bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Economic dynamics into Ecological Networks: The case of fishery sustainability
Authors: Glaum Paul , Cocco Valentin , Valdovinos Fernanda S. 
Published: November 2019

Summary/AbstractUnderstanding and sustainably managing anthropogenic impact on ecosystems requires studying the integrated economic -ecological dynamics driving coupled human-natural systems. Here, we expand ecological network theory to study fishery sustainability by incorporating economic drivers into food-web models to evaluate the dynamics of thousands of single-species fisheries across hundreds of generated food-webs and two management strategies. Analysis reveals harvesting high population biomass species can initially support fishery persistence, but threatens long term economic and ecological sustainability by indirectly inducing extinction cascades in non-harvested species. This dynamic is exacerbated in open access fisheries where profit driven growth in fishing effort increases perturbation strength. Results demonstrate the unique insight into both ecological dynamics and sustainability garnered from considering economically dynamic fishing effort in the network.One Sentence SummaryIntegrating economic drivers into ecological networks reveal non-linear drivers of sustainability in fisheries.
Differential effects of day-night cues and the circadian clock on the barley transcriptome
Authors: Müller Lukas M. , Mombaerts Laurent , Pankin Artem , Davis Seth J. , Webb Alex A. R. , Goncalves Jorge , von Korff Maria 
Published: November 2019

AbstractThe circadian clock is a complex transcriptional network that regulates gene expression in anticipation of the day-night cycle and controls agronomic traits in plants. However, in crops, information on the effects of the internal clock and day-night cues on the transcriptome is limited. We analysed the diel and circadian leaf transcriptomes in the barley cultivar Bowman and derived introgression lines carrying mutations in EARLY FLOWERING 3 (ELF3), LUX1, and EARLY MATURITY 7 (EAM7). Mutations in ELF3 and LUX1 abolished circadian transcriptome oscillations under constant conditions, whereas eam7 maintained oscillations of ≈30% of the circadian transcriptome. However, day-night cues fully restored transcript oscillations in all three mutants and thus compensated for a disrupted oscillator in the arrhythmic barley clock mutants elf3 and lux1. Nevertheless, elf3 but not lux1 affected the phase of the diel oscillating transcriptome and thus the integration of external cues into the clock. Using dynamical modelling, we predicted a structure of the barley circadian oscillator and interactions of its individual components with day-night cues. Our findings provide a valuable resource for exploring the function and output targets of the circadian clock and for further investigations into the diel and circadian control of the barley transcriptome.
Anthropomorphic left ventricular mesh phantom: a framework to investigate the accuracy of SQUEEZ using Coherent Point Drift for the detection of regional wall motion abnormalities
Authors: Manohar Ashish , Colvert Gabrielle , Schluchter Andrew , Contijoch Francisco , McVeigh Elliot R. 
Published: November 2019

AbstractWe present an anthropomorphically accurate left ventricular (LV) phantom derived from human CT data to serve as the ground truth for the optimization and the spatial resolution quantification of a CT-derived regional strain metric (SQUEEZ) for the detection of regional wall motion abnormalities. Displacements were applied to the mesh points of a clinically derived end-diastolic LV mesh to create analytical end-systolic poses with physiologically accurate endocardial strains. Normal function as well as regional dysfunction of four sizes (1, 2/3, 1/2, and 1/3 AHA (American Heart Association) segments as core diameter), each exhibiting hypokinesia (70% reduction in strain) and subtle hypokinesia (40% reduction in strain), were simulated. Regional shortening (RSCT) estimates were obtained by registering the end-diastolic mesh to each simulated end-systolic mesh condition using a non-rigid registration algorithm. Ground-truth models of normal function and of hypokinesia were used to identify the optimal parameters in the registration algorithm, and to measure the accuracy of detecting regional dysfunction of varying sizes and severities. For normal LV function, RSCT values in all 16 AHA segments were accurate to within ±5%. For cases with regional dysfunction, the errors in RSCT around the dysfunctional region increased with decreasing size of dysfunctional tissue.
The Time Varying Networks of the Interoceptive Attention and Rest
Authors: Martínez Ana Y. , Demertzi Athena , Bauer Clemens C.C. , Gracia-Tabuenca Zeus , Alcauter Sarael , Barrios Fernando A. 
Published: November 2019

