bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mediodorsal and ventromedial thalamus engage distinct L1 circuits in the prefrontal cortex
Authors: Anastasiades Paul G. , Collins David P. , Carter Adam G. 
Published: January 2020

SUMMARYInteractions between the thalamus and prefrontal cortex (PFC) play a critical role in cognitive function and arousal. Here we use anatomical tracing, electrophysiology, optogenetics, and 2-photon Ca2+ imaging to determine how ventromedial (VM) and mediodorsal (MD) thalamus target specific cell types and subcellular compartments in layer 1 (L1) of mouse PFC. We find thalamic inputs make distinct connections in L1, where VM engages NDNF+ cells in L1a, and MD drives VIP+ cells in L1b. These separate populations of L1 interneurons participate in different disinhibitory networks in superficial layers by targeting either PV+ or SOM+ interneurons. NDNF+ cells also inhibit the apical dendrites of L5 pyramidal tract (PT) cells, where they suppress AP-evoked Ca2+ signals. Lastly, NDNF+ cells mediate a unique form of thalamus-evoked inhibition at PT cells, selectively blocking VM-evoked dendritic Ca2+ spikes. Together, our findings reveal how two thalamic nuclei differentially communicate with the PFC through distinct L1 micro-circuits.
The effect of counterfactual information on outcome value coding in medial prefrontal and cingulate cortex: from an absolute to a relative neural code
Authors: Pischedda Doris , Palminteri Stefano , Coricelli Giorgio 
Published: January 2020

ABSTRACTAdaptive coding of stimuli in visual cortex is well documented in perception, where it supports efficient encoding over a broad range of possible percepts. Recently, a similar neural mechanism has been reported also in value-based decision, where it allows optimal encoding of vast ranges of values in PFC: neuronal response to value depends on the choice context (relative coding), rather than being invariant across contexts (absolute coding). Additionally, value learning is sensitive to the amount of feedback information: providing complete feedback (both obtained and forgone outcomes) instead of partial feedback (only obtained outcome) improves learning. However, it is unclear whether relative coding occurs in all PFC regions and how it is affected by feedback information. We systematically investigated univariate and multivariate feedback encoding in various PFC regions and compared three modes of neural coding: absolute, partially-adaptive and fully-adaptive.Twenty-eight human participants (both sexes) performed a learning task while undergoing fMRI scanning. On each trial, they chose between two symbols associated with a certain outcome. Then, the decision outcome was revealed. Notably, in half of the trials participants received partial feedback, while in the other half they got complete feedback. We used univariate and multivariate analysis to explore value encoding in different feedback conditions.We found that both obtained and forgone outcomes were encoded in mPFC, but with opposite sign in ventral and dorsal subdivisions. Moreover, we showed that increasing feedback information induced a switch from absolute to relative coding. Our results suggest that complete feedback information promotes context-dependent outcome encoding.SIGNIFICANCE STATEMENTThis study offers a systematic investigation of the effect of the amount of feedback information (partial vs. complete) on univariate and multivariate outcome value encoding, within multiple regions in mPFC/ACC critical for value-based decisions and behavioural adaptation. Moreover, we provide the first comparison of three possible models of neural coding (i.e., absolute, partially-adaptive, and fully-adaptive coding) of value signal in mPFC by using commensurable measures of model accuracy. Taken together, our results help build a more comprehensive picture of how the human brain encodes and processes outcome value. In particular, our results suggest that simultaneous presentation of obtained and foregone outcomes promotes relative value representation.
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads
Authors: Majidian Sina , Kahaei Mohammad Hossein , de Ridder Dick 
Published: January 2020

AbstractBackgroundHaplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads. By the advent of new sequencing technologies, new algorithms are needed to ensure long and accurate haplotypes. While a few linked-read haplotype assembly algorithms are available for diploid genomes, there are no algorithms yet for polyploids.ResultsThe first haplotyping algorithm designed for 10X linked reads generated from a polyploid genome is presented, built on a typical short-read haplotyping method, SDhaP. Using the input aligned reads and called variants, the haplotype-relevant information is extracted. Next, reads with the same barcodes are combined to produce molecule-specific fragments. Then, these fragments are clustered into strongly connected components which are then used as input of a haplotype assembly core in order to estimate accurate and long haplotypes.ConclusionsHap10 is a novel algorithm for haplotype assembly of polyploid genomes using linked reads. The performance of the algorithms is evaluated in a number of simulation scenarios and its applicability is demonstrated on a real dataset of sweet potato.
Expression-Based Inference of Cancer Metabolic Flux Differences
Authors: Wang Yiping , Gu Zhenglong 
Published: January 2020

1AbstractCancer cells display numerous differences in metabolic regulation and flux distribution from noncancerous cells, which are necessary to support increased cancer cell growth. However, current experimental methods cannot accurately measure such metabolic flux differences genome-wide. To address this short-coming, we apply FALCON, a computational algorithm for inferring metabolic fluxes from gene expression data, to analyze data from The Cancer Genome Atlas (TCGA). We found several major differences between tumor and control tissue metabolism. Cancer tissues have a considerably stronger correlation between RNA-seq expression and inferred metabolic flux, which may indicate a more streamlined and efficient use of metabolism. Cancer metabolic fluxes generally have high correlation with their normal control counterparts in the same tissue, but surprisingly, there are several cases where tumor samples in one tissue have even higher correlation with control samples in another tissue. Finally, we found several pathways that frequently have divergent flux between tumor and control samples. Among these are several previously implicated in tumorigenesis, including sphingolipid metabolism, methionine and cysteine synthesis, and bile acid transformations. Together, these findings show how cancer metabolism differs from normal tissues and may be targeted in order to control cancer progression.
Dissociable roles of central striatum and anterior lateral motor area in initiating and sustaining naturalistic behavior
Authors: Corbit Victoria L. , Piantadosi Sean C. , Wood Jesse , Liu Grace , Choi Clare J.Y. , Witten Ilana B. , Gittis Aryn H. , Ahmari Susanne E. 
Published: January 2020

AbstractAlthough much is known about how corticostriatal circuits mediate behavioral selection, most previous work has been conducted in highly trained animals engaged in instrumental tasks. Understanding how corticostriatal circuits mediate behavioral selection and initiation in a naturalistic setting is critical to understanding how the brain chooses and executes behavior in unconstrained situations. Central striatum (CS), an understudied region that lies in the middle of the motor-limbic topography, is well-poised to play an important role in these processes since its main cortical inputs (Corbit et al., 2019) have been implicated in behavioral flexibility (lateral orbitofrontal cortex (Kim and Ragozzino, 2005)) and response preparation (anterior lateral motor area, ALM) (Li et al., 2015), However, although CS activity has been associated with conditioned grooming behavior in transgenic mice (Burguiere et al., 2013), the role of CS and its cortical inputs in the selection of spontaneous behaviors has not been explored. We therefore studied the role of CS corticostriatal circuits in behavioral selection in an open field context.Surprisingly, using fiber photometry in this unconstrained environment, we found that population calcium activity in CS was specifically increased at onset of grooming, and not at onset of other spontaneous behaviors such as rearing or locomotion. Supporting a potential selective role for CS in the initiation of grooming, bilateral optogenetic stimulation of CS evoked immediate onset grooming-related movements. However, these movements resembled subcomponents of grooming behavior and not full-fledged grooming bouts, suggesting that additional input(s) are required to appropriately sequence and sustain this complex motor behavior once initiated. Consistent with this idea, optogenetic stimulation of CS inputs from ALM generated sustained grooming responses that evolved on a time-course paralleling CS activation monitored using single-cell calcium imaging. Furthermore, fiber photometry in ALM demonstrated a gradual ramp in calcium activity that peaked at time of grooming termination, supporting a potential role for ALM in encoding length of this spontaneous sequenced behavior. Finally, dual color dual region fiber photometry indicated that CS activation precedes ALM during naturalistic grooming sequences. Taken together, these data support a novel model in which CS activity is sufficient to initiate grooming behavior, but ALM activity is necessary to sustain and encode the length of grooming bouts. Thus, the use of an unconstrained behavioral paradigm has allowed us to uncover surprising roles for CS and ALM in the initiation and maintenance of spontaneous sequenced behaviors.
Structure of a consensus chitin-binding domain revealed by solution NMR
Authors: Heymann Dario , Mohanram Harini , Kumar Akshita , Verma Chandra S. , Lescar Julien , Miserez Ali 
Published: January 2020

