bluuebunny/crossref_metadata_2025_split huggingface dataset:
A population-based atlas of the human pyramidal tract in 410 healthy participants
Authors: Chenot Quentin , Tzourio-mazoyer Nathalie , Rheault François , Descoteaux Maxime , Crivello Fabrice , Zago Laure , Mellet Emmanuel , Jobard Gaël , Joliot Marc , Mazoyer Bernard , Petit Laurent 
Published: January 2018

AbstractWith the advances in diffusion MRI and tractography, numerous atlases of the human pyramidal tract (PyT) have been proposed but the inherent limitation of tractography to resolve crossing bundles within the centrum semiovale have so far prevented the complete description of the most lateral PyT projections. Here, we combined a precise manual positioning of individual subcortical regions of interest along the descending pathway of the PyT with a new bundle-specific tractography algorithm. This later is based on anatomical priors to improve streamlines tracking in crossing areas. We then extracted both left and right PyT in a large cohort of 410 healthy participants and built a population-based atlas of the whole-fanning PyT with a complete description of its most cortico-lateral projections. Clinical applications are envisaged, the whole-fanning PyT atlas being likely a better marker of corticospinal integrity metrics than those currently used within the frame of prediction of post-stroke motor recovery. The present population-based PyT, freely available, provides an interesting tool for clinical applications in order to locate specific PyT damage and its impact to the short and long-term motor recovery after stroke.
NormExpression: an R package to normalize gene expression data using evaluated methods
Authors: Wu Zhenfeng , Liu Weixiang , Jin Xiufeng , Yu Deshui , Wang Hua , Glusman Gustavo , Robinson Max , Liu Lin , Ruan Jishou , Shan Gao 
Published: January 2018

AbstractData normalization is a crucial step in the gene expression analysis as it ensures the validity of its downstream analyses. Although many metrics have been designed to evaluate the current normalization methods, the different metrics yield inconsistent results. In this study, we designed a new metric named Area Under normalized CV threshold Curve (AUCVC) and applied it with another metric mSCC to evaluate 14 commonly used normalization methods, achieving consistency in our evaluation results using both bulk RNA-seq and scRNA-seq data from the same library construction protocol. This consistency has validated the underlying theory that a sucessiful normalization method simultaneously maximizes the number of uniform genes and minimizes the correlation between the expression profiles of gene pairs. This consistency can also be used to analyze the quality of gene expression data. The gene expression data, normalization methods and evaluation metrics used in this study have been included in an R package named NormExpression. NormExpression provides a framework and a fast and simple way for researchers to evaluate methods (particularly some data-driven methods or their own methods) and then select a best one for data normalization in the gene expression analysis.
Effect of head volume conduction on directed connectivity estimated between reconstructed EEG sources
Authors: Anzolin Alessandra , Presti Paolo , Van de Steen Frederik , Astolfi Laura , Haufe Stefan , Marinazzo Daniele 
Published: January 2018

AbstractElectrical activity recorded on the scalp using electroencephalography (EEG) results from the mixing of signals originating from different regions of the brain as well as from artefactual sources. In order to investigate the role of distinct brain areas in a given experiment, the signal recorded on the sensors is typically projected back into the brain (source reconstruction) using algorithms that address the so-called EEG “inverse problem”. Once that the activity of sources located inside of the brain has been reconstructed, it is often desirable to study the statistical dependencies among them, in particular to quantify directional dynamical interactions between brain areas. Unfortunately, even when performing source reconstruction, the superposition of signals that is due to the propagation of activity from sources to sensors cannot be completely undone, resulting in potentially biased estimates of directional functional connectivity. Here we perform a set of simulations involving interacting sources, and quantify source connectivity estimation performance as a function of the location of the sources, their distance to each other, the noise level, the source reconstruction algorithm, and the connectivity estimator. The generated source activity was projected onto the scalp and projected back to the cortical level using two source reconstruction algorithms, Linearly Constrained Minimum Variance (LCMV) beamforming and ‘Exact’ Low-resolution Tomography (eLORETA). In source space, directed connectivity was estimated using Multi-Variate Granger Causality (MVGC), Time-Reversed Granger Causality (TRGC) and Partial Directed Coherence (PDC), and the estimated connectivity was compared with the imposed ground truth. Our results demonstrate that all considered factors significantly affect the connectivity estimation performance.
Key components of the delirium syndrome and mortality: greater impact of acute change and disorganised thinking in a prospective cohort study
Authors: Diwell RA , Davis D , Vickerstaff V , Sampson EL 
Published: January 2018