AbstractFocused attention to spontaneous sensations is a phenomenon that demands interoceptive abilities and a dynamic character of attentive processes. The lack of its control has been linked to neuropsychiatric disorders, such as illness-anxiety disorder. Regulatory strategies, like focused attention meditation, may enhance the ability to control attention particularly to body sensations, which can be reflected on functional neuroanatomy. Adopting a systems-level approach, we aimed at estimating the recurring fMRI functional connectivity (FC) patterns between regions of the dorsal attention network, default mode network, and frontoparietal network during 20 minutes of an attentional task to spontaneous sensations (Task), and at rest, before (Pre-task rs) and after the task (Post-task rs), in fifteen experienced meditators. Dynamic functional connectivity analysis was performed using sliding windows and k-means clustering on the grouped data finding five FC patterns. In both rest conditions the subjects remain longer in a low connectivity state, in contrast, during the task a higher proportion of time spent in complex organization states was preferred. Moreover, an impact over the post-task rs FC was observed as an effect of the preceding interoceptive task performance, with this remaining effect probably taking an active role in the learning process linked to cognitive training.
Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets
Authors: Chen Chao , Liu Songming , Li Bo 
Published: November 2019

AbstractThis study was aimed to investigate the mutations in colorectal cancer (CRC) for recurrent neoantigen identification. A total of 1,779 samples with whole exome sequencing (WES) data were obtained from 7 published CRC cohorts. Common HLA genotypes were used to predict the probability of neoantigens at high frequency mutants in the dataset. Based on the WES data, we not only obtained the most comprehensive CRC mutation landscape so far, but also found 1550 mutation sites which could be identified in at least 5 or more patients, includingKRASG12D (8%),KRASG12V (5.8%),PIK3CAE545K (3.5%),PIK3CAH1047R (2.5%) andBMPR2N583Tfs*44 (2.8%). These mutations can also be recognized by multiple common HLA molecules as potential ‘public’ neoantigens. Many of these mutations also have high mutation rates in metastatic pan-cancers, suggesting their value as therapeutic targets in different cancer types. Overall, our analysis provides recurrent neoantigens as potential cancer immunotherapy targets.
Production of Insoluble Starch-Like Granules in Escherichia coli by Modification of the Glycogen Synthesis Pathway
Authors: White Joseph J. , Cain Natasha , French Christopher E. 
Published: November 2019

AbstractWhile investigating the conversion of cellulosic biomass to starch-like materials for industrial use, it was observed that the overexpression of native ADP-glucose pyrophosphorylase GlgC in Escherichia coli led to the formation of insoluble polysaccharide granules within the cytoplasm, occupying a large fraction of the cell volume, as well as causing an overall increase in cellular polysaccharide content. TEM microscopy revealed that the granules did not have the lamellar structure of starch, but rather an irregular, clustered structure. On starvation, cells overexpressing GlgC appeared unable to fully degrade their polysaccharide material and granules were still clearly visible in cultures after 8 days of starvation. Interestingly, the additional overexpression of the branching enzyme GlgB eliminated the production of granules and led to a further increase in cellular polysaccharides. GlgC is generally thought to be responsible for the rate-limiting step of glycogen synthesis. Our interpretation of these results is that excess GlgC activity may cause the elongation of glycogen chains to outpace the addition of side branches, allowing the chains of adjacent glycogen molecules to reach lengths at which they spontaneously intertwine, forming dense clusters that are largely inaccessible to the host. However, upon additional upregulation of the GlgB branching enzyme, the branching of the polysaccharide is able to keep speed with the synthesis of linear chains, eliminating the granule phenotype. This study suggests potential avenues for increasing bacterial polysaccharide production and recovery.ImportanceIn this work, the polysaccharide stores of Escherichia coli were altered through the addition of extra copies of the bacteria’s own polysaccharide synthesis genes. In this way, bacteria were created that produced over twice the level of storage polysaccharide as a control strain, in the form of a granule that could potentially facilitate easy harvest. Another form of mutant Escherichia coli was created that produced over seven times the normal level of storage polysaccharide, and also grew to higher cell densities in liquid culture. In addition to increasing our understanding of glycogen synthesis, it is proposed that similarly modified bacteria, grown on inexpensive waste materials, may be a useful source of starch-like polysaccharides for industrial or agricultural use. In particular, the use of cyanobacterial glycogen as a carbon source for biofuels has recently been gaining interest, and the work presented here may well be applicable in this field.
Federated queries of clinical data repositories: balancing accuracy and privacy
Authors: Yu Yun William , Weber Griffin M 
Published: November 2019

