bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational model for human 3D shape perception from a single specular image
Authors: Shimokawa Takeaki , Nishio Akiko , Sato Masa-aki , Kawato Mitsuo , Komatsu Hidehiko 
Published: August 2018

AbstractIn natural conditions the human visual system can estimate the 3D shape of specular objects even from a single image. Although previous studies suggested that the orientation field plays a key role for 3D shape perception from specular reflections, its computational plausibility and possible mechanisms have not been investigated. In this study, to complement the orientation field information, we first add prior knowledge that objects are illuminated from above and utilize the vertical polarity of the intensity gradient. Then we construct an algorithm that incorporates these two image cues to estimate 3D shapes from a single specular image. We evaluated the algorithm with glossy and mirrored surfaces and found that 3D shapes can be recovered with a high correlation coefficient of around 0.8 with true surface shapes. Moreover, under a specific condition, the algorithm’s errors resembled those made by human observers. These findings show that the combination of the orientation field and the vertical polarity of the intensity gradient is computationally sufficient and probably reproduces essential representations used in human shape perception from specular reflections.
The borders ofcis-regulatory DNA sequences harbor the divergent transcription factor binding motifs in the human genome
Authors: Huang Jia-Hsin , Kwan Ryan Shun-Yuen , Tsai Zing Tsung-Yeh , Tsai Huai-Kuang 
Published: August 2018

AbstractChanges in thecis-regulatory DNA sequences and transcription factor (TF) repertoires provide major sources that shape the gene regulatory evolution in eukaryotes. However, it is currently unclear how dynamic change of DNA sequences introduce various divergence level of TF binding motifs in the genome over evolutionary time. Here, we estimated the evolutionary divergence level of the TF binding motifs, and quantified their occurrences in the DNase I hypersensitive sites. Results from ourin silicomotif scan and empirical TF-ChIP (chromatin immunoprecipitation) demonstrate that the divergent motifs tend to be introduced at the borders of thecis-regulatory regions, that are likely accompanied with the expansion through evolutionary time. Accordingly, we propose that an expansion by incorporating divergent motifs within thecis-regulatory regions provides a rationale for the evolutionary divergence of regulatory circuits.
Using an Optimal Set of Features with a Machine Learning-Based Approach to Predict Effector Proteins forLegionella pneumophila
Authors: Ashari Zhila Esna , Brayton Kelly A. , Broschat Shira L. 
Published: August 2018

AbstractType IV secretion systems exist in a number of bacterial pathogens and are used to secrete effector proteins directly into host cells in order to change their environment making the environment hospitable for the bacteria. In recent years, several machine learning algorithms have been developed to predict effector proteins, potentially facilitating experimental verification. However, inconsistencies exist between their results. Previously we analysed the disparate sets of predictive features used in these algorithms to determine an optimal set of 370 features for effector prediction. This work focuses on the best way to use these optimal features by designing three machine learning classifiers, comparing our results with those of others, and obtaining de novo results. We chose the pathogenLegionella pneumophilastrain Philadelphia-1, a cause of Legionnaires’ disease, because it has many validated effector proteins and others have developed machine learning prediction tools for it. While all of our models give good results indicating that our optimal features are quite robust, Model 1, which uses all 370 features with a support vector machine, has slightly better accuracy. Moreover, Model 1 predicted 760 effector proteins, more than any other study, 315 of which have been validated. Although the results of our three models agree well with those of other researchers, their models only predicted 126 and 311 candidate effectors.
Distinguishing between parallel and serial processing in visual attention from neurobiological data
Authors: Li Kang , Kadohisa Mikiko , Kusunoki Makoto , Duncan John , Bundesen Claus , Ditlevsen Susanne 
Published: August 2018

