bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining common principles of gene co-expression refines molecular stratification in cancer
Authors: Care Matthew A. , Westhead David R. , Tooze Reuben M. 
Published: July 2018

AbstractCancers converge onto shared patterns that arise from constraints placed by the biology of the originating cell lineage and microenvironment on recurrent programs driven by oncogenic events. This structure should be transferable to molecular stratification. We exploit expression data resources and a parsimonious and computationally efficient network analysis method to define consistent expression modules in colon and breast cancer. Comparison between cancer types identifies principles of gene co-expression: cancer hallmarks, functional and structural gene batteries, copy number variation and biology of originating lineage. Mapping outcome data at gene and module level onto these networks generates a detailed interactive resource. Testing the utility of the resulting modules in TCGA data defines specific associations of module expression with mutation state, identifying striking associations such as mast cell gene expression and mutation pattern in breast cancer. These analyses provide evidence for a generalizable framework to enhance molecular stratification in cancer.
Caspase-mediated cleavage of murine norovirus NS1/2 potentiates apoptosis and is required for persistent infection of intestinal epithelial cells
Authors: Robinson Bridget A. , Van Winkle Jacob A. , McCune Broc T , Peters A. Mack , Nice Timothy J. 
Published: July 2018

AbstractHuman norovirus (HNoV) is the leading cause of acute gastroenteritis and is spread by fecal shedding that can often persist for weeks to months after the resolution of symptoms. Elimination of persistent viral reservoirs has the potential to prevent outbreaks. Similar to HNoV, murine norovirus (MNV) is spread by persistent shedding in the feces and provides a tractable model to study molecular mechanisms of enteric persistence. Previous studies have identified non-structural protein 1 (NS1) from the persistent MNV strain CR6 as critical for persistent infection in intestinal epithelial cells (IECs), but its mechanism of action remains unclear. We now find that the function of CR6 NS1 is regulated by apoptotic caspase cleavage. Following induction of apoptosis in infected cells, caspases cleave the precursor NS1/2 protein, and this cleavage is prevented by mutation of caspase target motifs. These mutations profoundly compromise CR6 infection of IECs and persistence in the intestine. Conversely, NS1/2 cleavage is not required for acute replication in extra-intestinal tissues or in cultured myeloid cells, indicating an IEC-specific role. Intriguingly, we find that caspase cleavage of NS1/2 reciprocally promotes caspase activity, potentiates cell death, and amplifies spread among cultured IEC monolayers. Together, these data indicate that the function of CR6 NS1 is regulated by apoptotic caspases, and suggest that apoptotic cell death enables epithelial spread and persistent shedding.Author SummaryHuman Norovirus infection is highly contagious and the most common cause of acute gastroenteritis. Norovirus can be persistently shed after resolution of symptoms, perpetuating or initiating new outbreaks. Murine norovirus (MNV) is also persistently shed, enabling study of host and viral determinants of norovirus pathogenesis. We previously identified a critical role for MNV non-structural protein 1 (NS1), in persistence. Herein we find that regulation of NS1 by host apoptotic caspases is required for infection of intestinal epithelial cells, but not for extra-intestinal spread. Additionally, we demonstrate that NS1 reciprocally promotes cell death and spread among epithelial cells. These data identify regulation of NS1 by host proteases and suggest that apoptotic death is a determinant of epithelial spread and persistence.
Chromatin conformation analysis of primary patient tissue using a low input Hi-C method
Authors: Díaz Noelia , Kruse Kai , Erdmann Tabea , Staiger Annette M. , Ott German , Lenz Georg , Vaquerizas Juan M. 
Published: July 2018

