bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infundibulocystic Structures and Prominent Squamous Metaplasia in Sebaceoma—A Rare Feature. A Clinicopathologic Study of 10 Cases
Authors: Flux Katharina , Kutzner Heinz , Rütten Arno , Plaza Jose A. , Gasparov Slavko , Michal Michal , Guenova Emmanuella , Kazakov Dmitry V. 
Published: January 2016

Abstract:
The authors describe 10 cases of sebaceoma that manifested prominent infundibulocystic structures in all cases and, additionally, conspicuous squamous metaplasia in 6 neoplasms. All tumors occurred on the scalp or the face (2 cases lacked clinical information) and presented as a solitary lesion, measuring from 5 to 20 mm. The patients' age ranged from 22 to 89 years. The main component of all tumors was small, uniform basaloid cells (immature sebocytes) intermixed with mature sebocytes clearly arranged in nodules, classifying the lesions as a sebaceoma. In all neoplasms, the tumor cells showed organoid growth patterns of sebaceoma, including rippled, sinusoidal/labyrinthine, and carcinoid-like, occurring alone or in combination. Additionally, numerous infundibulocystic structures were readily noticed and were either distributed multifocally or unilocular within the tumors. In some cases, they were segregated from the main tumor bulk. The authors posit that these structures, which are different from both sebaceous ductal differentiation and squamous metaplasia, represent an authentic follicular differentiation. The infundibulocystic features (combined with squamous metaplasia), when prominent and in a limited biopsy specimen, may cause a confusion with trichoadenoma or even microcystic adnexal carcinoma.
Assessing Variations in Areal Organization for the Intrinsic Brain: From Fingerprints to Reliability
Authors: Xu Ting , Opitz Alexander , Craddock R. Cameron , Wright Margaret , Zuo Xi-Nian , Milham Michael P. 
Published: January 2016

AbstractResting state fMRI (R-fMRI) is a powerful in-vivo tool for examining the functional architecture of the human brain. Recent studies have demonstrated the ability to characterize transitions between functionally distinct cortical areas through the mapping of gradients in intrinsic functional connectivity (iFC) profiles. To date, this novel approach has primarily been applied to iFC profiles averaged across groups of individuals, or in one case, a single individual scanned multiple times. Here, we used a publically available R-fMRI dataset, in which 30 healthy participants were scanned 10 times (10 minutes per session), to investigate differences in full-brain transition profiles (i.e., gradient maps, edge maps) across individuals, and their reliability. 10-minute R-fMRI scans were sufficient to achieve high accuracies in efforts to “fingerprint” individuals based upon full-brain transition profiles. Regarding testretest reliability, the image-wise intraclass correlation coefficient (ICC) was moderate, and vertex-level ICC varied depending on region; larger durations of data yielded higher reliability scores universally. Initial application of gradient-based methodologies to a recently published dataset obtained from twins suggested inter-individual variation in areal profiles might have genetic and familial origins. Overall, these results illustrate the utility of gradient-based iFC approaches for studying inter-individual variation in brain function.
Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system
Authors: Rutter Jack W. , Dekker Linda , Fedorec Alex J. H. , Gonzales David T. , Wen Ke Yan , Tanner Lewis E. S. , Donovan Emma , Ozdemir Tanel , Thomas Geraint , Barnes Chris P. 
Published: January 2016

AbstractWhole-cell biosensors hold potential in a variety of industrial, medical and environmental applications. These biosensors can be constructed through the repurposing of bacterial sensing mechanisms, including the common two-component system. Here we report on the construction of a range of novel biosensors that are sensitive to acetoacetate, a molecule that plays a number of roles in human health and biology. These biosensors are based on the AtoSC two-component system. An ODE model to describe the action of the AtoSC two-component system was developed and sensitivity analysis of this model used to help inform biosensor design. The final collection of biosensors constructed displayed a range of switching behaviours, at physiologically relevant acetoacetate concentrations and can operate in severalEscherichia colihost strains. It is envisaged that these biosensor strains will offer an alternative to currently available commercial strip tests and, in future, may be adopted for more complexin vivoor industrial monitoring applications.
Identification of the ventral occipital visual field maps in the human brain
Authors: Winawer Jonathan , Witthoft Nathan 
Published: January 2016