AbstractSerial and parallel processing in visual search have been long debated in psychology but the processing mechanism remains an open issue. Serial processing allows only one object at a time to be processed, whereas parallel processing assumes that various objects are processed simultaneously. Here we present novel neural models for the two types of processing mechanisms based on analysis of simultaneously recorded spike trains using electrophysiological data from prefrontal cortex of rhesus monkeys while processing task-relevant visual displays. We combine mathematical models describing neuronal attention and point process models for spike trains. The same model can explain both serial and parallel processing by adopting different parameter regimes. We present statistical methods to distinguish between serial and parallel processing based on both maximum likelihood estimates and decoding the momentary focus of attention when two stimuli are presented simultaneously. Results show that both processing mechanisms are in play for the simultaneously recorded neurons, but neurons tend to follow parallel processing in the beginning after the onset of the stimulus pair, whereas they tend to serial processing later on. This could be explained by parallel processing being related to sensory bottom-up signals or feedforward processing, which typically occur in the beginning after stimulus onset, whereas top-down signals related to cognitive modulatory influences guiding attentional effects in recurrent feedback connections occur after a small delay, and is related to serial processing, where all processing capacities are being directed towards the attended object.Author summaryA fundamental question concerning processing of visual objects in our brain is how a population of cortical cells respond when presented with more than a single object in their receptive fields. Is one object processed at a time (serial processing), or are all objects processed simultaneously (parallel processing)? Inferring the dynamics of attentional states in simultaneously recorded spike trains from sensory neurons while being exposed to a pair of visual stimuli is key to advance our understanding of visual cognition. We propose novel statistical models and measures to quantify and follow the time evolution of the visual cognition processes right after stimulus onset. We find that in the beginning processing appears to be predominantly parallel, which develops into serial processing 150 – 200 ms after stimulus onset in prefrontal cortex of rhesus monkeys.
Toxoplasma gondiiROP18 Inhibits Human Glioblastoma Cell Apoptosis through Mitochondrial Pathway by Targeting Host Cell P2X1
Authors: Zhou Li-Juan , Chen Min , He Cheng , Xia Jing , He Cynthia Y. , Deng Sheng-Qun , Peng Hong-Juan 
Published: August 2018

ABSTRACTIt is known thatToxoplasma gondiiinfection both initiates and inhibits host cell apoptosis through different proapoptotic signaling cascades, but the parasitic factors involved in these processes remain unclear.T. gondiivirulence factor ROP18 has been reported to regulate host cell apoptosis, but the results of this regulation are few reported and contradictory. In this study, we found that immune or neuro cells infected by any one of theT. gondiistrains (RH-type I, ME49-type II, and VEG-type III) showed a significantly lower apoptosis index than their uninfected controls when apoptosis was induced by staurosporine (STS). We further found that ROP18 of RH strain inhibited ATP induced apoptosis in human glioblastoma cells (SF268) with endogenous expression of human proapoptotic protein purinergic receptor 1 (P2X1), but had no effects on the immune cells of RAW264.7 and THP-1 without detectable P2X1 expression, which may indicate that ROP18’s inhibition of host cell apoptosis is related to P2X1. Interestingly, we further identified that ROP18 (RH strain) interacted with P2X1, and over-expression of ROP18 in COS-7 cells inhibited the cell apoptosis mediated by P2X1. We also found that ROP18 of RH strain inhibited P2X1-mediated Ca2+influx, translocation of cytochrome C from mitochondria to cytoplasm, and 1 ATP-triggered caspases activation. Collectively, these findings supported that ROP18 inhibited the host cell apoptosis through the intrinsic mitochondria pathway by targeting host cell P2X1, thereby suggesting a sensor role of the host proapoptotic protein P2X1 in this processAuthor summaryThe obligate intracellular protozoanToxoplasma gondiihas been shown to modulate cell apoptosis through different apoptotic pathways. However, the consequences are various and even contradictory, and the parasite effectors and the precise biological mechanisms remain unclear. Herein we showed thatT. gondiiof type I, II, and III strains could inhibit the apoptosis of neuro cells and immune cells.Toxoplasma gondiiROP18 (RH strain) inhibited apoptosis of human glioblastoma cell SF268 by targeting C terminal of host cell P2X1 protein, but not through proteasome-dependent degradation of P2X1.
Did a novel virus contribute to late blight epidemics?
Authors: Cai Guohong , Myers Kevin , Fry William E. , Hillman Bradley I. 
Published: August 2018

