bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organization of Area hV5/MT+ in Subjects with Homonymous Visual Field Defects
Authors: Papanikolaou Amalia , Keliris Georgios A. , Papageorgiou T. Dorina , Schiefer Ulrich , Logothetis Nikos K. , Smirnakis Stelios M. 
Published: January 2018

AbstractDamage to the primary visual cortex (V1) leads to a visual field loss (scotoma) in the retinotopically corresponding part of the visual field. Nonetheless, a small amount of residual visual sensitivity persists within the blind field. This residual capacity has been linked to activity observed in the middle temporal area complex (V5/MT+). However, it remains unknown whether the organization of hV5/MT+ changes following V1 lesions. We studied the organization of area hV5/MT+ of five patients with dense homonymous defects in a quadrant of the visual field as a result of partial V1+ or optic radiation lesions. To do so, we developed a new method, which models the boundaries of population receptive fields directly from the BOLD signal of each voxel in the visual cortex. We found responses in hV5/MT+ arising inside the scotoma for all patients and identified two possible sources of activation: 1) responses might originate from partially lesioned parts of area V1 corresponding to the scotoma, and 2) responses can also originate independent of area V1 input suggesting the existence of functional V1-bypassing pathways. Apparently, visually driven activity observed in hV5/MT+ is not sufficient to mediate conscious vision. More surprisingly, visually driven activity in corresponding regions of V1 and early extrastriate areas including hV5/MT+ did not guarantee visual perception in the group of patients with post-geniculate lesions that we examined. This suggests that the fine coordination of visual activity patterns across visual areas may be an important determinant of whether visual perception persists following visual cortical lesions.
Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples
Authors: Zheng Hong , Brennan Kevin , Hernaez Mikel , Gevaert Olivier 
Published: January 2018

ABSTRACTLong non-coding RNAs (lncRNAs) emerge as important regulators of various biological processes. Many lncRNAs with tumor-suppressor or oncogenic functions in cancer have been discovered. While many studies have exploited public resources such as RNA-Seq data in The Cancer Genome Atlas (TCGA) to study lncRNAs in cancer, it is crucial to choose the optimal method for accurate expression quantification of lncRNAs. In this benchmarking study, we compared the performance of pseudoalignment methods Kallisto and Salmon, and alignment-based methods HTSeq, featureCounts, and RSEM, in lncRNA quantification, by applying them to a simulated RNA-Seq dataset and a pan-cancer RNA-Seq dataset from TCGA. We observed that full transcriptome annotation, including both protein coding and noncoding RNAs, greatly improves the specificity of lncRNA expression quantification. Pseudoalignment-based methods detect more lncRNAs than alignment-based methods and correlate highly with simulated ground truth. On the contrary, alignment-based methods tend to underestimate lncRNA expression or even fail to capture lncRNA signal in the ground truth. These underestimated genes include cancer-relevant lncRNAs such as TERC and ZEB2-AS1. Overall, 10–16% of lncRNAs can be detected in the samples, with antisense and lincRNAs the two most abundant categories. A higher proportion of antisense RNAs are detected than lincRNAs. Moreover, among the expressed lncRNAs, more antisense RNAs are discordant from ground truth than lincRNAs when measured by alignment-based methods, indicating that antisense RNAs are more susceptible to mis-quantification. In addition, the lncRNAs with fewer transcripts, less than three exons, and lower sequence uniqueness tend to be more discordant. In summary, pseudoalignment methods Kallisto or Salmon in combination with the full transcriptome annotation is our recommended strategy for RNA-Seq analysis for lncRNAs.AUTHOR SUMMARYLong non-coding RNAs (lncRNAs) emerge as important regulators of various biological processes. Our benchmarking work on both simulated RNA-Seq dataset and pan-cancer dataset provides timely and useful recommendations for wide research community who are studying lncRNAs, especially for those who are exploring public resources such as TCGA RNA-Seq data. We demonstrate that using full transcriptome annotation in RNA-Seq analysis is strongly recommended as it greatly improves the specificity of lncRNA quantification. What’s more, pseudoalignment methods Kallisto and Salmon outperform alignment-based methods in lncRNA quantification. It is worth noting that the default workflow for TCGA RNA-Seq data stored in Genomic Data Commons (GDC) data portal uses HTSeq, an alignment-based method. Thus, reanalyzing the data might be considered when checking gene expression in TCGA datasets. In summary, pseudoalignment methods Kallisto or Salmon in combination with full transcriptome annotation is our recommended strategy for RNA-Seq analysis for lncRNAs.
Finding the balance between model complexity and performance: Using ventral striatal oscillations to classify feeding behavior in rats
Authors: Dwiel Lucas L. , Khokhar Jibran Y. , Connerney Michael A. , Green Alan I. , Doucette Wilder T. 
Published: January 2018