AbstractResearchers use large federated clinical data networks that connect dozens of healthcare organizations to access data on millions of patients. However, because patients often receive care from multiple sites in the network, queries frequently double-count patients. Using the probabilistic streaming algorithm HyperLogLog and adding obfuscation, we developed a scalable method for estimating the number of distinct lives that match a query, which balances accuracy and privacy in a “tunable” way.
Inter-subject phase synchronization differentiates neural networks underlying physical pain empathy
Authors: Xu Lei , Bolt Taylor , Nomi Jason S. , Li Jialin , Zheng Xiaoxiao , Fu Meina , Kendrick Keith M. , Becker Benjamin , Uddin Lucina Q. 
Published: November 2019

AbstractRecent approaches for understanding the neural basis of pain empathy emphasize the dynamic construction of neural networks underlying this multifaceted social cognitive process. Inter-subject phase synchronization (ISPS) is an approach for exploratory analysis of task-based fMRI data that reveals brain networks dynamically synchronized to task-features across participants. We applied ISPS to task-fMRI data assessing vicarious pain empathy in a large sample of healthy participants (n=238). The task employed physical (limb) and affective (faces) painful and corresponding non-painful visual stimuli. ISPS revealed two distinct networks synchronized during physical pain observation, one encompassing anterior insula and midcingulate regions strongly engaged in (vicarious) pain, and another encompassing parietal and inferior frontal regions associated with social cognitive processes which may further modulate and support the physical pain empathic response. No robust network synchronization was observed while processing affective pain, possibly reflecting high inter-individual variation in response to socially transmitted pain experiences. ISPS also revealed networks related to task onset or general processing of physical (limb) or affective (face) stimuli which encompassed networks engaged in object manipulation or face processing, respectively. Together, the ISPS approach permits segregation of networks engaged in different psychological processes, providing additional insight into shared neural mechanisms of empathy for physical pain, but not affective pain, across individuals.
Extracellular vesicles from monocyte/platelet aggregates modulate human atherosclerotic plaque responses
Authors: Oggero S , de Gaetano M , Marcone S , Barry M , Montero-Melendez T , Cooper D. , Norling L V , Brennan E P , Godson G , Perretti M 
Published: November 2019

AbstractIn atherosclerosis, a chronic disease characterized by lipid accumulation, fibrosis and vascular inflammation, extracellular vesicles (EVs) are emerging as key players in different stages of disease development. Here we provide evidence that EVs released by mixed aggregates of monocytes and platelets in response to TNF-α are both CD14+ and CD41+. Tempering platelet activation with Iloprost™ impacted the quality and quantity of EV produced. Proteomics of EVs from cells activated with TNF-α alone or in presence Iloprost™ revealed distinct proteome, with selective hits like gelsolin. EVs from TNF-α stimulated monocytes augmented release of cytokines, and modulated more than 500 proteins by proteomics, when added to human atherosclerotic plaques. In contrast, EVs generated by TNF-α and Iloprost™ produced minimal plaque activation. In conclusion, attenuating platelet activation has an effect on EV composition released from monocyte/platelet aggregates with downstream modulation of their pro-inflammatory actions and contribution to the development and progression of atherosclerosis.
Comparative Genomics and Full-Length TprK Profiling ofTreponema pallidumsubsp.pallidumReinfection
Authors: Addetia Amin , Tantalo Lauren C. , Lin Michelle J. , Xie Hong , Huang Meei-Li , Marra Christina M. , Greninger Alexander L. 
Published: November 2019

