induces chronic inflammation and tissue damage in the stomach, increasing risk for gastric cancer. Paradoxically, these tissue alterations may promote loss of H. pylori infection during cancer progression. H. pylori’s role in cancer progression beyond initiation is unclear. Geographic variation in gastric cancer risk has been attributed to variation in carriage and type of the H. pylori oncogene cagA.

Methods

To investigate possible differences in H. pylori load in the stomach and shedding in stool, H. pylori load and cagA genotype were assessed using droplet digital PCR assays on gastric mucosa and stool samples from 49 urea breath test-positive individuals, including 25 gastric cancer and 24 non-cancer subjects at Henan Cancer Hospital, Henan, China.

Results

Quantitation of H. pylori DNA indicated similar gastric loads among cancer and non-cancer cases, but the gastric cancer group had a median H. pylori load in the stool that was six times higher than that of the non-cancer subjects. While the cagA gene was uniformly present among study subjects, only 70% had the East Asian cagA allele, which was significantly associated with gastric cancer (Fisher’s Exact Test, p = 0.03).

Conclusion

H. pylori persists in a subset of gastric cancer cases and thus may contribute to cancer progression. In this East Asian population with a high prevalence of the cagA gene, the East Asian allele could still provide a marker for gastric cancer risk.

Impact

This study contributes to our understanding of H. pylori dynamics in the context of pathological changes.
Models that learn how humans learn: the case of decision-making and its disorders
Authors: Dezfouli Amir , Griffiths Kristi , Ramos Fabio , Dayan Peter , Balleine Bernard W.
Published: March 2018

Popular computational models of decision-making make specific assumptions about learning processes that may cause them to underfit observed behaviours. Here we suggest an alternative method using recurrent neural networks (RNNs) to generate a flexible family of models that have sufficient capacity to represent the complex learning and decision-making strategies used by humans. In this approach, an RNN is trained to predict the next action that a subject will take in a decision-making task and, in this way, learns to imitate the processes underlying subjects’ choices and their learning abilities. We demonstrate the benefits of this approach using a new dataset drawn from patients with either unipolar (n=34) or bipolar (n=33) depression and matched healthy controls (n=34) making decisions on a two-armed bandit task. The results indicate that this new approach is better than baseline reinforcement-learning methods in terms of overall performance and its capacity to predict subjects’ choices. We show that the model can be interpreted using off-policy simulations and thereby provides a novel clustering of subjects’ learning processes – something that often eludes traditional approaches to modelling and behavioural analysis.
Immuno-genomic PanCancer Landscape Reveals Diverse Immune Escape Mechanisms and Immuno-Editing Histories
Authors: Mizuno Shinichi , Yamaguchi Rui , Hasegawa Takanori , Hayashi Shuto , Fujita Masashi , Zhang Fan , Koh Youngil , Lee Su-Yeon , Yoon Sung-Soo , Shimizu Eigo , Komura Mitsuhiro , Fujimoto Akihiro , Nagai Momoko , Kato Mamoru , Liang Han , Miyano Satoru , Zhang Zemin , Nakagawa Hidewaki , Imoto Seiya ,   on behalf of the PCAWG Mitochondrial Genome and Immunogenomics Working Group and The PCAWG Network
Published: March 2018

Immune reactions in the tumor micro-environment are one of the cancer hallmarks and emerging immune therapies have been proven effective in many types of cancer. To investigate cancer genome-immune interactions and the role of immuno-editing or immune escape mechanisms in cancer development, we analyzed 2,834 whole genomes and RNA-seq datasets across 31 distinct tumor types from the PanCancer Analysis of Whole Genomes (PCAWG) project with respect to key immuno-genomic aspects. We show that selective copy number changes in immune-related genes could contribute to immune escape. Furthermore, we developed an index of the immuno-editing history of each tumor sample based on the information of mutations in exonic regions and pseudogenes. Our immuno-genomic analyses of pan-cancer analyses have the potential to identify a subset of tumors with immunogenicity and diverse background or intrinsic pathways associated with their immune status and immuno-editing history.
Productivity definition of the chilling requirement reveals underestimation of the impact of climate change on winter chill accumulation
Authors: Campoy José Antonio , Darbyshire Rebecca , Dirlewanger Elisabeth , Quero-García José , Wenden Bénédicte
Published: March 2018

