bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Assessment of Muscular Stiffness in Children With Chronic Kidney Disease Using Acoustic Radiation Force Impulse Ultrasound Elastography
Authors: Bekci Tumay , Bilgici Meltem Ceyhan , Tekcan Demet , Ulus Yasemin , Akyuz Behic 
Published: June 2019

Abstract
The aim of this study was to evaluate the feasibility of quantitative analysis of muscle stiffness in the rectus femoris muscle (RFM) by acoustic radiation force impulse (ARFI) ultrasound elastography in children with chronic kidney disease (CKD). Twenty-three children with CKD and 22 healthy children participated in the study in our radiology department. The strength of each CKD group and healthy group participants' tight extensors was assessed by a physiatrist using a handheld dynamometer. Acoustic radiation force impulse was used to measure the shear wave velocities (SWVs) of the RFM. The mean SWV value of the RFM correlated with the strengths of the tight extensors in the CKD and healthy groups. The mean ± SD SWV values of the RFM in the CKD group for the right (n = 23) and left sides (n = 21) were 1.23 ± 0.25 and 1.26 ± 0.30 m/s, respectively. The mean ± SD SWV values of the RFM in the healthy group for the right (n = 23) and left sides (n = 21) were 1.62 ± 0.33 and 1.65 ± 0.35 m/s, respectively. The SWV of the RFM significantly decreased in the patients with CKD when compared with controls (P < 0.001). The SWV values were not correlated to the handheld dynamometry. The interobserver agreement expressed as the interclass correlation coefficient was 0.65 (95% confidence interval, 0.33–0.84; P < 0.001). The acoustic radiation force impulse demonstrates a difference in RFM muscle stiffness between the CKD and healthy groups. This method is a feasible imaging method for the noninvasive assessment of muscle weakness in children with CKD.
Metagenomic Next-generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Central Nervous System Infections: A Multicentre Prospective Study
Authors: Fan Siyuan , Wang Xiaojuan , Hu Yafang , Shi Jingping , Zou Yueli , Zhao Weili , Qiao Xiaodong , Wang Chunjuan , Chin Jerome H. , Liu Lei , Qin Lingzhi , Wang Shengnan , Li Hongfang , Yue Wei , Zhang Weihe , Li Xiaohua , Ge Ying , Wu Honglong , Chen Weijun , Li Yongjun , Guan Tianjia , Li Shiying , Wu Yihan , Zhou Gaoya , Liu Zheng , Piao Yushun , Zhang Jianzhao , Ren Changhong , Cui Li , Liu Caiyun , Ren Haitao , Zhao Yanhuan , Feng Shuo , Jiang Haishan , Wang Jiawei , Bu Hui , Guo Shougang , Peng Bin , Cui Liying , Li Wei , Guan Hongzhi 
Published: June 2019

ABSTRACTBackgroundInfectious encephalitis and meningitis are often treated empirically without identification of the causative pathogen. Metagenomic next-generation sequencing (mNGS) is a high throughput technology that enables the detection of pathogens independent of prior clinical or laboratory information.MethodsThe present study was a multicentre prospective evaluation of mNGS of cerebrospinal fluid (CSF) for the diagnosis of suspected central nervous system infections.ResultsA total of 276 patients were enrolled in this study between Jan 1, 2017 and Jan 1, 2018. Identification of an etiologic pathogen in CSF by mNGS was achieved in 101 patients (36.6%). mNGS detected 11 bacterial species, 7 viral species, 2 fungal species, and 2 parasitic species. The five leading positive detections were varicella-zoster virus (17), Mycobacterium tuberculosis (14), herpes simplex virus 1 (12), Epstein-Barr virus (12), and Cryptococcus neoformans (7). False positives occurred in 12 (4.3%) patients with bacterial infections known to be widespread in hospital environments. False negatives occurred in 16 (5.8%) patients and included bacterial, viral and fungal aetiologies.ConclusionsmNGS of CSF is a powerful diagnostic method to identify the pathogen for many central nervous system infections.
Hyperspectral environmental illumination maps: Characterizing directional spectral variation in natural environments
Authors: Morimoto Takuma , Kishigami Sho , Linhares João M.M. , Nascimento Sérgio M.C. , Smithson Hannah E. 
Published: June 2019