ABSTRACTBackgroundDelirium increases the risk of mortality during an acute hospital admission. Full syndromal delirium (FSD) is associated with greatest risk and subsyndromal delirium (SSD) is associated with intermediate risk, compared to patients with no delirium - suggesting a dose-response relationship. It is not clear how individual diagnostic symptoms of delirium influence the association with mortality. Our objectives were to measure the prevalence of FSD and SSD, and assess the effect that FSD, SSD and individual symptoms of delirium (from the Confusion Assessment Method-short version (s-CAM)) have on mortality rates.MethodsExploratory analysis of a prospective cohort (aged ≥ 70 years) with acute (unplanned) medical admission (4/6/2007-4/11/2007). The outcome was mortality (data censored 6/10/2011). The principal exposures were FSD and SSD compared to no delirium (as measured by the CAM), along with individual delirium symptoms on the CAM. Cox regression was used to estimate the impact FSD and SSD and individual CAM items had on mortality.ResultsThe cohort (n=610) mean age was 83 (SD 7); 59% were female. On admission, 11% had FSD and 33% had SSD. Of the key diagnostic symptoms for delirium, 17% acute onset, 19% inattention, 17% disorganised thinking and 17% altered level of consciousness. Unadjusted analysis found FSD had an increased hazard ratio (HR) of 2.31 (95%CI 1.71, 3.12), for SSD the HR was 1.26 (1.00, 1.59). Adjusted analysis remained significant for FSD (1.55 95%CI 1.10, 2.18) but nonsignificant for SSD (HR=0.92 95% CI 0.70, 1.19). Two CAM items were significantly associated with mortality following adjustment: acute onset and disorganised thinking.ConclusionWe observed a dose-response relationship between mortality and delirium, FSD had the greatest risk and SSD having intermediate risk. The CAM items “acute onset” and “disorganised thinking” drove the associations observed. Clinically, this highlights the necessity of identifying individual symptoms of delirium.
The universal mechanism of intermediate filament transport
Authors: Robert Amélie , Tian Peirun , Adam Stephen A. , Goldman Robert D. , Gelfand Vladimir I. 
Published: January 2018

ABSTRACTIntermediate filaments (IFs) are a major component of the cytoskeleton that regulates a wide range of physiological properties in eukaryotic cells. In motile cells, the IF network has to adapt to constant changes of cell shape and tension. In this study, we used two cell lines that express vimentin and keratins 8/18 to study the dynamic behavior of these IFs. We demonstrated that both IF types undergo extensive transport along microtubules. This was an unexpected result as keratin filament remodeling has been described to depend on actin dynamics. We established the role of kinesin-1 in vimentin and keratin IF transport by knocking out KIF5B, the ubiquitous isoform of kinesin-1. Futhermore, we demonstrated that unlike typical membrane cargoes, transport of both types of IFs does not involve kinesin light chains, but requires the presence of the same region of the kinesin-1 tail, suggesting a unified mechanism of IF transport.
Unbiased construction of a temporally consistent morphological atlas of neonatal brain development
Authors: Schuh Andreas , Makropoulos Antonios , Robinson Emma C. , Cordero-Grande Lucilio , Hughes Emer , Hutter Jana , Price Anthony N. , Murgasova Maria , Teixeira Rui Pedro A. G. , Tusor Nora , Steinweg Johannes K. , Victor Suresh , Rutherford Mary A. , Hajnal Joseph V. , Edwards A. David , Rueckert Daniel 
Published: January 2018

