bluuebunny/crossref_metadata_2025 huggingface dataset:
Alternate Realms of Authority
Authors: Mody Sujata S.
Published: February 2019

Chapter 5 examines two landmark Hindi short stories that contested aspects of Dwivedi’s literary agenda. In ‘Dulāīvālī’ (quilt-woman), Banga Mahila used regional and domestic women’s speech in addition to Dwivedi’s preferred standard, Khari Boli prose. Her fictional exploration of the impact of nationalist ideals on middle-class Bengali women in the Hindi-belt further challenged the patriarchal authority with which Dwivedi and other nationalists sought to shape an emergent nation. Chandradhar Sharma ‘Guleri’, in ‘Usne kahā thā’ (she had said), employed regional/ethnic speech that was also gendered, as masculine and vulgar, once again flouting Dwivedi’s preferences for an upright, Khari Boli standard. His story, featuring a Sikh soldier fighting in Europe during World War I, upheld some nationalist ideals, but also defied conventional mores. Both stories underwent extensive editorial revisions, yet there remains a record in their final published versions of their authors’ defiance, and of Dwivedi’s strategic responses to such challenges.
Shooting a Tiger
Authors: Mandala Vijaya Ramadas
Published: February 2019

The main contention of Shooting a Tiger is that hunting during the colonial period was not merely a recreational activity, but a practice intimately connected with imperial governance. The book positions shikar or hunting at the heart of colonial rule by demonstrating that, for the British in India, it served as a political, practical, and symbolic apparatus in the consolidation of power and rule during the nineteenth and early twentieth centuries. The book analyses early colonial hunting during the Company period, and then surveys different aspects of hunting during the high imperial decades in the later nineteenth and early twentieth centuries. The book draws upon an impressive array of archival material and uses a wide range of evidence to support its contentions. It examines hunting at a variety of social and ethnic levels—military, administrative, elite, princely India, Indian professional hunters, and in terms of Indian auxiliaries and (sometimes) resisters. It also deals with different geographical contexts—the plains, the mountains, north and south India. The exclusive privilege of hunting exercised by the ruling classes, following colonial forest legislation, continued to be extended to the Indian princes who played a critical role in sustaining the lavish hunts that became the hallmark of the late nineteenth-century British Raj. Hunting was also a way of life in colonial India, undertaken by officials and soldiers alike alongside their everyday duties, necessary for their mental sustenance and vital for the smooth operation of the colonial administration. There are also two final chapters on conservation, particularly the last chapter focusing on two British hunter-turned-conservationists, Jim Corbett and Colonel Richard Burton.
Nimrods on the Hills—Hunting, Environment, and Its Fauna
Authors: Mandala Vijaya Ramadas
Published: February 2019

Drawing on rich archival material, sportsmen’s memoirs and colonial documents, this chapter develops the argument that hill-sport was another important feature of British social and cultural life in colonial India. Hill-sport played a significant role in shaping and transforming their cultural identity from the beginning of the nineteenth century. While scholarship to date has not touched upon this subject, chapter two traces the historical antecedents of the British military conquest, which led to exploration and the discovery of new geographies, that is, mountain and hill terrains in the north and south of India. It is possible to argue that the Nilgiris and the Doon Valley had the advantage of favourable climatic conditions and better hunting grounds, and therefore plentiful opportunities for hill-sport, which in turn provided the healthier lifestyle to the Britons living on the hill stations. In such mountain peripheries, there emerged aesthetic preferences among the colonial sporting fraternity, which were born out of their hunting experiences in the cultural geography of the Himalayas and the Nilgiris. Furthermore, this chapter also suggests that the British hunters in colonial India also created a dichotomy of difference in terms of the ecology and wild fauna of the mountains, which also influenced their development of different genres of hill-sport. In addition, this chapter offers a fresh perspective on the notions of masculinity and virile energy enshrined in the big-game hunting tradition in relation to mountain geographies in colonial India.
Vidyapati and Mithila
Authors: Jha Pankaj
Published: February 2019