AbstractObjects placed in real-world scenes receive incident light from every direction, and the spectral content of this light may vary from one direction to another. In computer graphics, environmental illumination is approximated using maps that specify illumination at a point as a function of incident angle. However, to-date, existing public databases of environmental illumination maps specify only three colour channels (RGB). We have captured a new set of 12 environmental illumination maps (eight outdoor scenes; four indoor scenes) using a hyperspectral imaging system with 33 spectral channels. The data reveal a striking directional variation of spectral distribution of lighting in natural environments. We discuss limitations of using daylight models to describe natural environmental illumination.
PHISDetector: a tool to detect diverse in silico phage-host interaction signals for virome studies
Authors: Zhang Fan , Zhou Fengxia , Gan Rui , Ren Chunyan , Jia Yuqiang , Yu Ling , Huang Zhiwei 
Published: June 2019

AbstractPhage-microbe interactions not only are appealing systems to study coevolution but also have been increasingly emphasized due to their roles in human health, diseases, and novel therapeutic development. Meanwhile, their interactions leave diverse signals in bacterial and phage genomic sequences, defined as phage-host interaction signals (PHISs), such as sequence composition, CRISPR targeting, prophage, and protein-protein interaction signals. We infer that proper detection and integration of these diverse PHISs will allow us to predict phage-host interactions. Here, we developed PHISDetector, a novel tool to predict phage-host interactions by detecting and integrating diverse in silico PHISs and scoring the probability of phage-host interactions using machine-learning models based on PHIS features. PHISDetector is available as a one-stop web service version for general users to study individual inputs. A stand-alone software version is also provided to process massive phage contigs from virome studies. PHISDetector is freely available at http://www.microbiome-bigdata.com/PHISDetector/ and https://github.com/HIT-ImmunologyLab/PHISDector.
Leveraging Family History in Case-Control Analyses of Rare Variation
Authors: Solis-Lemus Claudia R. , Fischer S. Taylor , Todor Andrei , Liu Cuining , Leslie Elizabeth J. , Cutler David J. , Ghosh Debashis , Epstein Michael P. 
Published: June 2019

AbstractStandard methods for case-control association studies of rare variation often treat disease outcome as a dichotomous phenotype. However, both theoretical and experimental studies have demonstrated that subjects with a family history of disease can be enriched for risk variation relative to subjects without such history. Assuming family history information is available, this observation motivates the idea of replacing the standard dichotomous outcome variable used in case-control studies with a more informative ordinal outcome variable that distinguishes controls (0), sporadic cases (1), and cases with a family history (2), with the expectation that we should observe increasing number of risk variants with increasing category of the ordinal variable. To leverage this expectation, we propose a novel rare-variant association test that incorporates family history information based on our previous GAMuT framework (Broadaway et al., 2016) for rare-variant association testing of multivariate phenotypes. We use simulated data to show that, when family history information is available, our new method outperforms standard rare-variant association methods like burden and SKAT tests that ignore family history. We further illustrate our method using a rare-variant study of cleft lip and palate.
Distinct extracellular-matrix remodeling events precede symptoms of inflammation
Authors: Shimshoni Elee , Adir Idan , Afik Ran , Solomonov Inna , Shenoy Anjana , Adler Miri , Puricelli Luca , Ghini Veronica , Mouhadeb Odelia , Gluck Nathan , Fishman Sigal , Werner Lael , Shouval Dror S. , Varol Chen , Podestà Alessandro , Turano Paola , Geiger Tamar , Milani Paolo , Luchinat Claudio , Alon Uri , Sagi Irit 
Published: June 2019