AbstractDeveloping a vaccine againstTreponema pallidumsubspeciespallidum, the causative agent of syphilis, remains a public health priority. Syphilis vaccine design efforts have been complicated by lack of an in vitroT. pallidumculture system, prolific antigenic variation in outer membrane protein TprK, and lack of functional annotation for nearly half of the genes. Understanding the genetic basis ofT. pallidumreinfection can provide insights into variation among strains that escape cross-protective immunity. Here, we present comparative genomic sequencing and deep, full-lengthtprKprofiling of twoT. pallidumisolates from blood from the same patient that were collected six years apart. Notably, this patient was diagnosed with syphilis four times, with two of these episodes meeting the definition of neurosyphilis, during this interval. Outside of the highly variabletprKgene, we identified 14 coding changes in 13 genes. Nine of these genes putatively localized to the periplasmic or outer membrane spaces, consistent with a potential role in serological immunoevasion. Using a newly developed full-lengthtprKdeep sequencing protocol, we profiled the diversity of this gene that far outpaces the rest of the genome. Intriguingly, we found that the reinfecting isolate demonstrated less diversity across eachtprKvariable region compared to the isolate from the first infection. Notably, the two isolates did not share any full-length TprK sequences. Our results are consistent with an immunodominant-evasion model in which the diversity of TprK explains the ability ofT. pallidumto successfully reinfect individuals, even when they have been infected with the organism multiple times.Author SummaryThe causative agent of syphilis,Treponema pallidumsubspeciespallidum, is capable of repeat infections in people, suggesting that the human immune response does not develop sufficiently broad or long-lasting immunity to cover treponemal diversity. Here, we examined the genomes from two blood-derived isolates ofT. pallidumderived 6 years apart from a patient who had syphilis four times during the same period to understand the genetic basis of reinfection. We found a paucity of coding changes across the genome outside of the highly variabletprKgene. Using deep profiling of the full-lengthtprKgene, we found surprisingly that the two isolates did not share any full-length TprK sequences.
Zika virus infects pericytes in the choroid plexus and enters the central nervous system through the blood-cerebrospinal fluid barrier
Authors: Kim Jihye , Hetman Michal , Hattab Eyas M. , Joiner Joshua , Alejandro Brian , Schroten Horst , Ishikawa Hiroshi , Chung Dong-Hoon 
Published: November 2019

ABSTRACTZika virus (ZIKV) can infect and cause microcephaly and Zika-associated neurological complications in the developing fetal and adult brains. In terms of pathogenesis, a critical question is how ZIKV overcomes the barriers separating the brain from the circulation and gains access to the central nervous system (CNS). Despite the importance of ZIKV pathogenesis, the route ZIKV utilizes to cross CNS barriers remains unclear.Here we show that in mouse models, ZIKV-infected cells initially appeared in the periventricular regions of the brain, including the choroid plexus and the meninges, prior to infection of the cortex. The appearance of ZIKV in cerebrospinal fluid (CSF) preceded infection of the brain parenchyma. We show that ZIKV infects pericytes in the choroid plexus, and that ZIKV infection of pericytes is dependent on AXL receptor tyrosine kinase. Using an in vitro Transwell system, we highlight the possibility of ZIKV to move from the blood side to CSF side, across the choroid plexus epithelial layers, via a nondestructive pathway (e.g., transcytosis). Finally, we demonstrate that brain infection is significantly attenuated by neutralization of the virus in the CSF, indicating that ZIKV in the CSF at the early stage of infection might be responsible for establishing a lethal infection of the brain. Taken together, our results suggest that ZIKV invades the host brain by exploiting the blood-CSF barrier rather than the blood-brain barrier.AUTHOR SUMMARYZika virus invades the human brains and causes Zika-associated neurological complications; however, the mechanism(s) by which Zika virus accesses the central nerves system remain unclear. Understanding of the cellular and molecular mechanisms will shed light on development of novel therapeutic and prophylactic targets for Zika virus and other neurotropic viruses. Here we use in vivo and in vitro models to understand how Zika virus enters the brain. In mouse models, we found that Zika virus infects pericytes in the choroid plexus at very early stages of infection and neutralization of Zika virus in the cerebrospinal fluid significantly attenuate the brain infection. Further we show evidence that Zika virus can cross the epithelial cell layers in the choroid plexus from the blood side. Our research highlights that ZIKV invades the host brain by exploiting the blood-CSF barrier rather than the blood-brain barrier.
Differences in international accreditation: Kyrgyzstan and Kazakhstan
Authors: Merrill Martha 
Published: November 2019