AbstractPremature birth increases the risk of developing neurocognitive and neurobe-havioural disorders. The mechanisms of altered brain development causing these disorders are yet unknown. Studying the morphology and function of the brain during maturation provides us not only with a better understanding of normal development, but may help us to identify causes of abnormal development and their consequences. A particular difficulty is to distinguish abnormal patterns of neurodevelopment from normal variation. The Developing Human Connectome Project (dHCP) seeks to create a detailed four-dimensional (4D) connectome of early life. This connectome may provide insights into normal as well as abnormal patterns of brain development. As part of this project, more than a thousand healthy fetal and neonatal brains will be scanned in vivo. This requires computational methods which scale well to larger data sets. We propose a novel groupwise method for the construction of a spatio-temporal model of mean morphology from cross-sectional brain scans at different gestational ages. This model scales linearly with the number of images and thus improves upon methods used to build existing public neonatal atlases, which derive correspondence between all pairs of images. By jointly estimating mean shape and longitudinal change, the atlas created with our method overcomes temporal inconsistencies, which are encountered when mean shape and intensity images are constructed separately for each time point. Using this approach, we have constructed a spatio-temporal atlas from 275 healthy neonates between 35 and 44 weeks post-menstrual age (PMA). The resulting atlas qualitatively preserves cortical details significantly better than publicly available atlases. This is moreover confirmed by a number of quantitative measures of the quality of the spatial normalisation and sharpness of the resulting template brain images.
Cyclic dominance emerges from the evolution of two inter-linked cooperative behaviours in the social amoeba
Authors: Shibasaki Shota , Shimada Masakazu 
Published: January 2018

AbstractEvolution of cooperation has been one of the most important problems in sociobiology, and many researchers have revealed mechanisms that can facilitate the evolution of cooperation. However, most studies deal only with one cooperative behaviour, even though some organisms perform two or more cooperative behaviours. The social amoebaDictyostelium discoideumperforms two cooperative behaviours in starvation: fruiting body formation and macrocyst formation. Here, we constructed a model that couples these two behaviours, and we found that the two behaviours are maintained due to the emergence of cyclic dominance, although cooperation cannot evolve if only either of the two behaviours is performed. The common chemoattractant cyclic AMP is used in both fruiting body formation and macrocyst formation, providing a biological context for this coupling. Cyclic dominance emerges regardless of the existence of mating types or spatial structure in the model. In addition, cooperation can re-emerge in the population even after it goes extinct. These results indicate that the two cooperative behaviours of the social amoeba are maintained due to the common chemical signal that underlies both fruiting body formation and macrocyst formation. We demonstrate the importance of coupling multiple games when the underlying behaviours are associated with one another.
Local Delivery of Stromal Cell-Derived Factor-1α Improves the Pregnancy Rate of Injured Uterus through the Promotion of Endometrial and Vascular Regeneration
Authors: Cai Hongxai , Wu Bingbing , Liu Yixiao , Li Yu , Shi Libing , Gong Lin , Xia Yaxian , Heng BoonChin , Wu Huiling , Ouyang Hongwei , Zhu Zhenghua , Zou Xiaohui 
Published: January 2018

AbstractSevere infection and mechanical injury of the uterus may lead to infertility and miscarriage. Currently, there is a lack of effective treatment modality for functional repair of uterine injury. To address this clinical challenge, this study aimed to develop a chemotactic composite scaffold by incorporating recombinant human stromal cell-derived factor-1α (rhSDF-1α) into a silk fibroin-bacterial cellulose (SF-BC) membrane carrier. A rat model of uterine injury was utilized for this study, which was composed of three groups: blank control, implantation with SF-BC only or SF-BC loaded with rhSDF-1α. The tissue regeneration efficacy of the three groups were analyzed and compared. The results showed that SF-BC loaded with rhSDF-1α significantly enhanced endometrial regeneration and arteriogenesis of the injured rat uterus, which led to improved pregnancy outcomes, thus indicating much promise for functional uterine repair and regeneration.
Dynein-2 intermediate chains play crucial but distinct roles in primary cilia formation and function
Authors: Vuolo Laura , Stevenson Nicola L. , Heesom Kate J. , Stephens David J. 
Published: January 2018