AbstractPhytophthora infestansis the causal agent of potato and tomato late blight. In this study, we characterized a novel RNA virus, Phytophthora infestans RNA virus 2 (PiRV-2). The PiRV-2 genome is 11,170 nt and lacks a polyA tail. It contains a single large open reading frame (ORF) with short 5’- and 3’-untranslated regions. The ORF is predicted to encode a polyprotein of 3710 aa (calculated molecular weight 410.94 kDa). This virus lacks significant similarity to any other known viruses, even in the conserved RNA-dependent RNA polymerase region. Comparing isogenic strains with or without the virus demonstrated that the virus stimulated sporangia production inP. infestansand appeared to enhance its virulence. Transcriptome analysis revealed that it achieved sporulation stimulation likely through down-regulation of ammonium and amino acid intake inP. infestans. This virus was faithfully transmitted through asexual reproduction. Survey of PiRV-2 presence in aP. infestanscollection found it in most strains in the US-8 lineage, a very successful clonal lineage ofP. infestansin North America. We suggest that PiRV-2 may have contributed to its success, raising the intriguing possibility that a potentially hypervirulent virus may contribute to late blight epidemics.Author SummaryPotato late blight, the notorious plant disease behind the Irish Potato Famine, continues to pose a serious threat to potato and tomato production worldwide. While most studies on late blight epidemics focuses on pathogen virulence, host resistance, environmental factors and fungicide resistance, we present evidence in this study that a virus infecting the causal agent,Phytophthora infestans, may have played a role. We characterized a novel RNA virus, Phytophthora infestans RNA virus 2 (PiRV-2) and examined its effects on its host. By comparing identicalP. infestansstrains except with or without the virus, we found that PiRV-2 stimulated sporulation ofP. infestans(a critical factor in late blight epidemics) and increased its virulence. We also profiled gene expression in these strains and identified potential molecular mechanisms through which PiRV-2 asserted its sporulation stimulation effect. In a survey of PiRV-2 presence in aP. infestanscollection, we found PiRV-2 in most isolates of the US-8 clonal lineage, a very successfull ineage that dominated potato fields in North America for several decades. We suggest that PiRV-2 may have contributed to its success. Our findings raise the intriguing possibility that a potentially hypervirulent virus may contribute to late blight epidemics.
Mouse parabrachial neurons signal a relationship between bitter taste and nociceptive stimuli
Authors: Li Jinrong , Lemon Christian H. 
Published: August 2018

AbstractTaste and somatosensation both partly mediate protective behaviors. Bitter taste guides avoidance of ingestion of toxins while pain sensations, such as noxious heat, signal adverse conditions to ward off harm. Although brain pathways for taste and somatosensation are typically studied independently, prior data suggest they intersect, potentially reflecting their common protective role. To investigate this, we applied electrophysiologic and optogenetic techniques in anesthetized mice of both sexes to evaluate relationships between oral somatosensory and taste activity in the parabrachial nucleus (PbN), implicated for roles in gustation and pain. Spikes were recorded from taste-active PbN neurons tested with oral delivery of thermal and chemesthetic stimuli, including agonists of nocisensitive transient receptor potential (TRP) ion channels on somatosensory fibers. Gustatory neurons were also tested to follow electrical pulse stimulation of an oral somatosensory region of the spinal trigeminal subnucleus caudalis (Vc), which projects to the PbN. Neurons composed classic taste groups, including sodium, electrolyte, appetitive, or bitter oriented cells. Across groups, most neurons spiked to Vc pulse stimulation, implying trigeminal projections reach PbN gustatory neurons. Among such cells, agonists of nocisensitive TRP channels, including mustard oil, capsaicin, and noxious heat, were discovered to predominantly activate PbN bitter taste neurons tuned to the bitters quinine and cycloheximide. Such neurons populated the lateral PbN. Further, PbN bitter taste neurons showed suppressed oral nociceptive activity during optogenetic-assisted inhibition of the Vc, implying convergent trigeminal input contributed to such activity. Our results imply a novel role for PbN gustatory cells in crossmodal signaling related to protection.
Necessity and contingency in developmental genetic screens: LIN-3, Wnt and semaphorin pathways in vulval induction of the nematodeOscheius tipulae
Authors: Vargas-Velazquez Amhed M. , Besnard Fabrice , Félix Marie-Anne 
Published: August 2018