ABSTRACTThe location and topography of the first three visual field maps in the human brain, V1-V3, are well agreed upon and routinely measured across most laboratories. The position of 4thvisual field map, ‘hV4’, is identified with less consistency in the neuroimaging literature. Using magnetic resonance imaging (MRI) data, we describe landmarks to help identify the position and borders of hV4. The data consist of anatomical images, visualized as cortical meshes to highlight the sulcal and gyral patterns, and functional data obtained from retinotopic mapping experiments, visualized as eccentricity and angle maps on the cortical surface.Several features of the functional and anatomical data can be found across nearly all subjects and are helpful for identifying the location and extent of the hV4 map. The medial border of hV4 is shared with the posterior, ventral portion of V3, and is marked by a retinotopic representation of the upper vertical meridian. The anterior border of hV4 is shared with the VO-1 map, and falls on a retinotopic representation of the peripheral visual field, usually coincident with the posterior transverse collateral sulcus. The ventro-lateral edge of the map typically falls on the inferior occipital gyrus, where functional MRI artifacts often obscure the retinotopic data. Finally, we demonstrate the continuity of retinotopic parameters between hV4 and its neighbors; hV4 and V3v contain iso-eccentricity lines in register, whereas hV4 and VO-1 contain iso-polar angle lines in register.Together, the multiple constraints allow for a consistent identification of the hV4 map across most human subjects.
Comparative evaluation of the genomes of common bacterial members of theDrosophilaintestinal community
Authors: Petkau Kristina , Fast David , Duggal Aashna , Foley Edan 
Published: January 2016

AbstractDrosophila melanogasteris an excellent model to explore the molecular exchanges that occur between an animal intestine and their microbial passengers. For example, groundbreaking studies in flies uncovered a sophisticated web of host responses to intestinal bacteria. The outcomes of these responses define critical events in the host, such as the establishment of immune responses, access to nutrients, and the rate of larval development. Despite our steady march towards illuminating the host machinery that responds to bacterial presence in the gut, we know remarkably little about the microbial products that influence bacterial association with a fly host. To address this deficiency, we sequenced and characterized the genomes of three commonDrosophila-associated microbes:Lactobacillus plantarum, Lactobacillus brevisandAcetobacter pasteurianus. In each case, we compared the genomes ofDrosophila-associated strains to the genomes of strains isolated from alternative sources. This approach allowed us to identify molecular functions common toDrosophila-associated microbes, and, in the case ofA. pasteurianus, to identify genes that are essential for association with the host. Of note, many of the gene products unique to fly-associated strains have established roles in the stabilization of host-microbe interactions. We believe that these data provide a valuable starting point for a more thorough examination of the microbial perspective on host-microbe relationships.
Reverse signaling by Semaphorin-6A regulates cellular aggregation and neuronal morphology
Authors: Perez-Branguli Francesc , Zagar Yvrick , Shanley Daniel K. , Graef Isabella A. , Chédotal Alain , Mitchell Kevin J. 
Published: January 2016

AbstractThe transmembrane semaphorin, Sema6A, has important roles in axon guidance, cell migration and neuronal connectivity in multiple regions of the nervous system, mediated by context-dependent interactions with plexin receptors, PlxnA2 and PlxnA4. Here, we demonstrate that Sema6A can also signal cell-autonomously, in two modes, constitutively, or in response to higher-order clustering mediated by either PlxnA2-binding or chemically induced multimerisation. Sema6A activation stimulates recruitment of Abl to the cytoplasmic domain of Sema6A and phosphorylation of this cytoplasmic tyrosine kinase, as well as phosphorylation of additional cytoskeletal regulators. Sema6A reverse signaling affects the surface area and cellular complexity of non-neuronal cells and aggregation and neurite formation of primary neuronsin vitro. Sema6A also interacts with PlxnA2 incis, which reduces binding by PlxnA2 of Sema6Ain transbut not vice versa. These experiments reveal the complex nature of Sema6A biochemical functions and the molecular logic of the context-dependent interactions between Sema6A and PlxnA2.
Canvas: versatile and scalable detection of copy number variants
Authors: Roller Eric , Ivakhno Sergii , Lee Steve , Royce Thomas , Tanner Stephen 
Published: January 2016