AbstractThe ventral striatum (VS) is a central node within a distributed network that controls appetitive behavior, and neuromodulation of the VS has demonstrated therapeutic potential for appetitive disorders. Local field potential (LFP) oscillations recorded from deep brain stimulation electrodes within the VS are a pragmatic source of neural systems-level information about appetitive behavior that could be used in responsive neuromodulation systems. Here, we recorded LFPs from the bilateral nucleus accumbens core and shell (subregions of the VS) during limited access to palatable food across varying conditions of hunger and food palatability in male rats. We used standard statistical methods (logistic regression) as well as the machine learning algorithm lasso to predict aspects of feeding behavior using VS LFPs. These models were able to predict the amount of food eaten, the increase in consumption following food deprivation, and the type of food eaten. Further, we were able to predict whether the initiation of feeding was imminent up to 42.5 seconds before feeding began and classify current behavior as either feeding or not-feeding. In classifying this behavior, we found an optimal balance between model complexity and performance with models using 3 LFP features primarily from the alpha and high gamma frequencies. As shown here, unbiased methods can identify systems-level neural activity linked to symptoms of mental illness with potential application to the development and personalization of novel treatments.Author SummaryAs neuropsychiatry begins to leverage the power of computational methods to understand disease states and to develop better therapies, it is vital that we acknowledge the trade-offs between model complexity and performance. We show that computational methods can elucidate a neural signature of feeding behavior and show how these methods could be used to discover neural patterns related to other behaviors and used as therapeutic targets. Further, our results helps to contextualize both the limitations and potential of applying computational methods to neuropsychiatry by showing how changing the data being used to train predictive models (e.g., population vs. individual data) can have a large impact on how model performance generalizes across time, internal states and individuals.
Active avoidance requires inhibitory signaling in the rodent prelimbic prefrontal cortex
Authors: Diehl Maria M. , Bravo-Rivera Christian , Rodríguez-Romaguera Jose , Pagán-Rivera Pablo A. , Burgos-Robles Anthony , Quirk Gregory J. 
Published: January 2018

AbstractMuch is known about the neural circuits of conditioned fear and its relevance to understanding anxiety disorders, but less is known about other anxiety-related behaviors such as active avoidance. Using a tone-signaled, platform-mediated active avoidance task, we observed that pharmacological inactivation of the prelimbic prefrontal cortex (PL) delayed initiation of avoidance. However, optogenetic silencing of PL neurons did not delay avoidance. Consistent with this finding, inhibitory, but not excitatory, responses of rostral PL neurons to the tone were correlated with initiation of avoidance. To oppose inhibitory responses, we photoactivated rostral PL neurons during the tone to maintain pre-tone firing rate. Photoactivation of rostral PL (but not caudal PL) neurons at 4 Hz (but not 2 Hz) delayed or prevented avoidance. These findings suggest that the initiation of active avoidance requires inhibitory neuronal responses in rostral PL, and underscores the importance of designing behavioral optogenetic studies based on neuronal firing patterns.
Phospholipid flipping facilitates annexin translocation across membranes
Authors: Stewart Sarah E , Ashkenazi Avraham , Williamson Athena , Rubinsztein David C , Moreau Kevin 
Published: January 2018