AbstractChromatin conformation constitutes a fundamental level of eukaryotic genome regulation. However, our ability to examine its biological function and role in disease is limited by the large amounts of starting material required to perform current experimental approaches. Here, we present Low-C, a Hi-C method for low amounts of input material. By systematically comparing Hi-C libraries made with decreasing amounts of starting material we show that Low-C is highly reproducible and robust to experimental noise. To demonstrate the suitability of Low-C to analyse rare cell populations, we produce Low-C maps from primary B-cells of a diffuse large B-cell lymphoma patient. We detect a common reciprocal translocation t (3;14) (q27;q32) affecting the BCL6 and IGH loci and abundant local structural variation between the patient and healthy B-cells. The ability to study chromatin conformation in primary tissue will be fundamental to fully understand the molecular pathogenesis of diseases and to eventually guide personalised therapeutic strategies.
Engineered cell-to-cell signalling within growing bacterial cellulose pellicles
Authors: Walker Kenneth T , Goosens Vivianne J , Das Akashaditya , Graham Alicia E , Ellis Tom 
Published: July 2018

AbstractBacterial cellulose is a strong and flexible biomaterial produced at high yields by Acetobacter species and has applications in healthcare, biotechnology and electronics. Naturally, bacterial cellulose grows as a large unstructured polymer network around the bacteria that produce it, and tools to enable these bacteria to respond to different locations are required to grow more complex structured materials. Here, we introduce engineered cell-to-cell communication into a bacterial cellulose-producing strain of Komagataeibacter rhaeticus to enable different cells to detect their proximity within growing material and trigger differential gene expression in response. Using synthetic biology tools, we engineer Sender and Receiver strains of K. rhaeticus to produce and respond to the diffusible signalling molecule, acyl-homoserine lactone (AHL). We demonstrate that communication can occur both within and between growing pellicles and use this in a boundary detection experiment, where spliced and joined pellicles sense and reveal their original boundary. This work sets the basis for synthetic cell-to-cell communication within bacterial cellulose and is an important step forward for pattern formation within engineered living materials.
Organizational citizenship behavior in relation to employees’ intention to stay in Indian organizations
Authors: Shanker Meera 
Published: July 2018

PurposeThe purpose of this paper is to find out dimensions of organizational citizenship behavior (OCB) in Indian setting and to further examine the role of OCB that impacts employees’ intention to stay, with a view to draw on the deeper influences it carries on the quality work of the organization.Design/methodology/approachExperimental research design was used to find out the causal relationship between these constructs, i.e., dimensions of OCB and intention to stay. Probability sampling method was used to obtain the sample. In total, 475 respondents were approached for data collection. Data were collected using questionnaire method.FindingsFactor analysis result revealed five factors of OCB, namely: sportsmanship, altruism, courtesy, civic virtue and conscientiousness, having the reliability of 0.93, 0.89, 0.81, 0.82 and 0.69, respectively, single factor of intention to stay having the reliability 0.87. The findings of Pearson’s correlation, regression and structural equation modeling revealed unequivocal influence of OCB over employees’ intention to stay, suggesting a maneuvering capability of OCB with its influence over employees’ intention to stay in their present organizations.Research limitations/implicationsSince this study was conducted in India, to establish the external validity has to be judged carefully. The organizations approached for the study were of the MNC level.Practical implicationsThis study is important to understand the citizenship behavior of employees in relation with intention to stay in Indians setting in particular and the world in general. When individual does work, without any expectation, stay with the organization for longer time inculcating, imbibing working culture of the organization which enriches his experiences, utilized in increasing productivity and prosperity of the organizations.Social implicationsOverall, organizations are facing increased competition day by day; employees are expected to stretch themselves to be in the competition. After certain point of time, employees stop extending themselves, resulting in deteriorating the quality, performance and product. Retaining employees along with maintaining the quality becomes an important concern and issue for organizations. Importance of OCB is considered extensively in Industries in this regard.Originality/valueThis is an original research in Indian Setting, much researches are not available finding the relationship between OCB and intention to stay in turn which improves the quality of organizations. This research is valuable for business world, are facing problems of retaining the employees which affects their efficiency, productivity and profitability.
Active fault tolerant control design for stochastic Interval Type-2 Takagi-Sugeno fuzzy model
Authors: Maalej Imen , Ben Halima Abid Donia , Rekik Chokri 
Published: July 2018

Purpose
The purpose of this paper is to look at the problem of fault tolerant control (FTC) for discrete time nonlinear system described by Interval Type-2 Takagi–Sugeno (IT2 TS) fuzzy model subjected to stochastic noise and actuator faults.