ABSTRACTCarbohydrate-binding proteins (CBPs) are a versatile group of proteins found in almost every organism on earth. CBPs are involved in enzymatic carbohydrate degradation and also serve as templating scaffolds in the exoskeleton of crustaceans and insects. One specific chitin-binding motif found across a wide range of arthropods’ exoskeletons is the “extended Rebers and Riddiford” consensus (R&R). However, how the R&R motif binds chitin is unclear. Here, we report the 3D structure and molecular level interactions of a chitin-binding domain (CBD-γ) located in a CBP from the beak of the jumbo squid Dosidicus gigas. This CBP is one of four chitin-binding proteins identified in the beak mouthpart of D. gigas and is believed to interact with chitin to form a scaffold network that is infiltrated with a second set of structural proteins during beak maturation. We used solution state NMR spectroscopy to elucidate the molecular interactions between CBD-γ and the soluble chitin derivative pentaacetyl-chitopentaose (PCP) and find that folding of this domain is triggered upon its interaction with PCP. To our knowledge, this is the first experimental 3D structure of a CBP containing the R&R consensus motif, which can be used as a template to understand in more details the role of the R&R motif found in a wide range of CBP-chitin complexes. The present structure also provides molecular information for biomimetic synthesis of graded biomaterials using aqueous-based chemistry and biopolymers.
KLF4 coordinates corneal epithelial apicobasal polarity and plane of cell division, and is downregulated in ocular surface squamous neoplasia
Authors: Tiwari Anil , Swamynathan Sudha , Jhanji Vishal , Swamynathan Shivalingappa K. 
Published: January 2020

AbstractApicobasal polarity (ABP) is an important feature of many epithelial cells, including those in the stratified squamous corneal epithelium (CE). Previously, we demonstrated that KLF4 promotes CE homeostasis by suppressing epithelial-mesenchymal transition (EMT) and TGF-β signaling. As dysregulation of TGF-β signaling affects ABP, we investigated the role of KLF4 in regulating cell polarity and plane of division by spatiotemporally regulated ablation ofKlf4in adult ternary transgenicKlf4Δ/ΔCE(Klf4LoxP/LoxP/Krt12rtTA/rtTA/Tet-O-Cre) mouse CE.Klf4Δ/ΔCEcells displayed decreased expression and mis-localization of apical polarity markers Pals1 and Crumbs1, apicolateral Par3, and basolateral Scribble. Cdc42 was upregulated, while Rac and Rho were mis-localized in theKlf4Δ/ΔCEcytoplasm unlike their cortical expression in the control. Phalloidin staining revealed disrupted actin cytoskeleton in theKlf4Δ/ΔCEcells. Survivin and phospho-histone-H3 immunostaining revealed a tilt in the plane of cell division favoring symmetrical divisions with vertical axis in theKlf4Δ/ΔCEcompared with predominantly asymmetrical divisions with horizontal axis in the control. Human ocular surface squamous neoplasia (OSSN) tissues displayed signs of EMT and loss of ABP markers PAR3, PALS1 and SCRIB, coupled with downregulation of KLF4. By demonstrating thatKlf4ablation affects CE expression of ABP markers and Rho family GTPases, cytoskeletal actin organization and the plane of cell division, and that KLF4 is downregulated in OSSN tissues that display EMT and lack ABP, these results elucidate the key integrative role of KLF4 in coordinating CE cell polarity and plane of division, loss of which results in OSSN.
Multiple phosphatidylinositol(3)phosphate roles in retinal pigment epithelium membrane recycling
Authors: He Feng , Agosto Melina A. , Nichols Ralph M. , Wensel Theodore G. 
Published: January 2020

