bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing detects structural variants in cancer
Authors: Norris Alexis L. , Workman Rachael E. , Fan Yunfan , Eshleman James R. , Timp Winston 
Published: October 2015

ABSTRACTDespite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300bp) of 2ndgeneration sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20kb) possible with 3rdgeneration sequencing, specifically nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency.We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate theCDKN2A/p16andSMAD4/DPC4tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, with as few as 500 reads per sample. Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring.
Skin transcriptome profiles associated with coat color in goat
Authors: Peng Yongdong , Liu Xiaohui , Geng Liying , Zhang Chuansheng , Liu Zhengzhu , Gong Yuanfang , Li Hongqiang , Li Xianglong 
Published: October 2015

ABSTRACTCapra hircus, an economically important livestock, plays an indispensable role in the world animal fiber industry. To identify additional genes that may play important roles in coat color regulation, Illumina/Solexa high throughput sequencing technology was used to catalog the global gene expression profiles in the skin of three different coat colors goat (Lubei white goat (white), Jining gray goat (gray) and Jianyang big ear goat (brown)). The RNA-Seq analysis generated 83174342, 70222592 and 52091212 clean reads in white skin, gray skin and brown skin, respectively, which provided abundant data for further analysis. A total of 91 genes were differentially expressed between the gray skin and white skin libraries, with 74 upregulated and 17 genes downregulated. Between the brown skin and white skin libraries, there were 23 upregulated genes and 44 downregulated genes, while there were 33 upregulated genes and 121 downregulated genes between the brown skin and gray skin libraries. To our surprise,MC1R, MITF, TYR, KITandKITLGshowed no significant difference in the skin of three different coat colors and the expression ofASIPwas only detected in white skin and not in gray and brown skins. The expression ofPMEL,TRPM1,DCT,TYRP1andELOVL3was validated by real-time quantitative polymerase chain reaction (qPCR) and the results of the qPCR were consistent with the RNA-seq except the expression ofTYRP1between the gray skin and white skin libraries. This study provides several candidate genes that may be associated with the development of diferent coat colors goat skin. More importantly, the fact that theASIPgene was only detected in the white skin and not in the other dark skins and theMC1Rgene showed no significant difference in expression between the three different coat colors goat is of particular interest for future studies that aim to elucidate theirs functional role in the regulation of skin color. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goat and provide a foundation for future studies.
Democratization of genetic data: connecting government approval of clinical tests with data sharing
Authors: Ross Theodora S. 
Published: October 2015

AbstractWhen a doctor orders a genetic test, patients assume that the test will yield a useful result to guide how their physicians take care of them. That assumption is frequently correct, but not always. Until recently, a genetic test only interrogated the sequence of one or two genes. Now, DNA-sequencing technologies are so fast and cheap that they have enabled clinicians to sequence panels of genes that may or may not be relevant to the patient's condition. The technology has outpaced our ability to interpret the results. Connecting approval of clinical tests to data sharing could help close this gap.
Proactive treatment with calcipotriol reduces recurrence of plaque psoriasis
Authors: Ito Kotaro , Koga Monji , Shibayama Yoshitsugu , Tatematsu Saori , Nakayama Juichiro , Imafuku Shinichi 
Published: October 2015

AbstractTopical calcipotriol is a widely used treatment for plaque‐type psoriasis worldwide, and has been shown to improve psoriatic plaques as well as very potent corticosteroids. However, there remains the practical question of whether calcipotriol application should continue on healed pigmentation/depigmentation associated with psoriatic plaques. Therefore, we conducted a pilot clinical study to answer this question. Plaque‐type psoriatic patients not receiving systemic treatment were enrolled and treated with calcipotriol for 8 weeks (stage I) to achieve maximum effect. The patients were then divided into two groups: group A continued to apply calcipotriol to the entirety of the previous lesion (including pigmentation/depigmentation) regardless of whether skin was healed or not, while group B applied calcipotriol to the remaining lesion only. Patients were followed for 12 weeks (stage II) and dates of plaque recurrence were recorded. A total of 29 patients (13 men, 16 women) were enrolled. During stage I, reductions in scores for redness, induration and scale occurred in 40%, 47% and 55% of patients, respectively. After stage II was completed, group A (n = 19) showed a significantly better Kaplan–Meier curve of non‐recurrence than group B (n = 8, P < 0.01). The mean non‐recurrence duration was 76.8 ± 11.8 in group A and 35.0 ± 12.0 in group B. Our study showed that applying topical calcipotriol on seemingly healed psoriatic plaque lesions suppresses recurrence better than applying it only on remaining plaques. This finding may be important for instructing psoriatic patients on topical calcipotriol treatment.
Advice, authority and autonomy in shared decision‐making in antenatal screening: the importance of context
Authors: Pilnick Alison , Zayts Olga 
Published: October 2015

