bluuebunny/crossref_metadata_2025 huggingface dataset:
Landscape Heterogeneity and Dynamics
Authors: With Kimberly A.
Published: August 2019

Heterogeneity is a defining characteristic of landscapes and therefore central to the study of landscape ecology. Landscape ecology investigates what factors give rise to heterogeneity, how that heterogeneity is maintained or altered by natural and anthropogenic disturbances, and how heterogeneity ultimately influences ecological processes and flows across the landscape. Because heterogeneity is expressed across a wide range of spatial scales, the landscape perspective can be applied to address these sorts of questions at any level of ecological organization, and in aquatic and marine systems as well as terrestrial ones. Disturbances—both natural and anthropogenic—are a ubiquitous feature of any landscape, contributing to its structure and dynamics. Although the focus in landscape ecology is typically on spatial heterogeneity, disturbance dynamics produce changes in landscape structure over time as well as in space. Heterogeneity and disturbance dynamics are thus inextricably linked and are therefore covered together in this chapter.
Landscape Pattern Analysis
Authors: With Kimberly A.
Published: August 2019

The analysis of landscapes and other spatial patterns is a major focus of landscape ecology, being essential to the study of how landscape patterns affect ecological processes. Landscape pattern analysis has become a sine qua non for environmental monitoring, natural resource management, landscape planning, sustainable development, and species conservation. The intensification of human land use is a major global-change issue, requiring an in-depth analysis of how landscapes are being transformed over time, as well as how anthropogenic disturbances compare to the natural disturbance regime. This chapter covers the types and availability of landscape data, such as from historical land surveys and remote sensing; how spatial data are processed and manipulated within a Geographical Information System (GIS); and finally, how to analyze landscape structure using landscape metrics and spatial statistics, including a discussion of best practices.
Landscape Effects on Population Spatial Spread
Authors: With Kimberly A.
Published: August 2019

Range expansions, biological invasions, and disease spread are all inherently spatial processes that involve the successful introduction or colonization, establishment, and dispersal of organisms (or their propagules) into new areas. Population spatial spread thus involves the interaction of both dispersal and demography with landscape structure. This chapter begins by exploring landscape effects on species’ range shifts and the extent to which species can shift their distributions in response to future land-use and climate-change scenarios. Next, the chapter evaluates the effect that landscape structure might have on invasive spread, including an overview of spatial models that are used to predict whether, when, and how fast an invasive species is likely to spread. The chapter concludes with a discussion of disease spread in a landscape context (landscape epidemiology), which involves the study of how pathogens, vectors, and hosts interact with environmental heterogeneity to influence the incidence and persistence of disease in an area.
Landscape Effects on Ecosystem Structure and Function
Authors: With Kimberly A.
Published: August 2019

Landscape ecosystem ecology is concerned with the study of how landscape structure affects ecosystem structure and function, and how landscape heterogeneity in turn is generated or sustained by the redistribution of nutrients or organisms within and among ecosystems. This chapter begins with an overview of how landscape context influences ecosystem processes, including the effects of land management and land-cover change on nutrient dynamics and productivity. Next, the chapter considers the linkages among systems (metaecosystems) and how spatial subsidies are important for understanding ecosystem function in a landscape context. The chapter then explores under what conditions landscape function becomes disrupted, possibly precipitating irreversible system state changes, before concluding with a clarion call for landscape sustainability; that is, landscape management that preserves the productivity, multifunctionality, and ecological resilience of landscapes in the face of future societal demands, intensifying land use, and rapid climate change.
Collectives and Their Duties
Authors: Collins Stephanie
Published: August 2019

This chapter fleshes out the Tripartite Model’s conception of collectives and defends the attribution of duties to them. It begins by giving a detailed characterization of collectives and explaining how they have the specifically moral type of agency that’s at issue in duties. It explains that this conception of collectives is permissive (i.e. its conditions are easy to satisfy). The conception is compared with other prominent accounts of corporate agency or personhood. The final section argues in favour of including collectives’ duties within our ontology. This argument has two planks. First, collectives are able to make decisions based on duties. Second, those decisions are to produce an outcome that would not be produced if each of the collective’s members severally made decisions: the outcome of robust multilateralism (coordinated role-performance) amongst members. At a general level of description, a collective’s duty will be a duty to produce multilateralism amongst members—a decision that no member can sensibly take on their own.
Monetary Policy in the Digital Age
Authors: Zimmermann Claus D.
Published: August 2019

The potential of digital money to replace state-issued fiat money as the predominant means of payment for retail goods combined with its ability to flow freely across international borders is increasingly attracting attention among central bankers, the media, and scholars. The concern is that central banks could lose control over the monetary aggregates regulating the money supply for conducting monetary policy. This chapter examines important regulatory challenges that arise from the increasing use of virtual currency systems. Stable monetary regimes are expected to provide a level of resilience against three types of monetary stability risks: (i) structural ‘deflation’; (ii) lacking flexibility to respond to temporary shocks to money demand; and (iii) failing to fulfil the traditional key function of lender of last resort. It is against these three types of risks that the sustainability of virtual currency systems can be assessed. The chapter concludes that, as they attract increasing attention and account for increasing volumes of financial flows, virtual currency schemes may ultimately have to become subject to increasingly tight regulation on a global level.
Banking in a Digital Fiat Currency Regime
Authors: Grey Rohan
Published: August 2019