AbstractMotivation: Increased throughput and diverse experimental designs of large-scale sequencing studies necessi-tate versatile, scalable and robust variant calling tools. In particular, identification of copy number changes re-mains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on genome-wide sample properties, such as tumor polyploidy or polyclonality in cancer samples.Results: We have developed a new tool, Canvas, for identification of copy number changes from diverse se-quencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched and unmatched tumor-normal studies. In addition to variant calling, Canvas infers genome-wide parameters such as cancer ploidy, purity and heterogeneity. It provides fast and simple to execute workflows that can scale to thousands of samples and can be easily incorporated into existing variant calling pipelines.Availability: Canvas is distributed under an open source license and can be downloaded fromhttps://github.com/Illumina/canvas.Contact:eroller@illumina.comSupplementary information: Supplementary data are available atBioinformaticsonline.
Local opposite orientation preferences in V1: fMRI sensitivity to fine-grained pattern information
Authors: Alink Arjen , Walther Alexander , Krugliak Alexandra , Kriegeskorte Nikolaus 
Published: January 2016

The orientation of a visual grating can be decoded from human primary visual cortex (V1) using functional magnetic resonance imaging (fMRI) at conventional resolutions (2-3 mm voxel width, 3T scanner). It is unclear to what extent this information originates from different spatial scales of neuronal selectivity, ranging from orientation columns to global areal maps. According to the global-areal-map account, fMRI orientation decoding relies exclusively on fMRI voxels in V1 exhibiting a radial or vertical preference. Here we show, by contrast, that 2-mm isotropic voxels in a small patch of V1 within a quarterfield representation exhibit reliable opposite selectivities. Sets of voxels with opposite selectivities are locally intermingled and each set can support orientation decoding. This indicates that global areal maps cannot fully account for orientation information in fMRI and demonstrates that fMRI also reflects fine-grained patterns of neuronal selectivity.Significance statementConventional (3T)functional magnetic resonance imaging (fMRI) allows one measure brain activity at a spatial resolution of 2-3 mm. Brain response patterns in the primary visual cortex (V1) measured with fMRI have been shown to contain robust information about the orientation of visual grating stimuli. However, it is unclear whether this information arises only from global-areal patterns or also from more fine-grained patterns. Here we show that opposite orientation preferences are present and replicable within small V1 patches. This finding demonstrates that fine-grained fMRI patterns contribute to the orientation information present in fMRI data.
Identification and characterization of long non-coding RNAs as targets of mammary tumor cell proliferation and migration
Authors: Diermeier Sarah D. , Chang Kung-Chi , Freier Susan M. , Song Junyan , Krasnitz Alexander , Rigo Frank , Bennett C. Frank , Spector David 
Published: January 2016