Vidyapati was a polyglot poet and scholar, attached at different moments to courts of different chieftaincies of north Bihar and the terrain of Nepal. The chapter introduces his scholarly profile and provides the details of all his known compositions. The diversity of their themes, genres and languages is marked. Available information indicates how vibrant the intellectual milieu of Mithila was as a hub of Sanskrit learning during the 14th–16th centuries. The chapter traces the geographical background of the region. It also outlines the political setting with reference to the genealogies of the local rulers. These rulers were mostly ‘autonomous’ but ruled over a relatively tiny principality. Few historians have studied the region during the ‘medieval’ period, most of them local enthusiasts of Maithil culture and pride. The chapter provides a brief account of this historiography and its limitations.
Writing State and Order
Authors: Jha Pankaj
Published: February 2019

Careful documentation is an integral part of modern state system today. This development in medieval India is most visibly associated with Persian language and its patrons: Delhi Sultanate and the Mughal state. This chapter focuses on Likhanāvalī, a first of its kind text in Sanskrit that provided exemplary models of letters and documents for different official (and intimate) communications, occasions, and transactions. An attempt is made to trace the history of epistolary traditions in India both in Sanskrit and in Persian. The chapter historicizes the text to reveal how it drew on Persian traditions more than it did from the Sanskrit traditions. A close look at the imagined world of Likhanāvalī also reveals interesting perceptions of state, ethics, and the very craft of writing. How important was the cultivation of the skill of writing for the emergence of imperial states like the Mughal’s in the 16th century?
Political Ethics or the Art of Being a Man
Authors: Jha Pankaj
Published: February 2019

Turning to Vidyapati’s famous treatise on masculinity, Puruṣaparīkṣā, this chapter explores its framing and genre, its ideas and stories. This Sanskrit text sought to entertain and to educate young men about state building and ideal forms of manliness. The world of Sanskrit political thought found a contemporarized as well as classicized articulation in the text. The text attempted to weave discriminatory regimes of gender and caste into notions of ideal state and ethical conduct. Yet it is done through complex and entertaining stories, deriving its authority from history, common sense, and occasionally the Vedas. Again, the author is seen to be playing upon a conjunction of comparable features of Persian and Sanskrit literary tradition especially where articulations of exemplary masculinity (jawanmardi/paurusa) is concerned. The chapter also shows how a discourse on nīti (political ethics) was actually undergirded by precepts of dharma.
Introduction
Authors: Bhattacharya Sabyasachi
Published: February 2019

Usually, the archives are sites where historians conduct research into our past. They are not the objects of research. This work addresses that task. This is a subject somewhat out of the ordinary for the general reader or professional historians who tend to take the archives for granted. By way of introducing this book, I would like to share with the readers some thoughts that crossed my mind as I launched into this project....
Absence of a Definite Archives Policy
Authors: Bhattacharya Sabyasachi
Published: February 2019

After the termination of East India Company administration, there was an attempt to put in order the records of the Government of India. Since the issue of expenditure and financial stringency comes up repeatedly in the discussions on this matter, this chapter dwells on the nature and extent of financial stringency which formed the background to the first steps taken by the Government of India with regard to records after the termination of the East India Company’s rule. The chapter also explores some other key questions: Who were the people interested in and responsible for the organization and preservation of records after the takeover of the Indian government by the Crown? Were persons who had historical interest appointed to serve as members of the Records Committee, 1861–72? How did colonial historians address the issue of documenting their narratives before an archive came into existence? The chapter also looks at the legacy of Lord Macaulay.
Prehistory and Early Chronology of the Cult of Relics
Authors: Wiśniewski Robert
Published: February 2019

This chapter presents the framework which will be referred to throughout this book and begins with a presentation of the biblical ‘prehistory’ of the cult of relics. It demonstrates that the veneration of the martyrs in the pre-Constantinian period was clearly a distinct phenomenon from the cult of relics as it emerged in the mid-fourth century. The novelty of the latter phenomenon consisted in the belief in the miraculous power of relics and in the new, hitherto unknown practices it involved. Even though a few literary episodes found in late antique literature seem to attest that this belief and practices started to develop earlier, this chapter argues nevertheless that they cannot contradict its principal argument, namely that a profound change in the attitude toward saints’ bodies occurred no earlier than in the middle decades of the fourth century.
Defenders of Cities
Authors: Wiśniewski Robert
Published: February 2019