This chapter explores the future of banking in a digital fiat currency (‘DFC’) regime, defined as a monetary regime in which retail and wholesale consumers have direct access to public digital checking and payments services, independent of the existing bank-centric depository system. I argue that in such a regime, existing banks will continue to perform the valuable social function of underwriting loans and evaluating collateral, even as their checking and payments processing functions will be rendered obsolete. Such a system would improve payments system resiliency, while addressing the safe asset shortage issues associated with insurance caps on bank deposit accounts. At the same time, a DFC regime would necessarily clarify the public nature of the existing credit system, wherein commercial banks are (inherently) entrusted to underwrite loans and subjectively evaluate collateral. Thus, digital fiat currency technology represents more than a mere improvement in payment system efficiency—it has the potential to transform the banking industry, simplify financial regulation, and recast our collective understanding of how money and banking work in the modern economy.
‘Many Contests of the Trojans and Achaeans’: The Iliad’s Battle Books
Authors: Myers Tobias
Published: August 2019

Chapter 4 charts the continued use of the divine perspective to shape and reflect upon the dynamics of performance between Books 8 and 22. In these books, Homer continues to draw on the duel, daïs, and funerary paradigms to construct the battlefield contests as a live event commanding audience participation. The chapter’s first section examines patterns of divine and poetic ‘staging’, to demonstrate that the next three days of battle (in Books 8, 11–18, and 19–22 respectively), like the first day’s battle, are not only viewed from Zeus’ house on Olympus, but also closely patterned on the formal duel. The second section considers the significance of this strategy for the listening audience whom the poet is attempting to engage: they are invited to participate vicariously in the fighting, and also to reflect on their responses to the figure pulling the strings. The chapter’s third section focuses on the poet’s use of Zeus, primarily, to develop a perspective from which the contests trigger associations with funerary ritual. The chapter concludes with a metaperformative reading of the theomachia (‘battle of the gods’): the theomachia draws in new ways on both the duel and daïs paradigms, to present a provocative dramatization of poet-audience dynamics.
Past, Present, and Persecution
Authors: Harper Steven C.
Published: August 2019

Every memory has a culture, and Joseph Smith’s best-known account of his first vision (the 1838/39 account) consolidated in a hostile environment. Smith and his people were driven from Missouri by the governor’s executive order, he was jailed during the winter of 1838–39, and then he escaped to reunite with his exiled followers in Illinois. There he and associates renewed work on a manuscript history that begins with a defensive and defiant account of his first vision. The saints eventually canonized this version of Smith’s memory. It shapes their identity as a people persecuted for transcending creedal Christianity and accessing God directly. That outcome was not inevitable.
First Communication
Authors: Harper Steven C.
Published: August 2019

The long shadow cast by the minister’s rejection explains why Smith’s memory formed and re-formed as it did in the context of later experiences. In 1835 Joseph Smith consolidated, and his scribe recorded, a spontaneous memory of his first vision. It differs markedly from his other accounts primarily because it was cued spontaneously by a conversation, not by a premeditated effort to record autobiography. It shows that, given the right cues and context, he could make a memory that did not need to respond to the Methodist minister, whether to please him (as in 1832) or to rebuke him (as in 1838/39).
Extract from His History
Authors: Harper Steven C.
Published: August 2019

Joseph Smith grew up in a visionary family that lived in a visionary culture, but nothing in the historical record reveals that he told his family about his first vision in the 1820s. Many modern saints easily recall that, when Smith returned home after his vision, he told his mother. But all the historical record—an 1842 redaction to the 1838/39 account—says is that he told his mother what he learned, not how. There is no evidence that he told anyone but the Methodist minister for a decade. There is no known evidence of him relating his experience to family members or others. In 1832, Smith remembered that he could find no one that believed him.
Straightforward Recital
Authors: Harper Steven C.
Published: August 2019

Artistically written recursions of Joseph Smith’s first vision also began to appear in the 1880s, particularly through George Cannon and Andrew Jenson. These stories, while not intended to be historical representations, reflected and contributed to the recursion of collective memory and its transmission to the next generation. Distortion, while inevitable with retellings, occurs as the remembering entity favors coherence over accuracy. Forging collective memory from art, music, and print created by a shared memory and a multitude of individual ones, each inevitably distorted compared to Joseph Smith’s own memories of his first vision. But for all that, the collective memory the saints forged became incredibly strong, resilient, and extremely well known to them.
The Joseph (F.) Smith Story
Authors: Harper Steven C.
Published: August 2019