AbstractRecent genome-wide studies revealed that as much as 80% of the human genome can be transcribed whereas only 2% of this RNA is translated into proteins. Non-coding transcripts can be subdivided into several groups, with long non-coding RNAs (lncRNAs) representing the largest and most diverse class. With breast cancer being the most frequent malignancy in women worldwide, we set out to investigate the potential of lncRNAs as novel therapeutic targets. By performing RNA-Seq on tumor sections and mammary organoids from MMTV-PyMT and MMTV-Neu-NDL mice, modeling the luminal B and HER2/neu-amplified subtypes of human breast cancer respectively, we generated a comprehensive catalog of differentially expressed lncRNAs. We identified several hundred potentially oncogenic lncRNAs that were over-expressed in a subtype-specific manner as well as numerous lncRNAs up-regulated in both models. Among these lncRNA we defined a subset of 30 previously uncharacterized lncRNAs as Mammary Tumor Associated RNAs (MaTARs) and we identified human orthologs. We functionally validated the role of these MaTARs by antisense oligonucleotide (ASO) mediated knockdown in primary mammary tumor cells and 3Dex vivoorganoids. Upon independent knockdown of 15 MaTARs, we observed significantly reduced cell proliferation, invasion and/or collective cell migration in a cancer-specific context. Thus, MaTARs are likely key drivers of mammary tumor progression and/or metastasis and represent promising new therapeutic targets.
Evaluation of TagSeq, a reliable low-cost alternative for RNAseq
Authors: Lohman Brian K , Weber Jesse N , Bolnick Daniel I 
Published: January 2016

AbstractRNAseq is a relatively new tool for ecological genetics that offers researchers insight into changes in gene expression in response to a myriad of natural or experimental conditions. However, standard RNAseq methods (e.g., Illumina TruSeq®or NEBNext®) can be cost prohibitive, especially when study designs require large sample sizes. Consequently, RNAseq is often underused as a method, or is applied to small sample sizes that confer poor statistical power. Low cost RNAseq methods could therefore enable far greater and more powerful applications of transcriptomics in ecological genetics and beyond. Standard mRNAseq is costly partly because one sequences portions of the full length of all transcripts. Such whole-mRNA data is redundant for estimates of relative gene expression. TagSeq is an alternative method that focuses sequencing effort on mRNAs 3-prime end, thereby reducing the necessary sequencing depth per sample, and thus cost. Here we present a revised TagSeq protocol, and compare its performance against NEBNext®, the gold-standard whole mRNAseq method. We built both TagSeq and NEBNext®libraries from the same biological samples, each spiked with control RNAs. We found that TagSeq measured the control RNA distribution more accurately than NEBNext®, for a fraction of the cost per sample (∽10%). The higher accuracy of TagSeq was particularly apparent for transcripts of moderate to low abundance. Technical replicates of TagSeq libraries are highly correlated, and were correlated with NEBNext®results. Overall, we show that our modified TagSeq protocol is an efficient alternative to traditional whole mRNAseq, offering researchers comparable data at greatly reduced cost.
Cell Assembly Dynamics of Sparsely-connected Inhibitory Networks: a Simple Model for the Collective Activity of Striatal Projection Neurons
Authors: Angulo-Garcia David , Berke Joshua D. , Torcini Alessandro 
Published: January 2016

AbstractStriatal projection neurons form a sparsely-connected inhibitory network, and this arrangement may be essential for the appropriate temporal organization of behavior. Here we show that a simplified, sparse inhibitory network of Leaky-Integrate-and-Fire neurons can reproduce some key features of striatal population activity, as observed in brain slices. In particular we develop a new metric to determine the conditions under which sparse inhibitory networks form anti-correlated cell assemblies with time-varying activity of individual cells. We find that under these conditions the network displays an input-specific sequence of cell assembly switching, that effectively discriminates similar inputs. Our results support the proposal that GABAergic connections between striatal projection neurons allow stimulus-selective, temporally-extended sequential activation of cell assemblies. Furthermore, we help to show how altered intrastriatal GABAergic signaling may produce aberrant network-level information processing in disorders such as Parkinson’s and Huntington’s diseases.Author SummaryNeuronal networks that are loosely coupled by inhibitory connections can exhibit potentially useful properties. These include the ability to produce slowly-changing activity patterns, that could be important for organizing actions and thoughts over time. The striatum is a major brain structure that is critical for appropriately timing behavior to receive rewards. Striatal projection neurons have loose inhibitory interconnections, and here we show that even a highly simplified model of this striatal network is capable of producing slowly-changing activity sequences. We examine some key parameters important for producing these dynamics, and help explain how changes in striatal connectivity may contribute to serious human disorders including Parkinson’s and Huntington’s diseases.
From backyard to commercial hog production
Authors: Huang Weiming , Qiao Fangbin , Liu Huaiju , Jia Xiangping , Lohmar Bryan 
Published: January 2016

Purpose
– The purpose of this paper is to analyze the impact of structural changes in hog production manure management practices.