Evaluation of chilling requirements (CR) of cultivars of temperate fruit trees provides key information to assess regional suitability, according to winter chill, for both industry expansion and ongoing profitability as climate change continues. Traditional methods for calculating CR use climate controlled chambers and define CR using a fixed budburst percentage, usually close to 50% (CR-50%), without considering the productivity level associated to this percentage. This CR-50% definition may underestimate the real CR of tree crops for optimal productivity. This underestimation is particularly important to consider as winter chill accumulation is declining in many regions due to climate change. In this work we used sweet cherry to analyse the traditional method for calculating CR in many Rosaceae species (CR-50%) and compared the results with more a restrictive, productivity focused method, with CR defined with a 90% bud break level (90%, CRm-90%) close to the optimal budburst which assures productivity. Climate projections of winter chill suitability across Europe using CR-50% and CRm-90% were calculated. Regional suitability landscape was highly dependent on the method used to define CR and differences were found for a wide area of the European geography, both cold and mild winter areas. Our results suggest a need to use an optimal budburst level for the assessment of CR for sweet cherry. The use of traditional methods to determine CR can result in an underestimation of productivity CR with negative consequences for the fruit industry, particularly as climate change advances.
Exploring the Impact of Analysis Software on Task fMRI Results
Authors: Bowring Alexander , Maumet Camille , Nichols Thomas E.
Published: March 2018

A wealth of analysis tools are available to fMRI researchers in order to extract patterns of task variation and, ultimately, understand cognitive function. However, this ‘methodological plurality’ comes with a drawback. While conceptually similar, two different analysis pipelines applied on the same dataset may not produce the same scientific results. Differences in methods, implementations across software packages, and even operating systems or software versions all contribute to this variability. Consequently, attention in the field has recently been directed to reproducibility and data sharing. Neuroimaging is currently experiencing a surge in initiatives to improve research practices and ensure that all conclusions inferred from an fMRI study are replicable.

In this work, our goal is to understand how choice of software package impacts on analysis results. We use publically shared data from three published task fMRI neuroimaging studies, reanalyzing each study using the three main neuroimaging software packages, AFNI, FSL and SPM, using parametric and nonparametric inference. We obtain all information on how to process, analyze, and model each dataset from the publications. We make quantitative and qualitative comparisons between our replications to gauge the scale of variability in our results and assess the fundamental differences between each software package. While qualitatively we find broad similarities between packages, we also discover marked differences, such as Dice similarity coefficients ranging from 0.000 - 0.743 in comparisons of thresholded statistic maps between software. We discuss the challenges involved in trying to reanalyse the published studies, and highlight our own efforts to make this research reproducible.
Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis
Authors: Sun Guiling , Xu Yuxing , Liu Hui , Sun Ting , Zhang Jingxiong , Hettenhausen Christian , Shen Guojing , Qi Jinfeng , Qin Yan , Li Jing , Wang Lei , Chang Wei , Guo Zhenhua , Baldwin Ian T. , Wu Jianqiang
Published: March 2018

Dodders (Cuscuta spp., Convolvulaceae) are globally distributed root- and leafless parasitic plants that parasitize a wide range of hosts. The physiology, ecology, and evolution of these obligate parasites are still poorly understood. A high-quality reference genome (size 266.74 Mb and contig N50 of 3.63 Mb) of Cuscuta australis was assembled. Our analyses reveal that Cuscuta experienced accelerated evolution, and Cuscuta and the convolvulaceous morning glory (Ipomoea) shared a common whole-genome triplication event before their divergence. Importantly, C. australis genome harbors only 19805 protein-coding genes, and 11.7% of the conserved orthologs in autotrophic plants are lost in C. australis. Many of these gene loss events likely result from the plant’s parasitic lifestyle and large changes in its body plan. Moreover, comparison of the gene expression patterns in Cuscuta prehaustoria/haustoria and various tissues of closely related autotrophic plants suggests that Cuscuta haustorium genes largely evolved from roots. The C. australis genome provides important resources for studying the evolution of parasitism, regressive evolution, and evo-devo in plant parasites.
Down-regulated Long Noncoding RNAHOXA11-ASaffects trophoblast cell proliferation and migration by regulatingRND3andHOXA7expression in preeclampsia
Authors: Xu Yetao , Wu Dan , Liu Jie , Ma Zhonghua , Hui Bingqing , Wang Jing , chen Yanzi , Wang Sailan , Lian Yifan , Sun Lizhou
Published: March 2018