Design/methodology/approach
An IT2 fuzzy augmented state observer is first developed to estimate simultaneously the system states and the actuator faults since this estimation is required for the design of the FTC control law. Furthermore, based on the information of the states and the faults estimate, an IT2 fuzzy state feedback controller is conceived to compensate for the faults effect and to ensure a good tracking performance between the healthy system and the faulty one. Sufficient conditions for the existence of the IT2 fuzzy controller and the IT2 fuzzy observer are given in terms of linear matrix inequalities which can be solved using a two-step computing procedure.

Findings
The paper opted for simulation results which are applied to the three-tank system. These results are presented to illustrate the effectiveness of the proposed FTC strategy.

Originality/value
In this paper, the problem of active FTC design for noisy and faulty nonlinear system represented by IT2 TS fuzzy model is treated. The developed IT2 fuzzy fault tolerant controller is designed such that it can guarantee the stability of the closed-loop system. Moreover, the proposed controller allows to accommodate for faults, presents a satisfactory state tracking performance and outperforms the traditional type-1 fuzzy fault tolerant controller.
Students’ mobility attitudes and sustainable transport mode choice
Authors: Cattaneo Mattia , Malighetti Paolo , Morlotti Chiara , Paleari Stefano 
Published: July 2018

PurposeThis study aims to explore the propensity of university students to use different sustainable transport modes, taking into account individual and specific trip characteristics, as well as students’ psychological traits (i.e. attitudes).Design/methodology/approachUsing the transport mode preferences of 827 students who responded to a travel survey, a two-step analysis is conducted. The first step examines the effects of individual characteristics, travel experience and origin or destination features on students’ stated preferences (i.e. self-selected values assigned to personal attitudes). The second step analyses students’ travel mode choices, given their intrinsic mobility attitudes.FindingsThe results suggest that informing students about environmental issues increases their propensity to use sustainable mobility, leading to an average decrease in private transport usage of 5.8 per cent. Interestingly, improving the public transport service and promoting sustainable transport mobility have different impacts on individual campus areas. For campuses located in the city centre and in the historical hamlet, improvements in public transport are found to decrease solo driving by 3.3 per cent and 5.3 per cent, respectively. In suburban areas, this value increases to 9.5 per cent.Originality/valueThis work makes two contributions to the literature. First, it focuses on an unexplored setting, namely, that of a multi-campus university, with districts located in three different areas. This is used to explain how students are influenced by their travel experience and the cultural framework in which they are embedded. Second, the two-step analysis leads to a deeper understanding of the differences between attitudes and “intrinsic attitudes”, and their relative influence on the preferred alternative.
Farm to Consumer: Factors Affecting the Organoleptic Characteristics of Coffee. II: Postharvest Processing Factors
Authors: Hameed Ahsan , Hussain Syed Ammar , Ijaz Muhammad Umair , Ullah Samee , Pasha Imran , Suleria Hafiz Ansar Rasul 
Published: July 2018