AbstractThe low-abundance lipid phosphatidylinositol-3-phosphate (PI(3)P) is important for membrane dynamics in autophagy, endosome processing, and phagocytosis. In retinal pigmented epithelial cells (RPE) all three pathways are important, but phagocytosis of disk membranes shed from adjacent photoreceptors is especially important for ensuring health of photoreceptors and preventing retinal degeneration. By eliminating Vps34, the kinase responsible for synthesizing PI(3)P in RPE, we have found that PI(3)P plays distinct roles in each pathway. In phagocytosis it is not required for disk engulfment or phagosome transport but is essential for recruitment and lipidation of LC3. In contrast, initiation of autophagy and LC3 recruitment to autophagosomes does not require PI(3)P, which can be bypassed by an alternative mechanism of ATG16L recruitment that does not require PI(3)P, Rab11a, or WIPI2. In all three pathways, PI(3)P is essential for fusion with lysosomes; autophagosomes, phagosomes, and Rab7-positive late endosomes, as well as enlarged lysosomes, accumulate in large numbers in the absence of Vps34, leading to cell death.
Transcriptome analysis reveals evolutionary co-option of neural development and signaling genes for the wing pigmentation pattern of the polka-dotted fruit fly
Authors: Fukutomi Yuichi , Kondo Shu , Toyoda Atsushi , Shigenobu Shuji , Koshikawa Shigeyuki 
Published: January 2020

AbstractHow evolutionary novelties have arisen is one of the central questions in evolutionary biology. Pre-existing gene regulatory networks or signaling pathways have been shown to be co-opted for building novel traits in several organisms. However, the structure of entire gene regulatory networks and evolutionary events of gene co-option for emergence of a novel trait are poorly understood. In this study, we used a novel wing pigmentation pattern of the polka-dotted fruit fly, and identified the complete set of genes for pigmentation pattern formation byde novogenome sequencing and transcriptome analyses. In pigmentation areas of wings, 151 genes were positively or negatively regulated bywingless, a master regulator of wing pigmentation. Genes for neural development, Wnt signaling, Dpp signaling, Zinc finger transcription factors, and effectors (such as enzymes) for melanin pigmentation were included among these 151 genes. None of the known regulatory genes that regulate pigmentation pattern formation in other fruit fly species were included. Our results suggest that the novel pigmentation pattern of the polka-dotted fruit fly emerged through multi-step co-options of multiple gene regulatory networks, signaling pathways, and effector genes, rather than recruitment of one large gene circuit.
Discriminant Analysis of Principle Component analyses of Physiological Data
Authors: Haidar Omar , Ball Samuel , Barrett-Jolley Richard 
Published: January 2020

AbstractThere are many situations in physiological and pharmacological analyses where multivariate data is collected. Frequently these are analysed with t-tests and multiple (Bonferroni) comparisons or ANOVA with post-hoc test. Increasingly, even with more powerful computers many variables and it seems that feature reduction would be a useful approach. The most commonly used method is principle component analyses, but in this report we compare this to a technique developed for genetic analyses, discriminant analysis of principle component (DAPC) analyses. A simple to use and well-maintained library exists for DAPC analyses, Adegenet2, and using this we find that DAPC detects differences between synthetic physiological datasets with significantly greater accuracy than traditional PCA.
Exploiting market-oriented collective learning cycle to leverage competitive advantage at a foreign subsidiary in emerging markets
Authors: Shehata Gamal Mohamed 
Published: January 2020

Purpose
The purpose of this paper is to examine how a foreign subsidiary operates in emerging markets and integrates market orientation with organizational learning to achieve a competitive lead. It is an attempt to fill an evident gap in the literature of integrating organizational learning into a market-oriented competitive strategy through using a four-step collective learning cycle at General Motors Egypt (GME).

Design/methodology/approach
The paper adopts a qualitative case study methodology to thoroughly examine the viewpoints of 90 respondents via in-depth and unstructured interviews with both managers and employees working in a variety of divisions inside GME. An integrative qualitative data analysis approach is used to explore, synthesize, interpret and derive relationships resulting from the collected data.