The long noncoding RNAHOXA11-ASreveals abnormal expression in numerous human diseases. However, its function and biological mechanisms remain unclear in Preeclampsia (PE). In this study, we report thatHOXA11-ASwas significantly downregulated in preeclampsic placental tissues and could contribute to the occurrence and development of Preeclampsia. Silencing ofHOXA11-ASexpression could significantly suppress trophoblast cell growth and migration, whereasHOXA11-ASoverexpression facilitated cell growth in HTR-8/SVneo, JEG3 and JAR cell lines. RNA-seq analysis also indicated thatHOXA11-ASsilencing preferentially regulated numerous genes associated with cell proliferation and cell migration. Mechanistic analyses showed thatHOXA11-AScould recruit Ezh2 and Lsd1 protein, and regulateRND3mRNA expression in nucleus. In cytoplasm,HOXA11-ASmodulateHOXA7expression by sponged miR-15b-5p, thus affecting trophoblast cell proliferation. Together, these resulting data confirm that aberrant expression ofHOXA11-ASis involved in the occurrence and development of Preeclampsia, and may act as a prospective diagnosis and therapeutic target in PE.
Structured priors in human forecasting
Authors: Quiroga Francisco , Schulz Eric , Speekenbrink Maarten , Harvey Nigel
Published: March 2018

Forecasting is an increasingly important part of our daily lives. Many studies on how people produce forecasts frame their behavior as prone to systematic errors. Based on recent evidence on how people learn about functions, we propose that participants’ forecasts are not irrational but rather driven by structured priors, i.e. situationally induced expectations of structure derived from experience with the real world. To test this, we extract participants’ priors over various contexts using a free-form forecasting paradigm. Instead of exhibiting systematic biases, our results show that participants’ priors match well with structure found in real-world data. Moreover, given the same data set, structured priors induce predictably different posterior forecasts depending on the evoked situational context.
Footprints of antigen processing boost MHC class II natural ligand binding predictions
Authors: Barra Carolina , Alvarez Bruno , Andreatta Massimo , Buus Søren , Nielsen Morten
Published: March 2018

Major Histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide:MHC-II binding are trained on binding affinity data, generatedin-vitroand therefore lacking information about antigen processing. For the first time, we here describe prediction models of peptide:MHC-II binding trained directly on naturally eluted peptides, and show that these, in addition to peptide binding to the MHC, incorporate identifiable rules of antigen processing. In fact, we observed detectable signals of protease cleavage at defined positions of the peptides. We also hypothesize a role of the length of the terminal ligand protrusions for trimming the peptide to the epitope presented. The results of integrating binding affinity and eluted ligand data in a combined model demonstrate improved performance for the prediction of MHC-II ligands, and foreshadow a new generation of improved peptide:MHC-II prediction tools of considerable importance for understanding and manipulating immune responses.
Genome wide association analysis identifies genetic variants associated with reproductive variation across domestic dog breeds and uncovers links to domestication
Authors: Phillips Julie Baker , Smith Samuel A. , Johnson Maddison L. , Abbot Patrick , Capra John A. , Rokas Antonis
Published: March 2018