AbstractThe production and consumption of coffee are increasing despite the roadblocks to its agriculture and global trade. The unique, refreshing, and stimulating final cupping quality of coffee is the only reason for this rising production and consumption. Coffee quality is a multifaceted trait and is inevitably influenced by the way it is successively processed after harvesting. Reportedly, 60% of the quality attributes of coffee are governed by postharvest processing. The current review elaborates and establishes for the first time the relationship between different methods of postharvest processing of coffee and its varying organoleptic and sensory quality attributes. In view of the proven significance of each processing step, this review has been subdivided into three sections, secondary processing, primary processing, and postprocessing variables. Secondary processing addresses the immediate processing steps on the farm after harvest and storage before roasting. The primary processing section adheres specifically to roasting, grinding and brewing/extraction, topics which have been technically addressed more than any others in the literature and by industry. The postprocessing attribute section deals generally with interaction of the consumer with products of different visual appearance. Finally, there are still some bottlenecks which need to be addressed, not only to completely understand the relationship of varying postharvest processing methods with varying in‐cup quality attributes, but also to devise the next generation of coffee processing technologies.
Out‐of‐hospital arrests attending an Australian tertiary paediatric emergency department over 13 years: An observational study
Authors: Day Elisabeth , Hort Jason R 
Published: July 2018

AbstractObjectiveIn paediatric cardiopulmonary arrest, International Liaison Committee on Resuscitation (ILCOR) states, ‘there are no simple guidelines to determine when resuscitative efforts become futile’. Considerations to assist this decision‐making include cause of arrest, pre‐existing medical conditions, age, site of arrest, duration of untreated cardiopulmonary arrest, witnessed arrest and presence of shockable rhythm. Outcomes are poor in out‐of‐hospital cardiac arrests (OHCA), particularly for infants. This single‐centre observational study describes the characteristics and outcomes of the subgroup of children presenting to our hospital's ED following OHCA still receiving cardiac compressions, to assist development of guidelines for future resuscitation efforts in our ED, particularly for cessation of cardiopulmonary resuscitation (CPR).MethodsThe ED database was searched for children presenting in cardiopulmonary arrest receiving cardiac compressions. Data were reviewed on pre‐hospital, ED and hospital management and outcome, particularly looking at considerations outlined by ILCOR.ResultsFrom January 2000 to December 2013, 60 children were identified: median age 1.71 years; 87% arresting at home; 68% with bystander CPR; median CPR duration pre‐hospital 42 min, and in ED 19.5 min; total CPR median 61 min. Fifty patients (83%) died in ED, 10 (17%) were admitted to intensive care but all died within 4 days.ConclusionChildren presenting to ED still receiving cardiac compressions following OHCA had a universally poor outcome, regardless of age and underlying cause. This implies resuscitative efforts could be discontinued earlier in this subgroup. A national, multicentre study is needed to determine if this finding is reproducible with a larger population.
Food supplementation by an invasive fleshy‐fruited shrub sustains body condition of a native frugivorous bird during winter
Authors: ROJAS Tobias Nicolas , VERGARA‐TABARES David Lautaro , VALDEZ Diego Javier , PONZIO Marina Flavia , PELUC Susana Inés 
Published: July 2018

AbstractBirds tend to adjust their behavior and physiology to changes in food availability in their environment. Seasonal fluctuation of food resources may act as an energetic challenge, augmenting hypothalamus–pituitary–adrenal axis (HPA axis) activity, leading to an increase in corticosterone concentrations and promoting the metabolism of energy stores. Plant invasions may alter seasonal food fluctuations by providing a food supply during scarce seasons. This could attenuate the energetic challenge, reducing HPA axis activity and the metabolism of reserves. Using a system with seasonal fluctuation in food availability, we tested if fruit supplementation by the invasive fleshy‐fruited Pyracantha angustifolia during the season of native fruit scarcity decreases the consumption of energy stores through activity attenuation of the HPA axis. We measured changes in body condition and circulating corticosterone (CORT) concentration in Turdus chiguanco occurring at sites both invaded and not invaded by P. angustifolia over 3 time periods that correspond to the periods prior to, during and after highest fruit production of the plant. Fruit scarcity in the ecosystem appears as an energetic challenge for T. chiguanco, given that body mass, fat score and residuals of body mass/tarsus length decreased during winter in a site not invaded by the exotic shrub. Conversely, the presence of the invasive plant seemed to attenuate the metabolism of energetic reserves, as we did not record changes in body condition in birds inhabiting the invaded site. Unexpectedly, plasma CORT concentration did not vary between sites or periods. Further evaluation is required to elucidate how enhanced body condition, resulting from the consumption of a fleshy‐fruited invasive plant, affects survivorship and reproductive performance in T. chiguanco.
Effects of maternal stress induced by predator odors during gestation on behavioral and physiological responses of offspring in Brandt's vole (Lasiopodomys brandtii)
Authors: GU Chen , WANG Wenjia , DING Xiaoqian , YANG Shengmei , WANG Aiqin , YIN Baofa , WEI Wanhong 
Published: July 2018