Following the death of Lorenzo Snow in 1901, Joseph F. Smith was next in the line of prophetic successors. Joseph F. became the prophet and president of The Church of Jesus Christ of Latter-day Saints in autumn. He ramped up efforts to commemorate Joseph Smith’s birthday and especially to rehearse his first vision. In the turn-of-the-century crisis that threatened to undermine Mormonism, Joseph F. Smith’s selection, relation, and repetition of the story of his uncle’s first vision helped the saints navigate their way to a new narrative, one in which plural marriage could be relinquished without eroding the saints’ faith in revelations received by their prophets past or present.
Under Attack
Authors: Harper Steven C.
Published: August 2019

Drawing on newly discovered accounts (1832, 1835) and lots of contextual research, James Allen and Milton Backman added an alternative memory to the buffer on which the saints could draw for memory resources. Believing historians formed a faithful, complex understanding of Smith’s vision that accounted for the incongruity the critics saw in the historical record. The believing historians selected and related new items to old ones. They showed how new elements could be integrated recursively with the long-established story. The laity hardly noticed, however. Compared to the expanding number of Mormons whose conversions were often tied to the canonized account of Smith’s first vision, Mormon historians were a tiny minority. Publishing their findings did almost nothing to alter the Mormon collective memory or make it more resilient to critics. The disruptive potential of the newly discovered records and ways of interpreting them remained latent, waiting for an information age to unleash it.
Afterword
Authors: Harper Steven C.
Published: August 2019

By 2015, Latter-day Saints were beginning to consolidate a more resilient cultural memory of Smith’s vision based on unabashed selection, relation, and repetition of Smith’s accounts in church curriculum. Curriculum a generation earlier had avoided any potential first vision controversies. Richard Bushman’s biography of Joseph Smith had been banned, not his interpretation of Smith’s accounts was the curriculum, having been officially selected, related, and repeated via media that was much more likely than a lecture or a textbook to modulate memory formation in young Latter-day Saints. The consolidation of their shared memory will take time. So will the recursion process by which elements are added or subtracted and new memories form. Within a generation, relatively few saints will remember any of the earlier versions of their shared knowledge. This book will preserve those memories.
Some Thoughts on Domestic Violence
Authors: Chakravarti Uma
Published: August 2019

By placing violence within structural relationships that form a part, and support patriarchal hierarchies within the family, the author demonstrates how violence against women is central to maintaining men’s power and privilege over the women at home. Historically, socially and culturally there has been a complete normalization of the violence men have inflicted upon women within the household. Husbands, fathers, brothers all use violence when their self-assumed authority appears to be challenged, while women do not speak about the violence, often, because it is associated with some wrongdoing on their part. Change began only when women began to question such violence. The chapter traces the progress in jurisprudence on domestic violence over the years, reflecting on the deep-rooted patriarchal attitude persistent in courts, and current approaches to addressing domestic violence in an environment where backlash continues to prejudice women’s fight against domestic violence.
Innovative Global Health Care Experiences for Nursing Students: Microsemesters and Internships
Authors: Graber Jennifer S. , Saylor Jennifer , Johnson Amy N.
Published: August 2019

Global experiential learning using clinical internships and microsemesters is expanding in nursing as an alternative to full-semester study abroad. When incorporated into the curriculum, students have a broader perspective on global health care issues. For example, students learn historic and cultural concepts that are uniquely Australian while studying diversity in a condensed two-week microsemester. We describe the development and incorporation of global internships and alternative global experiences for undergraduate nursing students.
Colorectal cancer risk factors in asymptomatic Chilean population: a survey of international collaboration between Japan and Chile
Authors: Okada Takuya , Odagaki Tomoyuki , López-Köstner Francisco , Zárate Alejandro J. , Ponce Alejandra , Kronberg Udo , Karelovic Stanko , Flores Sergio , Estela Ricardo , Ito Takashi , Yasuno Masamichi , Uetake Hiroyuki , Kojima Kazuyuki , Kitagawa Masanobu
Published: August 2019

In Chile, the mortality from colorectal cancer has been on the rise. A national screening program based on a fecal immunochemical test was started in 2012 as an international collaboration with Japan. This case-control study was designed to identify the risk factors for colorectal cancer, with a goal of increasing the participation rate for colorectal cancer screening. In accordance with the Strengthening the Reporting of Observational Studies in Epidemiology guidelines, we conducted a case-control study from 2012 to 2017; 23 845 asymptomatic participants were enrolled in the study. Participants who were fecal immunochemical test-positive or had a family history of colorectal cancer underwent a colonoscopy. We analyzed the odds ratio of the risk factors for colorectal cancer, including sex, age, family history, BMI, hypertension, diabetes, regular use of nonsteroidal anti-inflammatory drugs, alcohol consumption, smoking, physical activity, and daily intake of certain food items. For the screening program, 202 cases of colorectal cancer were detected, and 195 of them were evaluated pathologically after resection. Of these, 173 cases (88.7%) had colorectal cancer stage 0/1, 151 (77.4%) of which were treated with endoscopic resection. In the multivariate analysis, male sex, family history of colorectal cancer, and low intake of cereals or fibers were closely related to a high colorectal cancer incidence. Moreover, participants in their 60s and 70s had a higher incidence of colorectal cancer than those in their 50s. These results suggest that intensive screening of the high-risk population can help in improving the detection of colorectal cancer, whereas higher consumption of cereals or fibers can be effective in preventing its onset.
Adaptation to life on land at high O2via transition from ferredoxin-to NADH-dependent redox balance
Authors: Gould S. B. , Garg S. G. , Handrich M. , Nelson-Sathi S. , Gruenheit N. , Tielens A. G. M. , Martin W. F.
Published: August 2019

Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function—redox balance—served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2levels (21% v/v),Chlamydomonas reinhardtiiexpresses them with diurnal regulation. High O2environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.
Amycolatopsis eburnea sp. nov., an actinomycete associated with arbuscular mycorrhizal fungal spores
Authors: Chaiya Leardwiriyakool , Matsumoto Atsuko , Wink Joachim , Inahashi Yuki , Risdian Chandra , Pathom-aree Wasu , Lumyong Saisamorn
Published: August 2019

A novel actinomycete, designated strain GLM-1T, was isolated from arbuscular mycorrhizal fungal spores from Funneliformis mosseae RYA08, collected from Aquilaria crassna Pierre ex Lec. rhizosphere soil in Klaeng, Rayong Province, Thailand. Morphological characteristics of this strain included long chains of rod-like cells and squarish elements. The cell-wall composition of this novel isolate contained meso-diaminopimelic acid. The whole-cell diagnostic sugars were arabinose and galactose. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 and iso-C15 : 0. Only phosphatidylethanolamine was detected as a polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GLM-1T was closely related to

Amycolatopsis rhabdoformis

SB026T (99.11 %) with a low DNA–DNA hybridization value of 22.6–34.7 %. Genome sequencing revealed a genome size of 10 Mbp. There were obvious distinctions in the average nucleotide identity values between stain GLM-1T and its closely related strains at around 86–93 % (ANIb) and 89–94 % (ANIm). The digital DNA–DNA hybridization values between strain GLM-1T and type strains of phylogenetically related species were 34–55 %. The G+C content of the genomic DNA was 71.8 mol%. Based on these data, strain GLM-1T is considered to represent a novel species of the genus

Amycolatopsis

, for which the name

Amycolatopsis
eburnea sp. nov. is proposed. The type strain is GLM-1T (=TBRC 9315T=NBRC 113658T)
Behavioural mechanisms underlying the evolution of cooperative burrowing inPeromyscusmice
Authors: Bedford Nicole L. , Weber Jesse N. , Tong Wenfei , Baier Felix , Kam Ariana , Greenberg Rebecca A. , Hoekstra Hopi E.
Published: August 2019

While some behaviours are largely fixed and invariant, others can respond flexibly to different social contexts. Here, we leverage the unique burrowing behaviour of deer mice (genusPeromyscus) to investigate if and how individuals of three species adapt their behaviour when digging individually versus with partners. First, we find that pairs of mice from monogamous (P. polionotus) but not promiscuous (P. maniculatus, P. leucopus) species cooperatively construct burrows that are approximately twice as long as those dug by individuals and similar in size to burrows found in the wild. However, the length of burrows built byP. polionotuspairs differs: opposite-sex pairs construct longer burrows than same-sex pairs. By designing a novel behavioural assay in which we can observe and measure burrowing behaviour directly, we find that longer burrows are achieved not by changing individual behaviour, but instead because opposite-sex pairs are more socially cohesive and thus more likely to dig simultaneously, which is a more efficient mode of burrow elongation. Thus, across social contexts, individual burrowing behaviour appears largely invariant, even when the resultant burrow from pairs of mice differs from expectation based on individual behaviour, underscoring the fixed nature of burrowing behaviour inPeromyscusmice.
Electrochemical Roughening and Carbon Nanotube Coating of Tetrodes for Chronic Single-Unit Recording
Authors: Xia Zifeng , Arias-Gil Gonzalo , Deckert Martin , Vollmer Maike , Curran Andrew , Herrera-Molina Rodrigo , Brosch Marcel , Krug Kristine , Schmidt Bertram , Ohl Frank W. , Lippert Michael T. , Takagaki Kentaroh
Published: August 2019