This chapter studies early testimonies to the use of relics as efficient palladia and examines the sources of this phenomenon, which unlike exorcizing and healing had no parallels in the Bible: the prophets, Christ, and the Apostles were never portrayed as powerful protectors of cities. For this reason the Greek and Roman background of this phenomenon deserves a detailed study aimed at finding out if there was any connection between the saints’ relics and the guardian statues and amulets whose growing popularity is attested in the late antique sources. This chapter argues that the Christian belief in the protection provided by the saints ran in parallel with the widespread belief in the power of amulets and that despite evident interactions between Christian and non-Christian practices it cannot be seen as resulting directly from pagan beliefs.
Burials ad Sanctos
Authors: Wiśniewski Robert
Published: February 2019

Both textual and material evidence demonstrates that many Christians would go to great lengths to bury their kin ad sanctos, close to the tombs of saints. The beginnings of this practice are often dated to the late third century. This chapter argues that the basis for such an early dating is tenuous. It also deals with the character of physical proximity between the ordinary dead and the martyrs: how close were the bones of the former placed to those of the latter? Were the relics put inside their tombs? Also, this chapter seeks to explain the reasons why people buried their dead ad sanctos. While acknowledging their religious motivation it shows that some Christians simply desired to entomb their dead close to a famous hero rather than to the source of a beneficial power.
Finding Relics
Authors: Wiśniewski Robert
Published: February 2019

When the cult of relics developed in the mid-fourth century, very few tombs of saints whose remains were to be venerated in the centuries to come had been identified. This chapter presents the early history of the search for and finding of such graves, which started in the last decades of the fourth century. It seeks to explain the reasons which lay behind this process, focusing both on the needs of the congregation and the role of the discovery in church politics. It also analyses the sense of the literary pattern of inventio and tries to find out how much this pattern reflected reality. Finally, it presents a case study: a literary dossier of the discovery of the relics of Gervasius and Protasius by Bishop Ambrose of Milan in 386.
Displaying and Seeing Relics
Authors: Wiśniewski Robert
Published: February 2019

In Late Antiquity most relics, even after they had been discovered, remained hidden: ordinary people rarely had an opportunity to see them. Visual contact with them, however, was not entirely impossible. This chapter studies various aspects of this contact, trying to answer the following questions: Where were the reliquaries stored and were they visible for visitors to churches? What did their iconography say about their contents? Were they constructed in a way which made it possible to peek inside? Also, it discusses some exceptional situations in which the very bones of martyrs were put on display and explains why this happened.
Introduction
Authors: Wiśniewski Robert
Published: February 2019

The Introduction emphasizes both the novelty and importance of the cult of relics in late antique Christianity. It presents the state of the art, showing that while the early cult of relics attracts interest as an aspect of the cult of saints, it has hardly been hardly studied on its own. It also discusses the main research questions and the general plan of the book, in which the chapters are arranged according to a thematic order, but which also studies the diachronic development of the phenomenon. Finally, it discusses questions of terminology that are important for the cult of relics, and particularly presents its concise vocabulary in various languages of ancient Christianity.
Comparison in Practice: A Methodological Framework
Authors: Freiberger Oliver
Published: February 2019

This chapter seeks to connect the insights gained in Chapter 2 with comparative practice, outlining a methodological framework that identifies two sets of elements of the comparative enterprise. First it describes the general configuration of a comparative study, distinguishing modes, scales, and scopes of comparison. Each of these categories comprises several options, out of which the researcher selects those that are most appropriate for the study. Second, the chapter breaks down the comparative process into five operations: selection, description and analysis, juxtaposition, redescription, and rectification/theory formation. This methodological framework provides a vocabulary that enables us to talk about the elements of the comparative method. A comparativist may use it as a template or foil against which he or she devises a comparative study. It provides tools for questioning, reconsidering, and defending decisions made in the study. Second, the framework may be used to analyze and evaluate existing comparative studies.
It is time for an ethical, evidence-based approach to youth presenting to the ED with an opioid overdose
Authors: Warshawski Tom , Warf Curren
Published: February 2019

Currently, there is a dangerous inconsistency between our current understanding of adolescent development and the effects of drugs on cognition when compared to our collective approach to youth who present in the emergency department with an opioid overdose. We call upon practitioners to embrace a new paradigm and we ask the Canadian Pediatric Society (CPS) to spearhead the development of guidelines to advise on best practices to manage youth who present to the emergency department with an illicit drug overdose.
Development of a Species-Specific PCR for Detection and Quantification of Meloidogyne hapla in Soil Using the 16D10 Root-Knot Nematode Effector Gene
Authors: Gorny Adrienne M. , Wang Xiaohong , Hay Frank S. , Pethybridge Sarah J.
Published: February 2019