AbstractShared decision‐making (SDM) has been widely advocated across many branches of healthcare, yet there is considerable debate over both its practical application and how it should be examined or assessed. More recent discussions of SDM have highlighted the important of context, both internal and external to the consultation, with a recognition that decisions cannot be understood in isolation. This paper uses conversation analysis (CA) to examine how decision‐making is enacted in the context of antenatal screening consultations in Hong Kong. Building on previous CA work (Collins et al. , Toerien et al. 2013), we show that, whilst previously identified formats are used here to present the need for a decision, the overriding basis professionals suggest for actually making a decision in this context is the level of worry or concern a pregnant woman holds about potential foetal abnormality. Professionals take an unknowing ‘epistemic stance’ (Heritage ) towards this worry, and hence step back from involvement in decision‐making. We argue that this is linked to the non‐directive ethos that prevails in antenatal screening services, and suggest that more research is needed to understand how the enactment of SDM is affected by wider professional contexts and parameters.
A toolbox for studying thermal heterogeneity across spatial scales: from unmanned aerial vehicle imagery to landscape metrics
Authors: Faye Emile , Rebaudo François , Yánez‐Cajo Danilo , Cauvy‐Fraunié Sophie , Dangles Olivier 
Published: October 2015

Summary

A major barrier for the scientific community of climate change biologists is the spatial mismatch between the size of organisms and the resolution at which global climate data are collected and modelled. Thus, the development of integrative and quantitative tools for the monitoring and spatial characterization of microclimates across spatial scales is a key issue for climate change ecologists.

We proposed an integrative toolbox for quantifying the spatial heterogeneity in surface temperatures by bringing together procedures of unmanned aerial vehicles, thermal imagery, orthomosaic, GIS classification and spatial metrics. This toolbox permits to yield high‐resolution visual and infrared orthoimages that are processed into a GIS for selecting surfaces of interest in the landscape (e.g. soil, vegetation). Then, the thermal matrices of selected surfaces (i.e. temperature values of the pixels belonging to the selected surfaces only) are processed within r to generate a variety of thermal landscape metrics (e.g. thermal patch richness and density, thermal aggregation and cohesion index).

We applied this toolbox to the thermal characterization of mountainous agricultural landscapes in Ecuador with implications for ectothermic pest dynamics. UAV flights at a height of 60 m above‐ground level allowed us to acquired high‐resolution visual and thermal images (1 and 5 cm/pixel, respectively) for 12 potato fields with a mean surface of 1017 ± 117 m2. Landscape metrics on plant and soil surfaces showed that crop phenology drives the spatial patterns of surface temperatures and strongly modifies the overall thermal ecology of crop fields, with potential implications for ectothermic pest occurrence and dynamics.

Overall, our toolbox affords a timely and innovative methodological framework to better assess the thermal heterogeneity of natural landscapes across a wide range of spatial scales. In particular, this toolbox would be of topical interest for ecologists trying to bridge the gap between the resolution of their climatic data and the body size of their study organisms.
The Universal Floristic Quality Assessment (FQA) Calculator: an online tool for ecological assessment and monitoring
Authors: Freyman William A. , Masters Linda A. , Packard Stephen 
Published: October 2015

Summary

Floristic Quality Assessments (FQAs) are measurements of a natural area's ecological integrity based on their plant species composition. Widely used by government agencies and conservation organizations to monitor and assess natural areas, FQA data bases have been developed for much of the United States and beyond.

Here, we present the Universal FQA Calculator (http://universalFQA.org), a free, open‐source web‐based FQA Calculator. The calculator offers 30 FQA data bases (with more being added regularly) from across the United States and Canada and has been used to calculate thousands of assessments. The Universal FQA Calculator's growing repository for site inventory and transect data is accessible via a REST API and represents a valuable resource for data on the occurrence and abundance of plant species.

We describe the features and implementation of the Universal FQA Calculator, provide a summary of its increasing usage and discuss the benefits of cloud‐based storage of ecological assessment data.
Neural substrates of cue reactivity: association with treatment outcomes and relapse
Authors: Courtney Kelly E. , Schacht Joseph P. , Hutchison Kent , Roche Daniel J. O. , Ray Lara A. 
Published: October 2015