Recording from single neurons in the brain for long periods of time has been a central goal in both basic neuroscience and translational neurology, in order to understand mechanisms underlying brain processes such as learning and to understand the pathogenesis of neurodynamic disease states 1. Recent advances in materials engineering, digital signal acquisition, and analysis algorithms have brought us closer to achieving this goal, and the possibility has gathered much public attention 2,3. However, it remains a challenge to record from the same units for weeks to months. Here, we record many high-quality tetrode neuronal signals reliably over long periods of time in both deep and superficial areas of the brain. We achieve this by combining electrochemical roughening and carbon nanotube coating of a flexible platinum/iridium substrate, with materials, packaging, and insertion optimized to minimize tip movement with brain pulsation. This “Magdeburger” probe enables recordings with long-term signal stability and high signal-to-noise ratio at a reasonable cost in both rodent brains and in substantially larger primate brains. Robust tetrode tracking of identified neurons over longer time periods, in multiple independently targeted areas of the brain, will allow fundamental advances in the study of cognitive learning, aging, and pathogenesis, and opens new possibilities for brain interfaces in humans.
Detection of Enterovirus D68 in wastewater samples from the United Kingdom during outbreaks reported globally between 2015 and 2018
Authors: Majumdar Manasi , Wilton Thomas , Hajarha Yara , Klapsa Dimitra , Martin Javier
Published: August 2019

Detection of enterovirus D68 (EV-D68) in wastewater samples from the UK between December 2014 and December 2018 showed a marked seasonal distribution with a high proportion of samples containing EV-D68 during periods when identification of this virus in clinical samples was most common. This includes a recent upsurge of EV-D68 detection in respiratory samples from the United Kingdom between August and December 2018 associated with cases of acute flaccid myelitis, following similar reports in the USA. Phylogenetic analysis of EV-D68 sewage strains demonstrated that strains belonging to distinct genetic clades followed the same temporal distribution as that observed for EV-D68 clinical strains in the UK and that they showed very close genetic relationship with EV-D68 strains circulating elsewhere in the world during the same periods. The results demonstrated a clear association between detecting EV-D68 in wastewater and finding it in clinical samples which was somehow unexpected given that EV-D68 is rarely detected in stool samples. We conclude that the use of environmental surveillance is a valuable tool to detect and monitor outbreaks due to EV-68 infection.
Bayesian semi-nonnegative matrix tri-factorization to identify pathways associated with cancer phenotypes
Authors: Park Sunho , Kar Nabhonil , Cheong Jae-Ho , Hwang Tae Hyun
Published: August 2019

Accurate identification of pathways associated with cancer phenotypes (e.g., cancer sub-types and treatment outcome) could lead to discovering reliable prognostic and/or predictive biomarkers for better patients stratification and treatment guidance. In our previous work, we have shown that non-negative matrix tri-factorization (NMTF) can be successfully applied to identify pathways associated with specific cancer types or disease classes as a prognostic and predictive biomarker. However, one key limitation of non-negative factorization methods, including various non-negative bi-factorization methods, is their lack of ability to handle non-negative input data. For example, many molecular data that consist of real-values containing both positive and negative values (e.g., normalized/log transformed gene expression data where negative value represents down-regulated expression of genes) are not suitable input for these algorithms. In addition, most previous methods provide just a single point estimate and hence cannot deal with uncertainty effectively.

To address these limitations, we propose a Bayesian semi-nonnegative matrix trifactorization method to identify pathways associated with cancer phenotypes from a realvalued input matrix, e.g., gene expression values. Motivated by semi-nonnegative factorization, we allow one of the factor matrices, the centroid matrix, to be real-valued so that each centroid can express either the up- or down-regulation of the member genes in a pathway. In addition, we place structured spike-and-slab priors (which are encoded with the pathways and a gene-gene interaction (GGI) network) on the centroid matrix so that even a set of genes that is not initially contained in the pathways (due to the incompleteness of the current pathway database) can be involved in the factorization in a stochastic way specifically, if those genes are connected to the member genes of the pathways on the GGI network. We also present update rules for the posterior distributions in the framework of variational inference. As a full Bayesian method, our proposed method has several advantages over the current NMTF methods which are demonstrated using synthetic datasets in experiments. Using the The Cancer Genome Atlas (TCGA) gastric cancer and metastatic gastric cancer immunotherapy clinical-trial datasets, we show that our method could identify biologically and clinically relevant pathways associated with the molecular sub-types and immunotherapy response, respectively. Finally, we show that those pathways identified by the proposed method could be used as prognostic biomarkers to stratify patients with distinct survival outcome in two independent validation datasets. Additional information and codes can be found at https://github.com/parks-cs-ccf/BayesianSNMTF.
Expression of oxytocin receptors in the zebra finch brain during vocal development
Authors: Davis Matthew T. , Grogan Kathleen E. , Maney Donna L.
Published: August 2019

Juvenile male zebra finches memorize and learn to sing the song of a male caregiver, or “tutor”, during a complex vocal learning process. Juveniles are highly motivated to interact socially with their tutor, and these interactions are required for effective vocal learning. It is currently unknown what neurological mechanisms underlie attraction to tutors, but social motivation and affiliation in this and other species may be mediated by oxytocin and related nonapeptides. Here, we used qPCR to quantify expression of oxytocin receptor (OTR) mRNA in the lateral septum, auditory forebrain, and regions of the song control system in zebra finches throughout post-hatch development and vocal learning. We found that zebra finches express OTR mRNA in these regions from post-hatch day 5 to adulthood, encompassing the entire period of auditory and sensorimotor learning. We also mapped the binding of 125I-ornithine vasotocin, an oxytocin receptor antagonist that binds to oxytocin receptors in songbird brain, to understand the neuroanatomical distribution of oxytocin-like action during vocal development. This study provides the groundwork for the use of zebra finches as a model for understanding the mechanisms underlying social motivation and its role in vocal development.
Neuromuscular fatigue and recovery after strenuous exercise depends on skeletal muscle size and stem cell characteristics
Authors: Baumert P. , Temple S. , Stanley J.M. , Cocks M. , Strauss J.A. , Shepherd S.O. , Drust B. , Lake M.J. , Stewart C.E. , Erskine R.M.
Published: August 2019