AbstractIdentification of early processes leading to complex tissue pathologies, such as inflammatory bowel diseases, poses a major scientific and clinical challenge that is imperative for improved diagnosis and treatment. Most studies of inflammation onset focus on cellular processes and signaling molecules, while overlooking the environment in which they take place, the continuously remodeled extracellular matrix. In this study, we used colitis models for investigating extracellular-matrix dynamics during disease onset, while treating the matrix as a complete and defined entity. Through the analysis of matrix structure, stiffness and composition, we unexpectedly revealed that even prior to the first clinical symptoms, the colon displays its own unique extracellular-matrix signature and found specific markers of clinical potential, which were also validated in human subjects. We also show that the emergence of this pre-symptomatic matrix is mediated by sub-clinical infiltration of neutrophils and monocytes bearing remodeling enzymes. Remarkably, whether the inflammation is chronic or acute, its matrix signature converges at pre-symptomatic states. We suggest that the existence of a pre-symptomatic extracellular-matrix is general and relevant to a wide range of diseases.
Genome analysis and Hi-C assisted assembly of Elaeagnus angustifolia L., a deciduous tree belonging to Elaeagnaceae
Authors: Mao Yunfei , Hu Qin , Zhang Manman , Yang Lu , Zhang Lulu , Wang Yunyun , Yin Yijun , Pang Huiling , Liu Yeping , Su Xiafei , Li Song , Cui XinXing , Ma Fengwang , Duan Naibin , Zhang Donglin , Hu Yanli , Mao Zhiquan , Chen Xuesen , Shen Xiang 
Published: June 2019

AbstractElaeagnus angustifolia L. is a deciduous tree of the Elaeagnaceae family. It is widely used in the study of abiotic stress tolerance in plants and for the improvement of desertification-affected land due to its characteristics of drought resistance, salt tolerance, cold resistance, wind resistance, and other environmental adaptation. Here, we report the complete genome sequencing using the Pacific Biosciences (PacBio) platform and Hi-C assisted assembly of E. angustifolia. A total of 44.27 Gb raw PacBio sequel reads were obtained after filtering out low-quality data, with an average length of 8.64 Kb. And 39.56 Gb clean reads was obtained, with a sequencing coverage of 75×, and Q30 ratio > 95.46%. The 510.71 Mb genomic sequence was mapped to the chromosome, accounting for 96.94% of the total length of the sequence, and the corresponding number of sequences was 269, accounting for 45.83% of the total number of sequences. The genome sequence study of E. angustifolia can be a valuable source for the comparative genome analysis of the Elaeagnaceae family members, and can help to understand the evolutionary response mechanisms of the Elaeagnaceae to drought, salt, cold and wind resistance, and thereby provide effective theoretical support for the improvement of desertification-affected land.
The Typhoid Toxin Produced by the Nontyphoidal Salmonella Serovar Javiana Can Utilize Multiple Binding Subunits, which Compete for Inclusion in the Holotoxin
Authors: Gaballa A , Harrand AS , Cohn AR , Wiedmann M , Cheng RA 
Published: June 2019

AbstractSalmonella enterica encodes a wide array of virulence factors. One novel virulence factor, a DNA-damaging toxin known as the typhoid toxin (TT), was recently characterized in >40 nontyphoidal Salmonella (NTS) serovars. Interestingly, these NTS serovars, including S. enterica subsp. enterica serovar Javiana, also encode artB, a homolog of the binding subunit (PltB) of the TT. Here, we show that ArtB and PltB compete for inclusion in the pentameric binding subunit of the TT. Using a combination of in silico modeling, a bacterial two-hybrid system expressed in S. Javiana, and tandem affinity purification (TAP) of the holotoxin subunits, we show that ArtB and PltB interact in vivo. Furthermore, binding subunits composed of homo- and heteropentamers of ArtB and PltB are able to associate with CdtB and PltA to form biologically active toxins. As artB was, (i) conserved among S. Javiana isolates, and (ii) co-expressed with pltB and cdtB under Mg2+-limiting conditions, we hypothesized that ArtB and PltB compete for inclusion in the binding subunit. Using a novel competition assay, we show that PltB outcompetes ArtB for inclusion in the binding subunit, when cultured at neutral pH. Together, our results suggest that the TT produced by S. Javiana utilizes multiple configurations of the binding subunit, representing a novel toxin form and adaptation mechanism for the AB5 toxin family. Our work suggests that Salmonella serovars, including S. Javiana, evolved to encode and maintain multiple binding subunits that can be used to form an active toxin, which may enhance the variety of cells, tissues, or hosts susceptible to this novel form of the TT.
High-resolution mapping of forest vulnerability to wind for disturbance-aware forestry and climate change adaptation
Authors: Suvanto Susanne , Peltoniemi Mikko , Tuominen Sakari , Strandström Mikael , Lehtonen Aleksi 
Published: June 2019