AbstractThe dynein-2 microtubule motor is the retrograde motor for intraflagellar transport. Mutations in dynein-2 components cause skeletal ciliopathies, notably Jeune syndrome. Dynein-2 comprises a heterodimer of two non-identical intermediate chains, WDR34 and WDR60. Here, we use knockout cell lines to demonstrate that each intermediate chain has a distinct role in cilia function. Both proteins are required to maintain a functional transition zone and for efficient bidirectional intraflagellar transport, only WDR34 is essential for axoneme extension. In contrast, only WDR60 is essential for co-assembly of the other subunits. Furthermore, WDR60 cannot compensate for loss of WDR34 or vice versa. This work defines a functional asymmetry to match the subunit asymmetry within the dynein-2 motor. Analysis of causative point mutations in WDR34 and WDR60 can partially restore function to knockout cells. Our data show that Jeune syndrome is caused by defects in transition zone architecture as well as intraflagellar transport.SUMMARYHere, Vuolo and colleagues use engineered knockout human cell lines to define roles for dynein-2 intermediate chains. WDR34 is required for axoneme extension, while WDR60 is not. Both subunits are required for cilia transition zone organization and bidirectional intraflagellar transport.
Comparing phylogenetic trees according to tip label categories
Authors: Kendall Michelle , Eldholm Vegard , Colijn Caroline 
Published: January 2018

AbstractTrees that illustrate patterns of ancestry and evolution are a central tool in many areas of biology. Comparing evolutionary trees to each other has widespread applications in comparing the evolutionary stories told by different sources of data, assessing the quality of inference methods, and highlighting areas where patterns of ancestry are uncertain. While these tasks are complicated by the fact that trees are high-dimensional structures encoding a large amount of information, there are a number of metrics suitable for comparing evolutionary trees whose tips have the same set of unique labels. There are also metrics for comparing trees where there is no relationship between their labels: in ‘unlabelled’ tree metrics the tree shapes are compared without reference to the tip labels.In many interesting applications, however, the taxa present in two or more trees are related but not identical, and it is informative to compare the trees whilst retaining information about their tips’ relationships. We present methods for comparing trees whose labels belong to a pre-defined set of categories. The methods include a measure of distance between two such trees, and a measure of concordance between one such tree and a hierarchical classification tree of the unique categories. We demonstrate the intuition of our methods with some toy examples before presenting an analysis ofMycobacterium tuberculosistrees, in which we use our methods to quantify the differences between trees built from typing versus sequence data.
The actin cytoskeleton of the mouse sperm flagellum is organized in a helical structure
Authors: Gervasi María Gracia , Xu Xinran , Carbajal-Gonzalez Blanca , Buffone Mariano G , Visconti Pablo E , Krapf Diego 
Published: January 2018

AbstractConception of a new mammalian organism is determined by the fusion of a sperm cell with an oocyte during fertilization. Motility is one of the features of sperm that allows them to succeed in fertilization, and their flagellum is essential for this function. Longitudinally, the flagellum divides into the midpiece, the principal piece, and the end piece. A precise cytoskeletal architecture of the sperm tail is key for the acquisition of fertilization competence. It has been proposed that the actin cytoskeleton plays essential roles in the regulation of sperm motility, however, actin organization in sperm remains elusive. In the present work, we found different types of actin structures in the sperm tail, using stochastic optical reconstruction microscopy (STORM). In the principal piece, actin is radially distributed between the axoneme and the plasma membrane. The actin-associated proteins spectrin and adducin are also found in these structures. Strikingly, polymerized actin in the midpiece forms a double-helix that accompanies mitochondria. Our findings illustrate a novel specialized structure of actin filaments in a mammalian cell.
Receptive field center-surround interactions mediate context-dependent spatial contrast encoding in the retina
Authors: Turner Maxwell H. , Schwartz Gregory W. , Rieke Fred 
Published: January 2018