Hamstring muscle injury is highly prevalent in sports involving repeated maximal sprinting. Although neuromuscular fatigue is thought to be a risk factor, the mechanisms underlying the fatigue response to repeated maximal sprints are unclear. Here, we show that repeated maximal sprints induce neuromuscular fatigue accompanied with a prolonged strength loss in hamstring muscles. The immediate hamstring strength loss was linked to both central and peripheral fatigue, while prolonged strength loss was associated with indicators of muscle damage. The kinematic changes immediately after sprinting likely protected fatigued hamstrings from excess elongation stress, while larger hamstring muscle physiological cross-sectional area and lower myoblast:fibroblast ratio appeared to protect against fatigue/damage and improve muscle recovery within the first 48 h after sprinting. We have therefore identified novel mechanisms that likely regulate the fatigue/damage response and initial recovery following repeated maximal sprinting in humans.
Constrution of a genetic map of rils derived from wheat (T. aestivumL.) varieties pamyatii azieva x paragon using high-throughput snp genotyping platform kasp -competative allele specific PCR
Authors: Yermekbayev K , Griffiths S , Chettry M , Liverington-Waite M , Orford S , Amalova A , Abugalieva S , Turuspekov Y
Published: August 2019

The main purposes of the study were i) to develop a first mapping population for bread wheat grown in Kazakhstan, ii) to construct its genetic map for further identification of genes associated with important agronomic traits.

To the best of our knowledge this is the first segregating population and genetic map developed for Kazakh bread wheat. The work is an example of how plant breeding programs in Kazakhstan have started successfully deploying next generation plant breeding methods.

The KASP (Compatative Allele Specific PCR) technology of LGC Group and SNP DNA-markers have been exploited to genotype and build a genetic map of the segregating population. The total length of the map was 1376 cM. A total 157 out of initial 178 SNP markers used formed 26 linkage groups leaving 1 duplicated and 20 unassigned markers. The threshold distance between markers was set ≤ 30 cM. Therefore, two linkage groups were obtained for chromosomes such as 2A, 2B, 2D, 3A, 5A, 6B and 7A. Despite one duplicated and 20 unassigned markers, the 157 KASP SNP markers that were mapped spanned A, B and D genomes of wheat. Kosambi Mapping function was employed to calculate recombination units between makers. RILs were developed through SSD method up to F4 generation. Almost 97% of identified alleles were useful in evaluating the population’s genetic diversity; the remaining 3% showed no outcome. As a result, 77 DNA markers were mapped for A, 74 for B and 27 for D genomes. The mapping population will be genotyped using high marker density array planform such as Illumina iSelect to obtain a genetic map with a relatively high coverage. Then, the population and high-resolution genetic map will be used to identify genes influencing wheat adaptation in Kazakhstan.
An ultrasensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data
Authors: Chen Si-Yi , Zhang Qiong , Liu Chun-Jie , Guo An-Yuan
Published: August 2019

T-cell receptors (TCRs) recognizing antigens play vital roles in T-cell immunology. Surveying TCR repertoires by characterizing complementarity-determining region 3 (CDR3) can provide valuable insights into the immune community underlying pathologic conditions, which will benefit neoantigen discovery and cancer immunotherapy. Here we present a novel tool named CATT, which can apply on TCR sequencing (TCR-Seq), RNA-Seq, and single-cell TCR(RNA)-Seq data to characterize CDR3 repertoires. CATT integrated maximum-network-flow based micro-assembly algorithm, data-driven error correction model, and Bayes classification algorithm, to self-adaptively and ultra-sensitively characterize CDR3 repertoires with high accuracy. Benchmark results of datasets from in silico and real conditions demonstrated that CATT showed superior recall and precision compared with other prevalent tools, especially for datasets with short read length and small data size. By applying CATT on a TCR-Seq dataset from aplastic anemia patients, we found the skewing of TCR repertoire was due to the oligoclonal expansion of effector memory T-cells. CATT will be a powerful tool for researchers conducting TCR and immune repertoire studies. CATT is freely available at http://bioinfo.life.hust.edu.cn/CATT.
The sodium leak channel complex is modulated by voltage and extracellular calcium
Authors: Chua Han Chow , Wulf Matthias , Weidling Claudia , Rasmussen Lise Pilgaard , Pless Stephan Alexander
Published: August 2019