Design/methodology/approach
– The data used in this study are obtained from a large-scale nationwide hog producers’ survey in rural China conducted by the Center for Chinese Agricultural Policy, Chinese Academy of Sciences, in 2010. A descriptive analysis between hog manure management and its main determinants was conducted. Based on the collected data, an econometric model on the determinants of hog manure management was constructed and used for analysis.

Findings
– The results of this study suggest that the scale of hog production has an important impact on the pattern of hog manure management. Moreover, the results from descriptive statistics and multivariate estimation suggest that smaller hog producers are more likely to apply hog manure to their own lands, while larger hog producers are more likely to sell the manure or find other ways to dispose of it.

Originality/value
– This study contributes to the existing literature by examining the impact of structural changes in hog production on hog manure management and the environment.
Trans-disciplinary community groups: an initiative for improving healthcare
Authors: Sideras James Demetri 
Published: January 2016

Purpose– In the context of budget constraints and the current quality crisis facing UK healthcare, the purpose of this paper is to examine the use of trans-disciplinary community groups (TCG) – an innovative and inexpensive initiative for improving patient care.Design/methodology/approach– Using an action research study, TCG was implemented within a private healthcare firm for vulnerable adults. Qualitative data were gathered over 12 months from 33 participants using depth interviews and focus groups.Findings– TCG led to improved patient activities and increased patient decision-making and confidence in self-advocacy. Key prerequisites were top management commitment, democratic leadership and employee empowerment. However, staff nurses resisted TCG because they were inclined to using managerial control and their own independent clinical judgements.Research limitations/implications– Whilst the findings from this study should not be generalized across all healthcare sectors, its results could be replicated in contexts where there is wide commitment to TCG and where managers adopt a democratic style of leadership. Researchers could take this study further by exploring the applicability of TCG in public healthcare organizations or other multi-disciplinary service contexts.Practical implications– The findings of this research paper provide policy makers and healthcare managers with practical insights on TCG and the factors that are likely to obstruct and facilitate its implementation.Originality/value– Adopting TCG could enable healthcare managers to ameliorate their services with little or no extra cost, which is especially important in a budget constraint context and the current quality crisis facing UK healthcare.
Factors influencing change in clinical practice
Authors: Rajasekhar Praveen T , Rees Colin J , Nixon Catherine , East James E , Brown Sally 
Published: January 2016

Purpose
– The quality improvement in colonoscopy study was a region wide service improvement study to improve adenoma detection rate at colonoscopy by implementing evidence into routine colonoscopy practice. Implementing evidence into clinical practice can be challenging. The purpose of this paper is to perform a qualitative interview study to evaluate factors that influenced implementation within the study.

Design/methodology/approach
– Semi-structured interviews were conducted with staff in endoscopy units taking part in the quality improvement in colonoscopy study, after study completion. Units and interviewees were purposefully sampled to ensure a range of experiences was represented. Interviews were conducted with 11 participants.

Findings
– Key themes influencing uptake of the quality improvement in colonoscopy evidence bundle included time, study promotion, training, engagement, positive outcomes and modifications. Areas within themes were increased awareness of quality in colonoscopy (QIC), emphasis on withdrawal time and empowerment of endoscopy nurses to encourage the use of quality measures were positive outcomes of the study. The simple, visible study posters were reported as useful in aiding study promotion. Feedback sessions improved engagement. Challenges included difficulty arranging set-up meetings and engaging certain speciality groups.

Originality/value
– This evaluation suggests that methods to implement evidence into clinical practice should include identification and empowerment of team members who can positively influence engagement, simple, visible reminders and feedback. Emphasis on timing of meetings and strategies to engage speciality groups should also be given consideration. Qualitative evaluations can provide important insights into why quality improvement initiatives are successful or not, across different sites.