The Northern root-knot nematode (Meloidogyne hapla) is an important soilborne pathogen of numerous agricultural crops in temperate regions. Accurate detection and quantification is vital to supporting informed pest management decisions. However, traditional methods of manual nematode extraction and morphology-based identification are time-consuming and require highly specialized training. Molecular methods may expand the diagnostician’s toolkit beyond those methods that rely on this disappearing specialized skillset. However, molecular assays targeting the internal transcribed spacer region may lead to inaccurate results because of intraspecific variability. The Meloidogyne spp. effector gene 16D10 was assessed as a target for a SYBR Green I quantitative PCR (qPCR) assay for detection and quantification of M. hapla. M. hapla-specific qPCR primers were developed and evaluated for specificity against five M. hapla isolates and 14 other plant-parasitic nematodes. A standard curve was generated by relating the quantification cycle (Cq) to the log of M. hapla population densities artificially introduced into soil. The influence of soil inhibitors on quantitative amplification was assessed by generating a dilution series from DNA extracted from pure nematode cultures and inoculated soil. Extracts from soil produced significantly higher Cq values than those produced from pure culture extracts. The utility of the qPCR was evaluated using soil samples collected from three naturally infested potato fields, resulting in a significant positive relationship between populations estimated using qPCR and populations derived from manual counting. The qPCR developed in this study provides a useful method for detecting and quantifying M. hapla in soil and demonstrates the utility of effector genes in plant-parasitic nematode diagnostics. The ability to use effector genes as targets for qPCR and other molecular detection and quantification methods may open additional avenues of novel research and support development of improved species-level diagnostics.
Post-traumatic endophthalmitis caused by Nocardia nova
Authors: Rodríguez-Lozano Jesús , Armiñanzas Castillo Carlos , Ruiz de Alegría Puig Carlos , Ventosa Ayarza Juan Antonio , Fariñas Maria Carmen , Agüero Jesús , Calvo Jorge
Published: February 2019

Introduction.

Nocardia nova

complex has been associated with infections in both immunocompetent and immunocompromised patients. Infection can be localized or disseminated, affecting skin and soft tissues, the respiratory system, bones and joints, the circulatory system and especially the central nervous system. Ocular infections such as keratitis, scleritis, conjunctivitis, dacryocystitis, orbital cellulitis and endophthalmitis due to

Nocardia

spp. are infrequently reported, and usually described after penetrating corneal trauma or ocular contact with plants and soils.

Case presentation. An immunocompetent male presented with a history of penetrating ocular trauma that had evolved to infectious endophthalmitis, which was refractory to different antibiotic treatments. No micro-organisms were isolated from repeated conjunctival smear and corneal scraping cultures between the ocular trauma (August 2014) and the endophthalmitis diagnosis (November 2015). After this period,

N. nova
sensu stricto was isolated in aqueous humour aspirate. Treatment was adjusted and clinical improvement was obtained after an adequate microbiological procedure, including an optimal sampling and an antimicrobial-susceptibility testing report.

Conclusion.

Nocardia

identification to the species level and performance of antimicrobial-susceptibility tests are both essential tools for treatment adjustment and clinical improvement.
Regulation of food intake by astrocytes in the brainstem dorsal vagal complex
Authors: MacDonald Alastair J. , Holmes Fiona E. , Beall Craig , Pickering Anthony E. , Ellacott Kate L.J.
Published: February 2019