The sodium leak channel (NALCN) is essential for survival in mammals: NALCN mutations are life-threatening in humans and knockout is lethal in mice. However, the basic functional and pharmacological properties of NALCN have remained elusive. Here, we found that the robust function of NALCN in heterologous systems requires co-expression of UNC79, UNC80 and FAM155A. The resulting NALCN channel complex is constitutively active, conducts monovalent cations but is blocked by physiological concentrations of extracellular divalent cations. Our data support the notion that NALCN is directly responsible for the increased excitability observed in a variety of neurons in reduced extracellular Ca2+. Despite the smaller number of voltage-sensing residues in the putative voltage sensors of NALCN, the channel complex shows voltage-dependent modulation of the constitutive current, suggesting that voltage-sensing domains can give rise to a broader range of gating phenotypes than previously anticipated. Our work points towards formerly unknown contributions of NALCN to neuronal excitability and opens avenues for pharmacological targeting.

Highlights

Function of NALCN requires UNC79, UNC80 and FAM155A

The complex is permeable to monovalent cations, but is blocked by divalent cations

The complex displays a constitutively active, voltage-modulated current phenotype

Positively charged side chains in S4 of NALCN VSD I and II confer voltage sensitivity
Stromal ISLR promotes intestinal regeneration and cancer by suppressing epithelial Hippo signaling via FAT1
Authors: Xu Jiuzhi , Tang Yang , Sheng Xiaole , Tian Yuhua , Deng Min , Du Sujuan , Lv Cong , Song Yongli , Lou Pengbo , Luo Yongting , Li Yuan , Zhang Bing , Chen Yanmei , Liu Zhanju , Cong Yingzi , Plikus Maksim V. , Meng Qingyong , Zhou Zhaocai , Yu Zhengquan
Published: August 2019

The YAP signaling activation in epithelial cells is essential for intestinal regeneration and tumorigenesis. However, the molecular mechanism linking stromal signals to YAP-mediated intestinal regeneration and tumorigenesis is poorly defined. Here we report a stroma-epithelia YAP signaling axis essential for stromal cells to modulate epithelial cell growth during intestinal regeneration and tumorigenesis. Specifically, upon inflammation and in cancer, an oncogenic transcription factor ETS1 in stromal cells induces expression of a secreted protein ISLR that can directly binds to a transmembrane protocadherin FAT1 on the surface of epithelial cells. This binding suppressed the Hippo signaling by disrupting MST1-FAT1 association, resulting in YAP signaling activation. Deletion of Islr in stromal cells in mice markedly impaired intestinal regeneration, and suppressed tumorigenesis in the colon. Moreover, the expression of stromal cell-specific ISLR and ETS1 significantly increased in inflamed mucosa of human IBD patients and in human colorectal adenocarcinoma, accounting for the epithelial YAP hyperactivation. Collectively, our findings uncovered a molecular mechanism governing signals for communication between stroma and epithelium during tissue regeneration and tumorigenesis.
Gene networks and expression quantitative trait loci associated with platinum-based chemotherapy response in high-grade serous ovarian cancer
Authors: Choi Jihoon , Tarnouskaya Anastasiya , Nesdoly Sean , Topouza Danai G. , Koti Madhuri , Duan Qing Ling
Published: August 2019

Background

A major impediment in the treatment of ovarian cancer is the relapse of platinum-resistant tumors, which occurs in approximately 25% of patients. A better understanding of the biological mechanisms underlying platinum-based response will improve treatment efficacy through genetic testing and novel therapies.

Methods

Using data from high-grade serous ovarian carcinoma (HGSOC) patients in the Cancer Genome Atlas (TCGA), we classified those who remained progression-free for 12 months following platinum-based chemotherapy as “chemo-sensitive” (N=160) and those who had recurrence within six months as “chemo-resistant” (N=110). Univariate and multivariate analysis of expression microarrays identified differentially expressed genes and co-expression gene networks associated with chemotherapy response. Moreover, we integrated genomics data to determine expression quantitative trait loci (eQTL).

Results

Differential expression of the Valosin-containing protein (VCP) gene and five co-expression gene networks were associated with chemotherapy response in HGSOC. VCP and the gene networks contribute to protein processing in the endoplasmic reticulum, which has been implicated in chemotherapy response. These findings were successfully replicated using independent replication cohort. Furthermore, 192 QTLs were associated with these gene networks and BRCA2 expression.