AbstractMaternal effects play a crucial role in regulating populations of small mammals and anti‐predator behaviors of offspring. The present study investigated the effects of maternal stress induced by exposure to predator odors during gestation on the behavioral and physiological responses of offspring in Brandt's vole (Lasiopodomys brandtii). Effects included changes in growth, behaviors, hormone levels in serum, and fosB/ΔfosB mRNA and FosB/ΔFosB protein expression in the hypothalamus. Our results showed that when pregnant voles were exposed to cat and rabbit urine odors for 18 days (1 h/day), the weight of the female offspring decreased; however, the thymus and ovary indices increased, compared with the control group. Male offspring of voles exposed to cat odor spent more time exploring and foraging, and showed a decrease in corticosterone (CORT) compared with voles in the control group. Both fosB/ΔfosB mRNA and FosB/ΔFosB protein expressions were downregulated in the hypothalamus of male offspring in the cat odor‐exposed group compared to that in offspring in the control group. However, the mRNA levels of fosB/ΔfosB in the hypothalamus of female offspring did not decrease in response to cat urine odor. Our findings suggested that maternal stress induced by predator odors during gestation restrained the growth of female offspring and increased the duration of exploring and foraging behaviors of male offspring by regulating the HPA axis, which, in turn, reduced the sensitivity of offspring to unfamiliar environments and increased their probability of becoming prey.
Bromelain Kinetics and Mechanism on Myofibril from Golden Pomfret (Trachinotus blochii)
Authors: Feng Xiao , Hang Shasha , Zhou Yige , Liu Qin , Yang Hongshun 
Published: July 2018

AbstractBromelain was used to tenderize golden pomfrets (Trachinotus blochii). The enzyme kinetic model was , which indicated that the degree of hydrolysis (DH, x) was dependent on hydrolysis time (t), the initial concentration of myofibril (S0) and bromelain (E0). The relationship between the overall hydrolysis rate (v), S0, E0, and t is demonstrated as: . Sample of 0.40% E0/S0 was further used to study the effects of hydrolysis time on the changes of proteins, peptides, free amino acids (FAA), and protein nanostructure. SDS‐PAGE result showed that myosin heavy chain was degraded dramatically from 22.88% before treatment to 12.03% after 2 min bromelain treatment. Meanwhile, bromelain did not exhibit activity towards actin, trypomyosin, myosin light chain, and troponin C. A general increase of amino acids indicated the increased DH and the preferential cleavage sites of bromelain in the descending order of lysine, glutamic acid, glycine, ornithine, methionine sulfoxide, and alanine. Atomic force microscope images showed that the strip‐like structure of myofibril was considerably degraded by bromelain, and the granulation of protein after 20 min indicated possible self‐assembling of protein hydrolysate. Confocal laser scanning microscopy further confirmed the degradation of myofibril proteins and formation of protein aggregates.Practical ApplicationMeat of golden pomfrets is tough, thus not idea for fish balls or fish cakes. Tenderization is essential to achieve desired texture and consumer acceptance, especially for this fish meat with intrinsic hard texture. Bromelain can be extracted from pineapple processing waste. Enzymatic kinetics was studied to instruct industry to control the tenderness of the processed fish meat. The microstructural and mechanism study elucidate the process, thus could be applied to improve the quality of the seafood products correspondingly.