AbstractWindstorms cause major disturbances in European forests and forest management can play a key role in making forests more persistent to disturbances. However, better information is needed to support decision making that effectively accounts for wind disturbances. Here we show how empirical probability models of wind damage, combined with existing spatial datasets, can be used to provide fine-scale spatial information about disturbance probability over large areas. First, we created stand-level damage probability models with predictors describing forest characteristics, recent forest management history and local wind, soil, site and climate conditions. We tested three different methods for creating the damage probability models - generalized linear models (GLM), generalized additive models (GAM) and boosted regression trees (BRT). Then, the damage probability maps were calculated by combining the models (GLM, GAM and BRT) with GIS data sets representing the model predictors. Finally, we demonstrated the predictive performance of the maps with a large, independent test data, which shows that the damage probability maps are able to identify vulnerable forests also in new wind damage events (AUC > 0.7). Use of the more complex methods (GAM and BRT) was not found to improve the predictive performance of the map compared to GLM, and therefore we would suggest using the more simple GLM method that can be more easily interpreted. The map allows identification of vulnerable forest areas in high spatial resolution (16 × 16 m2raster resolution), making it useful in assessing the vulnerability of individual forest stands when making management decisions. The map is also a powerful tool for communicating disturbance risks to forest owners and managers and it has the potential to steer forest management practices to a more disturbance aware direction. Our study showed that in spite of the inherent stochasticity of the wind and damage phenomena at all spatial scales, it can be modelled with good accuracy across large spatial scales when existing ground and earth observation data sources are combined smartly. With improving data quality and availability, map-based risk assessments can be extended to other regions and other disturbance types.
Cause-related marketing: an exploration of new avenues through conjoint analysis
Authors: Kulshreshtha Kushagra , Bajpai Naval , Tripathi Vikas , Sharma Gunjan 
Published: June 2019

Purpose
Cause-related marketing (CrM) is one of the effective marketing concepts which draw high public exposure and make the cause and the organization known in the market. Further, it develops a higher inclination of the customers associating themselves with CrM-related campaigns. In this regard, CrM campaigns generally take hedonic products into consideration. The purpose of this paper (comprises two studies) is to: study 1, examine the attributes leading to successful CrM campaign and afterward when the results of Study 1 were found in line with the existing literature; and, Study 2, empirically examine the consumer preference for hedo-utilitarian products type in the CrM context.

Design/methodology/approach
A total of 316 respondents participated in the survey. For selecting the appropriate research technique under the CrM study, the systematic review was conducted to arrive at a decision. Finally, conjoint analysis, a decompositional approach, was used for its ability to provide real-world setup to the respondents and keeping the social desirability bias at the minimum while assessing the consumer preference in the context of CrM.

Findings
Much literature is available in favor of using hedonic products for successful CrM activities. However, none has conceptualized the hedo-utilitarian products that have an equally fair chance to succeed under CrM strategy. The present study confirmed the relevance of hedo-utilitarian products (utilitarian products having hedonic features) for attracting the consumers having cognitive and affective responses altogether.

Practical implications
The novel concept of hedo-utilitarian product is introduced and empirically examined. The propositions and findings will facilitate the organizations in developing the products and marketing strategies in the context of CrM, giving them the option beyond the two product categories, i.e. hedonic and utilitarian. Accordingly, the companies may also focus and strategize for the “causmers,” i.e. the consumers who pay heed to the cause of the campaign during the purchase.

Originality/value
While several of the dimensions in marketing have been explored, CrM is the least explored area in the Asian region. The attributes that may affect CrM were taken all together as another product feature/attribute under conjoint analysis exploring the attributes affecting CrM most, eventually, leading to higher consumer preference. Further, the concept of hedo-utilitarian products was introduced, empirically examined and recommended to future researchers for bringing it forward.
Dichotomies of disaster management: a reflection on the politics of efficient decision making
Authors: Kasdan David Oliver 
Published: June 2019

Purpose
The purpose of this paper is to explore the variety of dichotomies related to disaster management with an objective to gain a better understanding of how and when dichotomous thinking can improve disaster management, especially in the discourse of disaster management politics.