Food intake is controlled by the coordinated action of numerous brain regions but a complete understanding remains elusive. Of these brain regions the brainstem dorsal vagal complex (DVC) is the first site for integration of visceral synaptic and hormonal cues that act to inhibit food intake. The DVC consists of three nuclei: the nucleus of the solitary tract (NTS), area postrema (AP) and dorsal motor nucleus of the vagus (DMX). Targeted chemogenetic activation of appetite-responsive NTS neuronal populations causes short term decreases in food intake. Astrocytes are a class of glial cell which provide metabolic and structural support to neurons and play an active role in modulating neurotransmission. Within the hypothalamic arcuate nucleus (ARC) astrocytes are regulated by both positive and negative energy balance and express receptors for hormones that influence satiety and hunger. Chemogenetic activation of these ARC astrocytes alters food intake. Since NTS astrocytes respond to vagal stimulation, we hypothesised that they may be involved in mediating satiety. Here we show that NTS astrocytes show plastic alterations in morphology following excess food consumption and that chemogenetic activation of DVC astrocytes causes a decrease in food intake, by recruiting an appetite-inhibiting circuit, without producing aversion. These findings are the first using genetically-targeted manipulation of DVC astrocytes to demonstrate their role in the brain’s regulation of food intake.
Multidimensional Profiling of Drug-Treated Cells by Imaging Mass Cytometry
Authors: Bouzekri Alexandre , Esch Amanda , Ornatsky Olga
Published: February 2019

In pharmaceutical research, high-content screening is an integral part of lead candidate development. Drug responsein vitroover 40 parameters including biomarkers, signaling molecules, cell morphological changes, proliferation indexes and toxicity in a single sample could significantly enhance discovery of new therapeutics. As a proof of concept, we present a workflow for multidimensional Imaging Mass Cytometry™ (IMC™) and data processing with open source computational tools. CellProfiler was used to identify single cells through establishing cellular boundaries, followed by histoCAT™ (histology topography cytometry analysis toolbox) for extracting single-cell quantitative information visualized as t-SNE plots and heatmaps. Human breast cancer-derived cell lines SKBR3, HCC1143 and MCF-7 were screened for expression of cellular markers to generate digital images with a resolution comparable to conventional fluorescence microscopy. Predicted pharmacodynamic effects were measured in MCF-7 cells dosed with three target-specific compounds: growth stimulatory EGF, microtubule depolymerization agent nocodazole and genotoxic chemotherapeutic drug etoposide. We show strong pairwise correlation between nuclear markers pHistone3S28, Ki-67 and p4E-BP1T37/T46in classified mitotic cells and anti-correlation with cell surface markers. Our study demonstrates that IMC data expands the number of measured parameters in single cells and brings higher-dimension analysis to the field of cell-based screening in early lead compound discovery.
Anti-Asialo GM1 treatment during secondaryToxoplasma gondiiinfection is lethal and depletes T cells
Authors: Ivanova Daria L. , Denton Steve L. , Gigley Jason P.
Published: February 2019

Using vaccine challenge model ofT. gondiiinfection, we found that treatments with two commonly used for NK cell depletion antibodies resulted in different survival outcomes during secondary infection. Anti-ASGM1 resulted in 100% death and greater parasite burden at the site of infection than anti-NK1.1. Anti-NK1.1 treatment resulted in increased parasite burdens, but animals did not die. Further we found that anti-ASGM1 treatment depleted T cells. CD8+ T cells were more susceptible that CD4+ T cells to the treatment. ASGM1 was expressed on a higher percentage of CD8+ T cells than CD4+ T cells and CD8+ T cells. InT. gondii-immunized animals ASGM1 was enriched on effector memory (Tem) and central memory (Tcm) CD8+ T cells. However, Tem were more susceptible to the treatment. After secondary infection, Tem, Tcm, effector (Tef) and naïve (Tn) CD8+ T cells were positive for ASGM1. Anti-ASGM1 treatment during reinfection resulted in greater depletion of activated IFNγ+, Granzyme B+, Tem and Tef than Tcm and Tn CD8+ T cells. Anti-ASGM1 also depleted IFNγ+ CD4+ T cells. Recombinant IFNγ supplementation prolonged survival of anti-ASGM1 treated mice, demonstrating that this antibody eliminated IFNγ-producing T and NK cells important for control of the parasite. These results highlight that anti-ASGM1 antibody is not an optimal choice for targeting only NK cells and more precise approaches should be used. This study uncovers ASGM1 as a marker of activated effector T cells and the potential importance of changes in sialylation in lipid rafts for T cell activation duringT. gondiiinfection.
Haplotype-Based Noninvasive Prenatal Diagnosis for Duchenne Muscular Dystrophy: A pilot study in South China
Authors: Chen Min , Chen Chao , Li Yingting , Yuan Yuan , Lai Zhengfei , Guo Fengyu , Wang Yaoshen , Huang Xiaoyan , Li Shiquan , Wu Renhua , Peng Zhiyu , Sun Jun , Chen Dunjin
Published: February 2019

Objective

To explore the accuracy and feasibility of noninvasive prenatal diagnosis (NIPD) for Duchenne Muscular Dystrophy (DMD) based on the haplotype approach.