The diversity of eutherian reproductive strategies has led to variation in many traits, such as number of offspring, age of reproductive maturity, and gestation length. While reproductive trait variation has been extensively investigated and is well established in mammals, the genetic loci contributing to this variation remain largely unknown. The domestic dog,Canis lupus familiarisis a powerful model for studies of the genetics of inherited disease due to its unique history of domestication. To gain insight into the genetic basis of reproductive traits across domestic dog breeds, we collected phenotypic data for four traits – cesarean section rate (n = 97 breeds), litter size (n = 60), stillbirth rate (n = 57), and gestation length (n = 23) – from primary literature and breeders’ handbooks. By matching our phenotypic data to genomic data from the Cornell Veterinary Biobank, we performed genome wide association analyses for these four reproductive traits, using body mass and kinship among breeds as co-variates. We identified 14 genome-wide significant associations between these traits and genetic loci, including variants nearCACNA2D3with gestation length,MSRB3with litter size,SMOC2with cesarean section rate,MITFwith litter size and still birth rate,KRT71with cesarean section rate, litter size, and stillbirth rate, andHTR2Cwith stillbirth rate. Some of these loci, such asCACNA2D3andMSRB3, have been previously implicated in human reproductive pathologies. Many of the variants that we identified have been previously associated with domestication-related traits, including brachycephaly (SMOC2), coat color (MITF), coat curl (KRT71), and tameness (HTR2C). These results raise the hypothesis that the artificial selection that gave rise to dog breeds also shaped the observed variation in their reproductive traits. Overall, our work establishes the domestic dog as a system for studying the genetics of reproductive biology and disease.
Acetylation-Dependent Recruitment of the FACT Complex and Its Role in Regulating Pol II Occupancy Genome-Wide inSaccharomyces cerevisiae
Authors: Pathak Rakesh , Singh Priyanka , Ananthakrishnan Sudha , Adamczyk Sarah , Schimmel Olivia , Govind Chhabi K.
Published: March 2018

Histone chaperones, chromatin remodelers, and histone modifying complexes play a critical role in alleviating the nucleosomal barrier for DNA-dependent processes. Here, we have examined the role of two highly conserved yeast (Saccharomyces cerevisiae) histone chaperones, FACT and Spt6, in regulating transcription. We show that the H3 tail contributes to the recruitment of FACT to coding sequences in a manner dependent on acetylation. We found that deleting a H3 HAT Gcn5 or mutating lysines on the H3 tail impairs FACT recruitment atADH1andARG1genes. However, deleting the H4 tail or mutating the H4 lysines failed to dampen FACT occupancy in coding regions. Additionally, we show that FACT-depletion reduces Pol II occupancy in the 5’ ends genome-wide. In contrast, Spt6-depletion leads to reduction in Pol II occupancy towards the 3’ end, in a manner dependent on the gene-length. Severe transcription and histone eviction defects were also observed in a strain that was impaired for Spt6 recruitment (spt6Δ202) and depleted of FACT. Importantly, the severity of the defect strongly correlated with WT Pol II occupancies at these genes, indicating critical roles of Spt6 and Spt16 in promoting high-level transcription. Collectively, our results show that both FACT and Spt6 are important for transcription globally and may participate during different stages of transcription.
Tournaments of values at the European film market
Authors: Smits Roderik
Published: March 2018

Purpose

With film sales markets becoming increasingly popular events where the film business gathers several times each year, the purpose of this paper is to demonstrate that they should be understood as events where important gatekeeping process are taking place. That is to say, sales markets are the point where important decisions about films are made, where sales agencies negotiate access to international markets, and where they exert influence over the sort of access given to specific films.

Design/methodology/approach

Drawing on qualitative methods such as participant observation and interviews, the author develops a case study of the European Film Market (EFM) in Berlin. The author analyses value creation processes at the EFM, focussing specifically on the disposition of exhibition space and the importance of film screenings.

Findings

Drawing on the literature about tournaments of value, the author demonstrates that sales markets endow films with significant values, exercising a powerful role over the process of enabling cultural flow. The author also demonstrates that there is a symbiotic relationship between the EFM sales market and the Berlin International Film Festival, providing a context from which films can generate attention.