SummaryAntagonistic receptive field surrounds are a near-universal property of early sensory processing. A key assumption in many models for retinal ganglion cell encoding is that receptive field surrounds are added only to the fully formed center signal. But anatomical and functional observations indicate that surrounds are added before the summation of signals across receptive field subunits that creates the center. Here, we show that this receptive field architecture has an important consequence for spatial contrast encoding: the surround can control sensitivity to fine spatial structure by changing the way the center integrates visual information over space. The impact of the surround is particularly prominent when center and surround signals are correlated, as they are in natural stimuli. This role of the surround differs substantially from classic center-surround models and raises the possibility that the surround plays unappreciated roles in shaping ganglion cell sensitivity to natural inputs.
Food prices, money growth and informal cross-border trade: evidence from Uganda
Authors: Mawejje Joseph , Nampewo Dorothy 
Published: January 2018

PurposeThe purpose of this paper is to examine the potential role of money supply and agricultural informal cross-border trade (ICBT) in Uganda’s food price processes.Design/methodology/approachThe econometric analysis is based on two separate but complementary approaches: vector error correction modeling and Granger causality testing.FindingsThe results indicate that long-run domestic food prices adjust to money supply, agricultural output and exchange rate movements. However, the findings do not provide sufficient evidence to support the proposition that agricultural ICBT is an important long-run driver of food price in Uganda. The pair-wise Granger causality test results reveal a unidirectional causality from food prices to agricultural output; unidirectional causality from money supply to food prices; bidirectional causality between food prices and nominal exchange rates; unidirectional causality running from rainfall to food prices; and unidirectional causality running from agricultural ICBT to agricultural output.Social implicationsUnderstanding the underlying drivers of food inflation is critically important because food prices are critically important for food security, social stability and general household welfare.Originality/valueThe major innovation in this paper is attempt to model demand side determinants of food prices by focusing on the role of money and ICBT.
The impact of budgetary planning on resource allocation: evidence from a developing country
Authors: Kwarteng Amoako 
Published: January 2018

PurposeThe purpose of this paper is to empirically examine whether firms in Ghana allocate resources through the use of budgetary planning principles.Design/methodology/approachA survey was conducted using top business executive and budget holders of the firms listed on the Ghana Stock Exchange. The data were analyzed using the structural equation modeling (SEM) and, in particular, the PLS-SEM approach.FindingsThe study demonstrates that there is a statistically significant relationship between budgeting, performance management, and resource allocation constructs. The results indicate that performance management partially mediates the relations between budget planning and resource allocation. This indicates that firms in Ghana behave optimally by allocating resource using budgetary planning principles.Research limitations/implicationsThe study is limited to the firms listed on the Ghana Stock Exchange. As a policy implication, this study has established that efficiency revolves around making the possible use of a given set of resources and as such firms in Ghana allocate resources through the use of budget.Originality/valueThere have been just a few studies that tried to integrate budgeting, performance management, and resource allocation in a comprehensive framework to deal with agency problems.
Organizational trust in farmer organizations: evidence from the Chinese fresh apple industry
Authors: Jia Xiangping , James Harvey S. 
Published: January 2018

Purpose
The purpose of this paper is to examine the role and importance of trust in a type of Chinese farmer cooperative organization called “Farm Bases” (FBs), considering the extent to which trust affects their performance and how the relationship between trust and FB performance is affected by perceptions of risk and uncertainty and other considerations.

Design/methodology/approach
The authors interviewed a random sample of 355 farmers, most of whom are from 42 different FBs in China. The authors operationalized organizational trust by assessing the perception of trustworthiness and competence that farmers have in FB managers. The authors conducted a regression analysis of the data to answer the research questions.

Findings
The findings support a nuanced role of trust for performance measures of FBs. Trust matters but in limited and specific contexts. Specifically, trust does not correlate with the marketing volume of Chinese FBs and only weakly correlates with FB compliance of production standards.

Originality/value
FBs play an essential role in China’s agribusiness policies and are pervasive in Chinese business practices. Very little research has been conducted on Chinese FBs and of the role of trust in organizational performance.