AbstractGenetic screens in the nematodeCaenorhabditis elegansidentified the EGF/Ras and Notch pathways as central for vulval precursor cell fate patterning. Schematically, the anchor cell secretes EGF, inducing the P6.p cell to a 1° vulval fate; P6.p in turn induces its neighbors to a 2° fate through Delta-Notch signaling and represses Ras signaling. In the nematodeOscheius tipulae, the anchor cell successively induces 2° then 1° vulval fates. Here we report on the molecular identification of mutations affecting vulval induction inO. tipulae. A single Induction Vulvaless mutation was found, which we identify as a cis-regulatory deletion in a tissue-specific enhancer of theO. tipulae lin-3homolog, confirmed by CRISPR/Cas9 mutation. In contrast to this predictable Vulvaless mutation, mutations resulting in an excess of 2° fates unexpectedly correspond to the plexin/semaphorin pathway, which was not implicated in vulval fate induction inC. elegans. Hyperinduction of P4.p and P8.p in these mutants likely results from mispositioning of these cells due to a lack of contact inhibition. The third signaling pathway found by forward genetics inO. tipulaeis the Wnt pathway: decrease in Wnt pathway activity results in loss of vulval precursor competence and induction, and 1° fate miscentering on P5.p. Our results suggest that the EGF and Wnt pathways have qualitatively similar activities in vulval induction inC. elegansandO. tipulae, albeit with quantitative differences in the effects of mutation. This study highlights both necessity and contingency in forward genetic screens.100-word summaryGenetic screens in the nematodeCaenorhabditis elegansidentified EGF and Notch pathways as key for vulval precursor cell fate patterning. Here we report on the molecular identification of mutations affecting vulval induction in another nematode,Oscheius tipulae. The single mutation with reduced induction is identified as acis-regulatory deletion in theO. tipulae lin-3homolog, confirmed by CRISPR/Cas9 mutation. In contrast to this predictable Vulvaless mutation, mutations resulting in an excess of 2° vulval fates unexpectedly correspond to the plexin/semaphorin pathway, not implicated in vulval induction inC. elegans. This study highlights both necessity and contingency in forward genetic screens.
In praise of hospitality: the role extended by religious hosts as drivers of satisfaction and loyalty
Authors: Milman Ady , Oren Gila 
Published: August 2018

PurposeThis study aims to explore the hospitality and religious experience of Israeli travelers visiting the globally prevalent Jewish Orthodox Chabad Houses that provide religious, spiritual, educational and hospitality havens in their locales, regardless of the degree of observance.Design/methodology/approachUsing Schmitt’s (1999b) experiential consumption dimensions of Sense, Feel, Think, Relate and Act, this study measured the various visitors’ experiences, satisfaction and loyalty using a sample of 488 Israeli travelers obtained from online social media sites, popular with Israeli travelers.FindingsThe findings reveal that Israeli visits to Chabad Houses were primarily characterized by Act, Feel and Relate experiences like meeting fellow Israeli travelers, a sense of togetherness and a feeling of belonging. In predicting satisfaction and loyalty, the visitors’ religious experience did not play a major role, but rather the actual hospitality extended by their religious hosts, like a home-like feeling, comfort, tasty food and a sense of togetherness did.Research limitations/implicationsCollecting data from an online sample might yield results that would not be applicable to the typical Chabad House visitor. Due to the Chabad Houses’ global presence, their visitors’ experiences may vary from one house to another and the findings may not represent an accurate picture of the typical Chabad House visit.Practical implicationsTo continue its hospitality brand, the Chabad movement’s decision-makers should continue focusing on innovative visitor experiences and balance the religious and secular components of their hospitality, as well as consider carefully how to direct their marketing and operational budgets.Originality/valueAdding to the body of literature on travelers’ experience at religious sites, this research is a pioneering attempt to study and explore visitors’ religious and hospitality experiences while visiting small non-conspicuous religious centers that extend their global hospitality brand to travelers.
Remittances, poverty and human capital: evidence from developing countries
Authors: Huay Chong Siew , Bani Yasmin 
Published: August 2018

Purpose
The purpose of this paper is to analyze the relationship between remittances and poverty through the human capital channel in developing countries, which has received less attention in the literature.