AbstractAnnexins are phospholipid binding proteins that somehow translocate from the inner leaflet of the plasma membrane to the outer leaflet. For example, Annexin A2 is known to localise to the outer leaflet of the plasma membrane (cell surface) where it is involved in plasminogen activation leading to fibrinolysis and cell migration, among other functions. Despite having well described extracellular functions, the mechanism of annexin transport from the cytoplasmic inner leaflet to the extracellular outer leaflet of the plasma membrane remains unclear. Here, we show that phospholipid flipping activity is crucial for the transport of annexins A2 and A5 across membranes in cells and in liposomes. We identified TMEM16F (anoctamin-6) as a lipid scramblase required for transport of these annexins to the outer leaflet of the plasma membrane. This work reveals a mechanism for annexin translocation across membranes which depends on plasma membrane phospholipid flipping.
Representativeness and robustness of TCR repertoire diversity assessment by high-throughput sequencing
Authors: Chaara Wahiba , Mariotti-Ferrandiz Encarnita , Gonzalez-Tort Ariadna , Florez Laura , Six Adrien , Klatzmann David 
Published: January 2018

ABSTRACTHigh-throughput sequencing (HTS) has the potential to decipher the diversity of T cell repertoires and their dynamics during immune responses. Applied to T cell subsets such as T effector and T regulatory cells, it should help identify novel biomarkers of diseases. However, given the extreme diversity of TCR repertoires, understanding how the sequencing conditions, including cell numbers, biological and technical sampling and sequencing depth, impact the experimental outcome is critical to properly use of these data. Here we assessed the representativeness and robustness of TCR repertoire diversity assessment according to experimental conditions. By comparative analyses of experimental datasets and computer simulations, we found that (i) for small samples, the number of clonotypes recovered is often higher than the number of cells per sample, even after removing the singletons; (ii) high sequencing depth for small samples alters the clonotype distributions, which can be corrected by filtering the datasets using Shannon entropy as a threshold; (iii) a single sequencing run at high depth does not ensure a good coverage of the clonotype richness in highly polyclonal populations, which can be better covered using multiple sequencing. Altogether, our results warrant better understanding and awareness of the limitation of TCR diversity analyses by HTS and justify the development of novel computational tools for improved modelling of the highly complex nature of TCR repertoires.
Comprehensive mapping of Cystic Fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site
Authors: Molinski Steven V. , Shahani Vijay M. , Subramanian Adithya S. , MacKinnon Stephen S. , Woollard Geoffrey , Laforet Marcon , Laselva Onofrio , Morayniss Leonard D. , Bear Christine E. , Windemuth Andreas 
Published: January 2018

AbstractBackgroundCystic Fibrosis (CF) is caused by mutations in the CFTR gene, of which over 2000 have been reported to date. Mutations have yet to be analyzed in aggregate to assess their distribution across the tertiary structure of the CFTR protein, an approach that could provide valuable insights into the structure-function relationship of CFTR. In addition, the binding site of Class I correctors (VX-809, VX-661, C18) is not well understood.MethodsExonic CFTR mutations and mutant allele frequencies described in three curated databases (ABCMdb, CFTR1 and CFTR2, comprising >130,000 data points) were mapped to two different structural models: a homology model of full-length CFTR protein in the open-channel state, and a cryo-electron microscopy core-structure of CFTR in the closed-channel state. Immunoblotting confirmed the approximate binding site of Class I correctors, and molecular docking generated binding poses for their complex with the cryo-electron microscopy structure.ResultsResidue positions of six high-frequency mutant CFTR alleles were found to spatially co-localize in CFTR protein, and a significant cluster was identified at the NBD1:ICL4 interdomain interface. Further, Class I correctors VX-809, VX-661 and C18 were shown to act via a similar mechanism in vitro, and a putative multi-domain corrector binding site near residues F374-L375 was predicted in silico.ConclusionsOur results confirm the significance of interdomain interfaces as susceptible to disruptive mutation, and identify a putative corrector binding site. The structural pharmacogenomics approach of mapping mutation databases to protein models shows promise for facilitating drug discovery and personalized medicine for monogenetic diseases.
A review of emergency department visits made by youth and adults with autism spectrum disorder from the parent perspective
Authors: Lunsky Yona , Tint Ami , Weiss Jonathan A. , Palucka Anna , Bradley Elspeth 
Published: January 2018