Findings
This work advances the theory of organizational learning by testing the theme of collective learning cycle in a real work setting. It presents a real example of aligning market orientation into a collective learning cycle directed toward achieving competitive advantages.

Research limitations/implications
This study provides scholars and practitioners alike with a real scenario on how and why a four-step organizational learning cycle functions as a building block to generate a competitive advantage. It also discusses the elements of collective learning that are not captured by the four-step collective learning cycle. Factors facilitating market-based organizational learning are also explored. However, the results generated are contingent on the investigated case study circumstances, which are limited in generalizability.

Practical implications
The paper addresses a set of directions through which auto assembly firms leverage both collective learning practices and knowledge-driven strategy to gain competitive advantages. The GME paradigm indicates how a firm can use collective learning not only to respond to an internal need for change but also to react to external market forces and constraints.

Originality/value
This study is the first of its kind to investigate the value of the cyclic learning concept from a strategic viewpoint in a multinational organizational context. It enriches the primarily practitioner literature on aligning collective learning into strategy with rich empirical examination of the learning practices of a leading foreign subsidiary. It resolves a gap in the literature regarding how organizational learning and knowledge management processes are aligned to market-oriented competitive strategy. The paper draws a number of critical research issues that call for refinement of the organizational learning cycle theory.
Implementing HBIM on conservation heritage projects
Authors: Woodward Alexa , Heesom David 
Published: January 2020

PurposeHeritage or historic building information modelling (BIM), often referred to as HBIM, is becoming an established feature in both research and practice. The advancement of data capture technologies such as laser scanning and improved photogrammetry, along with the continued power of BIM authoring tools, has provided the ability to generate more accurate digital representations of heritage buildings which can then be used during renovation and refurbishment projects. Very often these representations of HBIM are developed to support the design process. What appears to be often overlooked is the issue of conservation and how this can be linked to the BIM process to support the conservation management plan for the building once it is given a new lease of life following the refurbishment process. The paper aims to discuss these issues.Design/methodology/approachThe paper presents a review of the context of conservation and HBIM, and then subsequently presents two case studies of how HBIM was applied to high-profile renovation and conservation projects in the UK. In presenting the case studies, a range of issues is identified which support findings from the literature noting that HBIM is predominantly a tool for the geometric modelling of historic fabric with less regard for the actual process of renovation and conservation in historic buildings.FindingsLessons learnt from the case studies and from existing literature are distilled to develop a framework for the implementation of HBIM on heritage renovation projects to support the ongoing conservation of the building as an integral part of a BIM-based asset management strategy. Five key areas are identified in the framework including value, significance, recording, data management and asset management. Building on this framework, a conceptual overlay is proposed to the current Level 2 BIM process to support conservation heritage projects.Originality/valueThis paper addresses the issue of HBIM application to conservation heritage projects. Whilst previous work in the field has identified conservation as a key area, there is very little work focusing on the process of conservation in the HBIM context. This work provides a framework and overlay which could be used by practitioners and researchers to ensure that HBIM is fully exploited and a more standardised method is employed which could be used on conservation heritage renovation projects.
Food image segmentation using edge adaptive based deep-CNNs
Authors: C. Burkapalli Vishwanath. , Patil Priyadarshini C. 
Published: January 2020

PurposeIndian food recognition can be considered as a case of fine-grained type visual recognition, where the several photos of same category generally have significant variability. Therefore, effective segmentation and classification technique is required to identify the particular cuisines and fine-grained analysis. The paper aims to discuss this issue.Design/methodology/approachIn this paper, the authors provided an effective segmentation approach through the proposed edge adaptive (EA)-deep convolutional neural networks (DCNNs) model, where each input images are divided into patches in order to provide much efficient and accurate structural description of data.FindingsEA-DCNNs starts with developing a coarse map of feature that obtained through DCNN, afterwards EA model is applied to construct the final segmented image.Originality/valueThe training model of EA-DCNN consists of pooling, rectified linear unit and convolution, which help convolutional network to optimize the performance of segmentation in a significant extent, which is much practical and relevant in the context of food image segmentation.