AbstractGiven the strong evidence for neurological alterations at the basis of drug dependence, functional magnetic resonance imaging (fMRI) represents an important tool in the clinical neuroscience of addiction. fMRI cue‐reactivity paradigms represent an ideal platform to probe the involvement of neurobiological pathways subserving the reward/motivation system in addiction and potentially offer a translational mechanism by which interventions and behavioral predictions can be tested. Thus, this review summarizes the research that has applied fMRI cue‐reactivity paradigms to the study of adult substance use disorder treatment responses. Studies utilizing fMRI cue‐reactivity paradigms for the prediction of relapse and as a means to investigate psychosocial and pharmacological treatment effects on cue‐elicited brain activation are presented within four primary categories of substances: alcohol, nicotine, cocaine and opioids. Lastly, suggestions for how to leverage fMRI technology to advance addiction science and treatment development are provided.
Morphology of the greater palatine grooves of the hard palate: a cone beam computed tomography study
Authors: Monsour P , Huang T 
Published: October 2015

AbstractBackgroundThere is increasing frequency of dentoalveolar and palatal implants placed in the posterior maxilla for prosthodontic and orthodontic purposes. The purpose of this study is to provide information on the location and morphology of the greater palatine grooves (GPG) in the hard palate and to promote awareness of this structure.MethodsEighty‐nine cone beam computed tomography (CBCT) scans were analysed for the presence of a groove, crest or bridging.ResultsThis study on the morphology of the GPG in the maxillary first and second molar regions showed three distinct appearances: (1) no palatal groove; (2) one palatal groove; (3) two palatal grooves. The detection frequency of no palatal groove in the first molar region was 60%, 34% had one groove and 6% having two grooves. The detection frequency of no palatal groove in the second molar region was 72%, 26% had one groove and 2% had two grooves. The number of crests in the first and second molar regions ranged from 0 to 3.ConclusionsThe present study demonstrates a great variation in morphology of the GPG of the hard palate. Knowledge of the GPG will decrease possible complications of implant surgery, particularly palatal implant surgery and to not confuse the GPG with pathology.
Immunolocalization and distribution of proteoglycans in carious dentine
Authors: Stankoska K , Sarram L , Smith S , Bedran‐Russo AK , Little CB , Swain MV , Bertassoni LE 
Published: October 2015

AbstractBackgroundCollagen type I, proteoglycans (PG) and non‐collagenous proteins represent important building blocks of the dentine matrix. While different PGs have been identified in dentine, changes in the distribution of these macromolecules with the progression of caries have been poorly characterized. The aim of this study was to compare the immunolocalization of three small collagen‐binding PGs (biglycan, fibromodulin and lumican) as well as collagen (types I and VI) in healthy versus carious dentine.MethodsLongitudinal demineralized sections of extracted teeth were stained with antibodies recognizing specific PG core proteins and collagens, as well as glycosaminoglycans (GAGs) with toluidine blue.ResultsIn healthy dentine, PGs appeared to be more abundant near the tubule walls and directly under the cusps. Conversely, in carious dentine, specific locations appeared to be more prone to PG degradation than others. These degradation patterns were well correlated with the progression of caries into the tissue, and also appeared to trigger interesting morphological changes in the tissue structure, such as the deformation of dentine tubules near highly infected areas and the lower concentration of PG in tertiary dentine.ConclusionsThis study presents new insights into the involvement of PGs in the progression of caries.
Effects of renal denervation on renal pelvic contractions and connexin expression in rats
Authors: Koenen A. , Steinbach A. , Schaper K. , Zimmermann U. , Miehe B. , Kurt B. , Rettig R. , Grisk O. 
Published: October 2015

AbstractAimsThe renal pelvis shows spontaneous rhythmic contractile activity. We assessed to what extent this activity depends on renal innervation and studied the role of connexins in pelvic contractions.MethodsRats underwent unilateral renal denervation or renal transplantation. Renal pelvic pressure and diuresis were measured in vivo. Spontaneous and agonist‐induced contractions of isolated renal pelves were investigated by wire myography. Rat and human renal pelvic connexin mRNA abundances and connexin localization were studied by real‐time PCR and immunofluorescence respectively.ResultsRenal denervation or transplantation increased renal pelvic pressure in vivo by about 60 and 150%, respectively, but did not significantly affect pelvic contraction frequency. Under in vitro conditions, isolated pelvic preparations from innervated or denervated kidneys showed spontaneous contractions. Pelves from denervated kidneys showed about 50% higher contraction frequencies than pelves from innervated kidneys, whereas contraction force was similar in pelves from denervated and innervated kidneys. There was no denervation‐induced supersensitivity to noradrenaline or endothelin‐1. Renal denervation did not increase pelvic connexin37, 40, 43 or 45 mRNA abundances. Gap junction blockade had no effect on spontaneous pelvic contractile activity.ConclusionsThe denervation‐induced effect on pelvic pressure may be the consequence of the enhanced diuresis. The mechanisms underlying the denervation‐induced effects on pelvic contraction frequency remain unknown. Our data rule out a major role for two important candidates, by showing that renal denervation neither induced supersensitivity to contractile agonists nor increased connexin mRNA abundance in the pelvic wall.
Smoking behaviour and knowledge of the health effects of smoking in patients with inflammatory bowel disease
Authors: De Bie C. , Ballet V. , Hendriks N. , Coenen S. , Weyts E. , Van Assche G. , Vermeire S. , Ferrante M. 
Published: October 2015