Originality/value

The author provides new insights into film sales processes within sales markets, and the role of sales agents in influencing such processes. The author argues that sales markets exert an important influence over gatekeeping by creating social and cultural hierarchies that impact on the sales process of films.
Marketing and consumption of art products: the movie industry
Authors: Ulker-Demirel Elif , Akyol Ayse , Simsek Gülhayat Gölbasi
Published: March 2018

Purpose

The purpose of this paper is to investigate the impact of the importance, assigned by audiences, of factors such as people, movie features, script, price, promotion, and distribution channels (defined as a movie marketing mix) on the audience’s buying intentions, as well as the impact of their buying intentions on word of mouth (WOM). In addition, the intention is to explore the relationship between the preference and frequency of people’s cultural event attendance with their buying intention and the relationship between people with extroverted personalities and WOM.

Design/methodology/approach

The data were collected from 904 valid surveys conducted in Beyoglu, one of the important centres for the culture and art life of the Istanbul.

Findings

The results show that promotion, actor or actress, and diversity of distribution channels have a positive effect on people’s purchase intention. In addition, the frequency of attendance to cultural events can be determinative of the audience and helpful for industry professionals.

Originality/value

Although there have been a number of studies that examine the simple relationships among some of these variables (movie marketing mix, attendance, purchase intention, WOM, extraversion), there is still a gap in the literature with regard to these variables in an integrated framework. Considering these variables in the same model and analysing the effects of each dimension individually provides a better explanation of consumer purchase intention and post-purchase behaviour in the movie industry. This study extends the previous research by incorporating the concept of movie marketing and consumption by improving the scale with data collected in Istanbul, Turkey.
“I Hope I Get It”: impact of Tony Award nominations and wins on Broadway production longevity
Authors: Warne Russell Thomas
Published: March 2018

Purpose

The purpose of this paper is to ascertain the relative impact of different Tony Award nominations and wins on the financial success of a Broadway theater production, as defined by the length of the production’s run.

Design/methodology/approach

Cox hazard regression was used to identify the impact of Tony Award nominations and wins (time-varying covariates), while controlling for several time-invariant covariates: type of production (play or musical, revival or original Broadway production), production costs (operationalized via the cast size), the month and year of opening, and initial marketing success (defined as the percentage of first full week’s tickets sold).

Findings

The award with the strongest relationship with production longevity was the Tony Award for Best Musical (nomination OR=0.566,p=0.110; win OR=0.323,p=0.020). Several other awards had a relationship with production longevity, but most were not statistically significant.

Research limitations/implications

The limitations include the low statistical power for many time-varying covariates and the cumulative impact of multiple awards was not investigated. Future researchers interested in the Broadway industry should not combine Tony Awards because of the varying impact on economic outcomes for a production.

Originality/value

This study is the first to investigate all 22 Tony Award nominations and wins and their individual impact on an economic outcome. This paper includes the study’s raw data and SPSS syntax to comply with open science practices. The author encourages readers to replicate the analysis.
Day, duration, and start time: are the arts providing what their audiences require?
Authors: Rhine Anthony S. , Murnin Patrick M.
Published: March 2018

Purpose

The purpose of this paper is to explore whether variations in factors such as start time, duration of event, and day of presentation might lead to improved attendance at performing arts events in the USA.

Design/methodology/approach

The research was conducted using a quantitative strategy. The approach consisted of a survey design that explored preference data for respondents. The data were examined to look for emergent themes in both raw data and cross-tabulations. The data collection also included survey questions for conjoint analysis, a form of regression analysis that compares consumer trade-offs for various levels of different attributes.

Findings

The researchers found that while anecdotal evidence regarding performing arts attendance largely holds up, there is room to explore the possibility that modern-day consumers require events of shorter duration, and that the utility of Saturday attendance is so overwhelming that start time preference can be manipulated within the Saturday level of that attribute with minimal effect on overall utility.

Originality/value

The study begins to fill a gap in the literature regarding attendance preference for the performing arts regarding several attributes. The study opens a discussion on how to address declining attendance figures by considering some of the factors that are likely contributing to the decline.