Design/methodology/approach
This is a reflective essay that surveys dichotomies from multiple disciplines in respect to their potential contributions to disaster management.

Findings
Thinking about disaster management as a collection or series of dichotomies may help to better understand the sources, vulnerabilities, approaches, modes, methods and modes for related decision-making scenarios, particularly in the political realm.

Research limitations/implications
The world is not so simply divided at every turn and dichotomous thinking may harbor biases, mask ignorance and/or offend postmodern notions of alterity.

Practical implications
Portraying disaster management through dichotomies is an efficient way for experts to convey information and structure decisions for political agendas.

Originality/value
This study presents a unique perspective of disaster management and how it may shape the thinking and decision making of disaster management politics.
The Ecovillage of Pescomaggiore (L’Aquila)
Authors: Tomassi Isabella , Forino Giuseppe 
Published: June 2019

Purpose
The purpose of this paper is to aim at exploring the relationship between community building and the changes occurred in the context of a post-disaster self-built ecovillage (EcoVillaggio Autocostruito (EVA)), spontaneously born after the L’Aquila earthquake in 2009. The community eventually dissolved in 2014, following a series of changes in the organization, that resulted in an increasingly centralized decision-making process, and in individual and community relationships, that were fueled by conflicts and contrasts.

Design/methodology/approach
Through a self-ethnography method, the paper provides the insider perspective of the lead author who was a part of EVA since the beginning. Self-ethnography allowed developing a narrative of EVA across its life course.

Findings
Findings reveal that the community into EVA was initially pursuing community-building goals through self-construction, sustainability, mutuality and reciprocity relationships out of market. However, several events occurred and changed community goals, organization and decision making. Eventually, individual goals and vertical decision making emerged among the community members, leading to the death of EVA.

Research limitations/implications
The paper just considered those main events that marked the collective and individual life of the lead author since the beginning until the end of the ecovillage. Others events, equally important, were not considered due to word length. In addition, self-ethnography is still considered by some authors as a subjective method.

Originality/value
The paper is one of the few exploring community experiences into post-disaster ecovillages. Moreover, there are no papers investigating post-disaster ecovillages through a self-ethnography approach. Therefore, the paper offers an innovative and original perspective on the under-investigated topic of post-disaster ecovillages and employs a promising research method in disaster studies.
Defensible decisions
Authors: Kurlychek Megan , Bushway Shawn , Denver Megan 
Published: June 2019

Purpose
Employers using criminal background checks to make hiring determinations must carefully balance the need to protect themselves and their clients against legal mandates designed to protect the rights of individuals with criminal records. Yet, surprisingly little research examines this balancing act. The purpose of this paper is to examine how one large agency, the New York Department of Health (DOH), navigates a myriad of mandates to convey and create legitimacy in compliance with complex legal mandates and contrasting interests.

Design/methodology/approach
Prior research on civil right legislation suggests that while companies may create regulations that appear to comply with such mandates, their actual practice does not always comply with their own rules (Dobbin et al., 1988). Therefore, this study addresses two key questions: do the DOH policies appear to comply with the relevant New York State law and does the DOH effectively implement the policies in a way that upholds New York State law. Specifically, this study estimates probit models on a sample of over 7,000 potential employees with criminal records to determine compliance with the criteria established by law and policy.

Findings
Findings show that the variables indicated by law/regulations such as offense severity and time since conviction work in the intended direction. Using only these criteria the models are able to correctly predict clearance decisions approximately of the time and that extra-legal factors such as race and gender do not further influence final determinations.

Practical implications
These findings have practical implications for employers as they show that it is possible for employers to design formal rules that navigate this complex landscape while still opening up employment opportunities for individuals with criminal records.

Originality/value
This is important as many employers either utilize criminal background checks without regulation or are fearful of embarking on efforts to meet regulations such as those promulgated by the EEOC. This research is the first of its kind to actually document and explore the ability of a large employer to conduct socially responsible criminal history background checks.