Conclusion

This study implicates both known and novel genes as well as biological networks underlying response to platinum-based chemotherapy among HGSOC patients.
Trading Genome Vulnerability for Stable Genetic Inheritance: Active Retrotransposons Help Maintain Pericentromeric Heterochromatin Required for Faithful Cell Division
Authors: Hao Yajing , Wang Dongpeng , Wu Shuheng , Li Xiao , Shao Changwei , Zhang Peng , Chen Jia-Yu , Lim Do-Hwan , Fu Xiang-Dong , He Shunmin , Chen Runsheng
Published: August 2019

Retrotransposons are extensively populated in vertebrate genomes, which, when active, are thought to cause genome instability with potential benefit to genome evolution. Retrotransposon-derived RNAs are also known to give rise to small endo-siRNAs to help maintain heterochromatin at their sites of transcription; however, as not all heterochromatic regions are equally active in transcription, it remains unclear how heterochromatin is maintained across the genome. Here, we attack these problems by defining the origins of repeat-derived RNAs and their specific chromatin registers inDrosophilaS2 cells. We demonstrate that repeat RNAs are predominantly derived from active Gypsy elements, and upon their processing by Dicer-2, these endo-siRNAs act incisandtransto help maintain pericentromeric heterochromatin. Remarkably, we show that synthetic repeat-derived siRNAs are sufficient to rescue Dicer-2 deficiency-induced defects in heterochromatin formation in interphase and chromosome segregation during mitosis, thus demonstrating that active retrotransposons are actually required for stable genetic inheritance.
The Impact of Genetic Background and Cell Lineage on the Level and Pattern of Position Effect Variegation
Authors: Wang Sidney H. , Elgin Sarah C.R.
Published: August 2019

Background

Chromatin-based transcriptional silencing is often described as a stochastic process, largely because of the mosaic expression observed in position effect variegation (PEV), where a euchromatic reporter gene is juxtaposed with heterochromatin. Here we closely examine the impact of genetic background on PEV phenotypes in the fruit fly,Drosophila melanogaster.

Results

Using consecutive generations of selective breeding, we isolated, from a single laboratory population, two inbred lines exhibiting contrasting degrees of variegation (A1: low expression, D1: high expression). Within each inbred population, remarkable similarity is observed in both the degree and the pattern of variegation. 89.63% of the differences between the two inbred lines in the degree of silencing can be explained by genotype, while a modest but significant sex effect is also observed. Further analyses of the PEV phenotype in the progeny of crosses between A1 and D1 suggest that the genotypic effect is the result of the combined effect of multiple independenttrans-acting loci. While the initial observations are based on a PEV phenotype scored in the fly eye (hsp70-whitereporter), similar degrees of silencing were observed using abeta-galreporter that can be scored across the whole fly. The pattern of variegatinghsp70-whiteexpression among individual flies becomes almost identical after five generations of inbreeding. Using a reporter inserted into the heterochromatic fourth chromosome, image analysis found significant enrichment of pigmentation in the ventral-posterior quadrant in both the A1 and D1 lines, and in the F1 and F2 progeny produced from a cross between A1 and D1, despite different degrees of expression.

Conclusions

Combining these results with the spreading model for local heterochromatin formation, we propose an augmented stochastic model to describe PEV. In this model, the genetic background, which determines the overall level of silencing, works with the cell lineage specific regulatory environment to determine the on/ off probability at the reporter locus in each cell. This model acknowledges cell-type specific events, as well as the general impact of heterochromatin formation.
Anaerobic degradation of syringic acid by an adapted strain ofRhodopseudomonas palustris
Authors: Oshlag J. Zachary , Ma Yanjun , Morse Kaitlin , Burger Brian T. , Lemke Rachelle A. , Karlen Steven D. , Myers Kevin S. , Donohue Timothy J. , Noguera Daniel R.
Published: August 2019

While lignin represents a major fraction of the carbon in plant biomass, biological strategies to convert the components of this heterogenous polymer into products of industrial and biotechnological value are lacking. Syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) is a byproduct of lignin degradation, appearing in lignocellulosic hydrolysates, deconstructed lignin streams, and other agricultural products.Rhodopseudomonas palustrisCGA009 is a known degrader of phenolic compounds under photoheterotrophic conditions, via the benzoyl-CoA degradation (BAD) pathway. However,R. palustrisCGA009 is reported to be unable to metabolizemeta-methoxylated phenolics such as syringic acid. We isolated a strain ofR. palustris(strain SA008.1.07), adapted from CGA009, which can grow on syringic acid under photoheterotrophic conditions, utilizing it as a sole source of organic carbon and reducing power. An SA008.1.07 mutant with an inactive benzoyl-CoA reductase structural gene was able to grow on syringic acid, demonstrating that the metabolism of this aromatic compound is not through the BAD pathway. Comparative gene expression analyses of SA008.1.07 implicated the involvement of products of thevanARBoperon (rpa3619-rpa3621), which has been described as catalyzing aerobic aromatic ring demethylation in other bacteria, in anaerobic syringic acid degradation. In addition, experiments with avanARBdeletion mutant demonstrated the involvement of thevanARBoperon in anaerobic syringic acid degradation. These observations provide new insights into the anaerobic degradation ofmeta-methoxylated and other aromatics byR. palustris.

IMPORTANCE

Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for production of aromatic-based biochemicals requires detailed knowledge of metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of aRhodopseudomonas palustrisstrain capable of syringic acid degradation reveals a previously unknown metabolic route for aromatic degradation inR. palustris. This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire to metabolize aromatic compounds from lignin and other renewable sources.