Purpose
The purpose of this paper is twofold: first, to count the number of international program accreditations at universities in Kyrgyzstan and Kazakhstan; and second, to understand why Kazakhstan has dramatically more such accreditations.

Design/methodology/approach
The methodology included identifying agencies working in each country, reviewing data on their websites, and analyzing government documents and relevant literature.

Findings
Findings were that Kazakhstan has 645 international program accreditations and Kyrgyzstan has 9. Analysis of the reasons for this difference includes strong government support and incentives for internationalization of higher education in Kazakhstan, furthering the government’s goal of becoming one of the world’s 30 most developed economies by 2050; Kazakhstan’s financial wherewithal to support internationalization policies; and its membership in the Bologna Process. In Kyrgyzstan, on the other hand, few rewards result from the costly and time-consuming process of international accreditation; only programs with existing international connections or institutions with large international student populations seem interested.

Research limitations/implications
Limitations are that the research was based on document analysis and did not include interviews with staff of programs seeking international accreditation.

Practical implications
One implication, i.e., international program accreditation, while an indicator of program quality, also denotes the financial and infrastructural wherewithal to carry it out, plus the perceived benefits and costs of doing so.

Originality/value
The value of this research is that it analyzes the reasons for divergence and different results in two countries that, 25 years ago, were part of the same higher education system.
Anthropomorphized vs objectified brands: which brand version is more loved?
Authors: Delgado-Ballester Elena , Palazón Mariola , Peláez Jenny 
Published: November 2019

PurposeThe purpose of this paper is to deal with the role of the human metaphor (anthropomorphism) and consumers’ liking for the humanized version of the brand as antecedents of three key components of brand love: self-brand integration, positive emotional connection and feelings of anticipated separation distress.Design/methodology/approachA sample of 399 consumers provided information about a brand from a stated list of 16 brands of clothing.FindingsBoth anthropomorphism and consumers’ liking for the humanized brand have positive effects on specific components of brand love. The results confirm that brand anthropomorphism is only desirable when the humanized version of the brand is attractive for consumers.Research limitations/implicationsA potential shortcoming is the qualitative technique employed to observe anthropomorphic thought. Collecting ratings of anthropomorphic and non-anthropomorphic traits could be viewed as a method more easily applied in market research surveys.Practical implicationsManagers have to control how consumers imagine the brand as a human entity because it affects brand love. For example, by tracking consumers’ opinions and traits of those people associated with the brand and brand user stereotypes can condition consumers’ imagination of the humanized brand.Originality/valueCompared to the limited number of studies about the relationship between anthropomorphism and brand love, this study focuses on the effects of anthropomorphism as a process, and not as a personal trait, on brand love. It also relies on consumers’ imagination instead of brand personification strategies to stimulate anthropomorphism.
Navigating ethnic entrepreneurship in religion and culture meld
Authors: Ojo Sanya 
Published: November 2019

PurposeThe purpose of this paper is to examine ethnic entrepreneurship within the contexts of religion, cultural hybridity, segregation, diasporic network and enterprise.Design/methodology/approachThe study collected two sets of data from 15 black African respondents/entrepreneurs through face-to-face interviews in London, UK.FindingsFindings point to immigrants’ entrepreneurial adaptation through traditional and dogmatic interpretations of religious beliefs in the informal sector.Originality/valueThe paper offers fresh insights into the religion/faith and socio-cultural meld in the sagacity of black African entrepreneurship. Such insights afford great opportunities to construct new sites of meaning or frame new explanations of entrepreneurship among the ethnic group – using religion and culture as important environmental munificence.