PurposePast research has shown individuals with autism spectrum disorder (ASD) visit hospital emergency departments (ED) at high rates. In order to assist individuals with ASD, their families and health care providers to improve ED care, it is important to understand these encounters in greater detail. The purpose of this paper is to provide a descriptive summary of the ED experiences of adolescents and adults with ASD, from the perspective of their families.Design/methodology/approachA subset of data from a larger prospective cohort study was used. Specifically, 46 parents of adolescents and adults with ASD provided details concerning 49 ED visits over a 12-month period.FindingsResults suggest a range of presentations requiring ED use, and also diverse profiles of those with ASD who visited the ED, in terms of age, gender, and ASD severity. While overall degree of satisfaction with care received in the ED was high, parents provided recommendations to improve the ED experiences for their family members with ASD.Originality/valueThis is the first study to provide detailed accounts of ED visits from the perspective of parents of adolescents and adults with ASD. Families play an important role in the lives of individuals with ASD across the lifespan and it is important to include their perspective to improve hospital-based care for those with ASD.
Moderating effect of absorptive capacity on the entrepreneurial orientation of international performance of family businesses
Authors: Hernandez-Perlines Felipe 
Published: January 2018

PurposeThe purpose of this paper is to analyse the moderating effect of absorptive capacity on the entrepreneurial orientation of international performance of family businesses.Design/methodology/approachThe sample for this study was collected from 218 family firms associated with the Family Business Institute (IEF). This paper used a structural equation model through PLS-SEM technique to test the proposed model and for contrasting the moderating effect of absorptive capacity on the entrepreneurial orientation of international performance of family businesses.FindingsThe main result of this work is that international performance of family businesses is determined, to a great extent, by the entrepreneurial orientation. In addition, this effect is reinforced by the absorption capacity, exerting a positive moderating role.Practical implicationsIf family firms want to improve their international results, they must act in the entrepreneurial orientation through the effect of absorption capacities.Originality/valueThe originality of this work comes from the discovery of the new moderating role of absorption capacities in family firms.
Take full advantage of unlabeled data for sentiment classification
Authors: La Lei , Cao Shuyan , Qin Liangjuan 
Published: January 2018

Purpose
As a foundational issue of social mining, sentiment classification suffered from a lack of unlabeled data. To enhance accuracy of classification with few labeled data, many semi-supervised algorithms had been proposed. These algorithms improved the classification performance when the labeled data are insufficient. However, precision and efficiency are difficult to be ensured at the same time in many semi-supervised methods. This paper aims to present a novel method for using unlabeled data in a more accurate and more efficient way.

Design/methodology/approach
First, the authors designed a boosting-based method for unlabeled data selection. The improved boosting-based method can choose unlabeled data which have the same distribution with the labeled data. The authors then proposed a novel strategy which can combine weak classifiers into strong classifiers that are more rational. Finally, a semi-supervised sentiment classification algorithm is given.

Findings
Experimental results demonstrate that the novel algorithm can achieve really high accuracy with low time consumption. It is helpful for achieving high-performance social network-related applications.

Research limitations/implications
The novel method needs a small labeled data set for semi-supervised learning. Maybe someday the authors can improve it to an unsupervised method.