Design/methodology/approach
The paper applied the system GMM developed by Arellano and Bond (1991) and Arellano and Bover (1995) containing 54 developing countries. This estimator is appropriate compared to a cross-section technique because it controls for the endogeneity of all explanatory variables, includes unobserved country-specific effects and allows for the inclusion of lagged dependent variables.

Findings
The results suggest that, while remittances reduced poverty, the effect is moderated via education. A 1 percent increase in remittances reduces the poverty headcount by 0.47 percent, while the reduction is 0.33 percent via education. The marginal effect of remittances is negatively related to the level of education, indicating that education mitigates the effect of remittances on poverty.

Practical implications
This paper includes the implications for the policymakers to justify the need for more effective approaches. It is useful to identify whether and how remittances and human capital interact in their effect on poverty when deciding the most desirable allocation of available resources between these two priorities.

Originality/value
This paper takes a step forward filling the limited evidence on the role of human capital in remittances–poverty relationship in developing countries. Different from the existing studies which have used the traditional panel estimators, this study utilizes the dynamic panel estimators such as system GMM to tackle the specification issues of endogeneity, measurement errors and heterogeneity.
Experimental investigations of force transmission characteristics in granular flow lubrication
Authors: Meng Fanjing , Liu Kun , Qin Tao 
Published: August 2018

Purpose
Granular lubrication is a new lubrication method and can be used in extreme working conditions; however, the obstacle of force transmission characteristics needs to be urgently solved to fully understand the mechanical and bearing mechanisms of granular lubrication.

Design/methodology/approach
A flat sliding friction cell is developed to study the force transmission behaviors of granules under shearing. Granular material, sliding velocity, granule size and granule humidity are considered in these experiments. The measured normal and shear force, which is transmitted from the bottom friction pair to the top friction pair via the granular lubrication medium, reveals the influence of these controlling parameters on the force transmission characteristics of granules.

Findings
Experimental results show that a low sliding velocity, a large granule size and a low granular humidity increase the measured normal force and shear force. Besides, a comparison experiment with other typical lubrication styles is also carried out. The force transmission under granular lubrication is mainly dependent on the force transmission path, which is closely related to the deconstruction and reconstruction of the force chains in the granule assembly.

Originality/value
These findings reveal the force transmission mechanism of granular lubrication and can also offer the helpful reference for the design of the new granular lubrication bearing.
Cleanliness unravelled: a review and integration of literature
Authors: Vos Martijn C. , Galetzka Mirjam , Mobach Mark P. , van Hagen Mark , Pruyn Ad T.H. 
Published: August 2018

Purpose
The purpose of this paper is to present a systematic literature review on stimulus, organism and response variables related to actual and perceived cleanliness and develop a conceptual framework to encourage future research on cleanliness.

Design/methodology/approach
The PRISMA statement methodology for systematic literature review was applied. After analysing 926 articles, 46 articles were included and reviewed.

Findings
Stimulus, organism and response variables related to cleanliness were identified and integrated in a conceptual framework. A distinction was made between articles evaluating the relationship between stimulus and organism variables; stimulus and response variables; and organism and response variables. First, actual cleanliness, staff behaviour, condition of the environment, scent and the appearance of the physical environment were identified as stimuli variables influencing perceived cleanliness and service quality. Second, the presence of litter, behaviour and presence of others, scent, disorder, availability of trash cans and informational strategies were identified as stimuli affecting littering and other kinds of unethical behaviour. Third, the effect of perceived cleanliness (and other organism variables) on satisfaction, approach behaviours, physical activity and pro-social behaviour was registered.

Practical implications
The findings of this review allow in-house and corporate facility managers to better understand and identify most effective interventions positively influencing actual and perceived cleanliness.

Originality/value
No systematic literature review on antecedents and consequences of a clean environment has previously been conducted.