SummaryBackgroundThe detrimental effect of smoking on development and progression of Crohn's disease (CD) is generally accepted.AimTo evaluate the awareness of smoking risks in a Belgian inflammatory bowel disease (IBD) population.MethodsIn the out‐patient clinic of a tertiary referral centre, 625 consecutive patients with CD, 238 patients with ulcerative colitis (UC) and 289 non‐IBD controls, filled out a simple questionnaire. This questionnaire included data on smoking behaviour and awareness of smoking‐related health effects, including effects on IBD.ResultsAt diagnosis, more CD patients were active smokers compared to UC (40% vs. 17%, P < 0.001). Remarkably, smoking cessation rates after diagnosis were similar for CD and UC (both 56%, P = 0.997). The great majority recognised a detrimental influence of smoking on general health (98–99%), lung cancer (95–97%), myocardial infarction (89–92%) and stroke (78–87%). Although CD patients more frequently acknowledged risks of smoking on their disease, only 37% were aware of a link with CD development, 30% of increased surgical rates and 27% of increased post‐operative CD recurrence. Active smokers more frequently denied an increased risk of surgery and higher post‐operative CD recurrence. Intriguingly, within the active smokers with CD, those not willing to quit smoking most often denied a potential bad influence of smoking. Taking into account disease duration, previous surgery, education level, working status and nicotine dependence, we were unable to define specific subgroups of patients requiring extra education.ConclusionAlthough patients with Crohn's disease were better informed on the detrimental effects of smoking, the awareness rate was still low.
Conception rates in farm mink (Neovison vison) in relation to first mating date, age and color variety
Authors: Felska‐Błaszczyk Lidia , Lasota Bogdan , Seremak Beata 
Published: October 2015

AbstractThe aim of the study was to analyze the effects of the first mating date, age and color variety on the conception rates in farm mink. We analyzed female mink reproductive performance in 492 Sapphire and 463 Standard Black females over 3 or 4 years. The analysis included the number of inefficient matings, the interval between the first inefficient mating and the efficient mating (copulation) and the conception rates. The results show a significant effect of female's age and color variety on the conception rates. The youngest, yearling females of either color needed a higher number of matings per conception, as compared to older, 2‐ and 3‐year‐old females. Black females demonstrated a higher number of inefficient matings (1.066), as compared with Sapphires (0.730). Yearling females were most often mated from 1 to 10 March, and older females from 11 to 20 March. Older females achieved better conception rates than the yearlings. Dates between 11 and 25 March proved to be the optimum for the first mating, since the highest conception rates were observed if the females had mated during this period.
Microscopic haematuria at time of diagnosis is associated with lower disease stage in patients with newly diagnosed bladder cancer
Authors: Ramirez Daniel , Gupta Amit , Canter Daniel , Harrow Brian , Dobbs Ryan W. , Kucherov Victor , Mueller Edward , Streeper Necole , Uhlman Matthew A. , Svatek Robert S. , Messing Edward M. , Lotan Yair 
Published: October 2015

ObjectivesTo determine whether the severity of haematuria (microscopic or gross) at diagnosis influences the disease stage at presentation in patients diagnosed with bladder cancer.Patients and MethodsWe conducted a multi‐institutional observational cohort study of patients who were newly diagnosed with bladder cancer between August 1999 and May 2012. We reviewed the degree of haematuria, demographic information, clinical and social history, imaging, and pathology. The association of haematuria severity with incident tumour stage and grade was evaluated using logistic regression.ResultsPatients diagnosed with bladder cancer presented with gross haematuria (GH; 1 083, 78.3%), microscopic haematuria (MH; 189, 13.7%) or without haematuria (112, 8.1%). High‐grade disease was found in 64% and 57.1% of patients presenting with GH and MH, respectively, and severity of haematuria was not associated with higher grade disease. Stage of disease at diagnosis for patients presenting with MH was Ta/carcinoma in situ (CIS) in 68.8%, T1 in 19.6%, and ≥T2 in 11.6%. Stage of disease at diagnosis for patients presenting with GH was Ta/CIS in 55.9%, T1 in 19.6%, and ≥T2 in 17.9%. On multivariate analyses, GH was independently associated with ≥T2 disease at diagnosis (odds ratio 1.69, 95% confidence interval 1.05–2.71, P = 0.03).ConclusionsAmong patients with newly diagnosed bladder cancer, presentation with GH is associated with a more advanced pathological stage. Earlier detection of disease, before development of GH, could influence survival in patients with bladder cancer. Type of haematuria at presentation does not impact grade of disease.