Practical implications
The mentioned method can be used in text mining, image classification, audio processing and so on, and also in an unstructured data mining-related field. Overcome the problem of insufficient labeled data and achieve high precision using fewer computational time.

Social implications
Sentiment mining has wide applications in public opinion management, public security, market analysis, social network and related fields. Sentiment classification is the basis of sentiment mining.

Originality/value
According to what the authors have been informed, it is the first time transfer learning be introduced to AdaBoost for semi-supervised learning. Moreover, the improved AdaBoost uses a totally new mechanism for weighting.
Entrepreneurial financing–alternatives for raising capital
Authors: Broude Paul D. , Levangie Joseph E. 
Published: January 2018

Most entrepreneurs are continually concerned about their finances. Their companies perhaps not yet profitable, they may have a fear of “running out of dry powder.” These entrepreneurs often have fallen in love with their company's technologies, products, and potential markets, but they require more resources. Invariably these emerging ventures shroud their fear of the grueling capital raising marathon by presenting voluminous business plans to potential investors. They often flaunt their “optimized business models.”” Investors, however, typically want to know why the potential investment is such a good deal. The entrepreneur often wants guidance regarding what to say to whom in a changing financing environment.
In this article, our “Practitioner's Corner” associate editor Joe Levangie collaborates with a long-time colleague Paul Broude to address how businesses should “make their capital-raising initiatives happen.” Levangie, a venture advisor and entrepreneur, first worked with Broude, a business and securities attorney, in 1985 when they went to London to pursue financing for an American startup. They successfully survived all-night drafting sessions, late-night clubbing by the company founder, and even skeet shooting and barbequing at the investment banker's country house to achieve the first “Greenfield” flotation by an American company on the Unlisted Securities Market of the London Stock Exchange. To ascertain how the entrepreneur can determine what financing options exist in today's investing climate, read on.
Outcomes of bevacizumab combined with chemotherapy in lung adenocarcinoma‐induced malignant pleural effusion
Authors: Tao Hong , Meng Qiyi , Li Mingzhi , Shi Liang , Tang Junfang , Liu Zhe 
Published: January 2018

BackgroundVEGF is critical in the pathogenesis of malignant pleural effusion (MPE). To understand the clinical benefits of antiangiogenic agents, the efficacy of chemotherapy containing bevacizmab was investigated in patients with lung adenocarcinoma‐induced MPE.MethodsThe data of lung adenocarcinoma patients with MPE treated with bevacizumab plus chemotherapy on day 1, every three weeks, for ≤ 6 cycles was retrospectively collected. Patients who achieved a response or stable disease were administered bevacizumab as maintenance therapy until progression. The primary outcomes of the study were MPE response rate (RR), MPE control rate, and pleural progression‐free survival (PPFS), while the secondary outcomes were PFS, overall survival (OS), changes to the lung volume and thoracic cage, and safety profiles.ResultsA total of 21 cases were collected, and all were evaluable for response, including 15 chemotherapy‐naïve patients and 6 who experienced relapse. The median cycle of treatments was 7 (1‐42) and 5 (2‐6) for bevacizumab and chemotherapy, respectively. The MPE RR reached 81.0%. The MPE control rate at 6, 12, 24, 48, and 96 weeks were 95.2%, 90.0%, 89.5%, 73.7%, and 43.8%, respectively. Median PPFS was significantly longer than PFS (22.2 vs. 7.8 months; P = 0.044), and median OS was 25.8 months. Nineteen (90.5%) patients experienced lung re‐expansion after treatment. Only one (4.8%) patient suffered thoracic volume decrease during treatment and the follow‐up period. No unexpected adverse events were observed.ConclusionsBevacizumab combined with chemotherapy demonstrated efficacious, persistence, and safety in controlling lung cancer‐induced MPE, indicating a potential superior therapeutic option.