Methods

We recruited singleton pregnancies at-risk of DMD at 12-25 weeks of gestation from 17 families who all had a proband children affected by DMD. We have identified the pathogenic mutations in probands and their mothers by multiplex ligation-dependent probe amplification (MLPA). To construct parental haplotypes, we performed captured sequencing on genomic DNA from parents and probands. The integration analysis of parental haplotypes and targeted sequencing results of maternal plasma DNA were used to infer the fetal haplotype and genotypes inDMDgene. FetalDMDgenotypes were further confirmed by invasive prenatal diagnosis.

Results

We have successfully performed the haplotype-based NIPD in all recruited families. Ten fetuses were identified as normal, including four female and six male fetuses. Four female fetuses were carriers and the other three male fetuses were affected byDMDwith exons 49-52 deletion, exons 8-37 deletion and c.628G > T mutation, respectively. The results of NIPD were consistent with those of invasive diagnosis.

Conclusion

Haplotype-based NIPD for DMD by targeted sequencing is promising and has potential for clinical application.
Additional layer of regulation via convergent gene orientation in yeasts
Authors: Gilet Jules , Conte Romain , Torchet Claire , Benard Lionel , Lafontaine Ingrid
Published: February 2019

Convergent gene pairs can produce transcripts with complementary sequences. We had shown that mRNA duplexes formin vivoinSaccharomyces cerevisiaevia interactions of their 3′-ends and can lead to post-transcriptional regulatory events. Here we show that mRNA duplex formation is restricted to convergent genes separated by short intergenic distance, independently of their 3′-UTR length. We disclose an enrichment in genes involved in biological processes related to stress among these convergent genes. They are markedly conserved in convergent orientation in budding yeasts, meaning that this mode of post-transcriptional regulation could be shared in these organisms, conferring an additional level for modulating stress response. We thus investigated the mechanistic advantages potentially conferred by 3′-UTR mRNA interactions. Analysis of genome-wide transcriptome data revealed that Pat1 and Lsm1 factors, having 3′-UTR binding preference and participating to the remodeling of messenger ribonucleoprotein particles, bind differently these mRNA duplexes in comparison to canonical mRNAs. Functionally, the translational repression upon stress also appears limited on mRNA duplexes. We thus propose that mRNA duplex formation modulates the regulation of mRNA expression by limiting their access to translational repressors. Our results thus show that post-transcriptional regulation is an additional factor that determine the order of coding genes.
Evolutionary dynamics determines adaptation to inactivation of an essential gene
Authors: Rodrigues João V. , Shakhnovich Eugene I.
Published: February 2019

Genetic inactivation of essential genes creates an evolutionary scenario distinct from escape from drug inhibition, but the mechanisms of microbe adaptations in such cases remain unknown. Here we inactivateE.colidihydrofolate reductase (DHFR) by introducing D27G,N,F chromosomal mutations in a key catalytic residue with subsequent adaptation by serial dilutions. The partial reversal G27->C occurred in three evolutionary trajectories. Conversely, in one trajectory for D27G and in all trajectories for D27F,N strains adapted to grow at very low supplement folAmix concentrations but did not escape entirely from supplement auxotrophy. Major global shifts in metabolome and proteome occurred upon DHFR inactivation, which were partially reversed in adapted strains. Loss of function mutations in two genes,thyAanddeoB, ensured adaptation to low folAmix by rerouting the 2-Deoxy-D-ribose-phosphate metabolism from glycolysis towards synthesis of dTMP. Multiple evolutionary pathways of adaptation to low folAmix converge to highly accessible yet suboptimal fitness peak.
Accurate fetal variant calling in the presence of maternal cell contamination
Authors: Nabieva Elena , Sharma Satyarth Mishra , Kapushev Yermek , Garushyants Sofya K. , Fedotova Anna V. , Moskalenko Viktoria N. , Serebrenikova Tatyana , Glazyrina Eugene , Kanivets Ilya V. , Pyankov Denis V. , Neretina Tatyana V. , Logacheva Maria D. , Bazykin Georgii A. , Yarotsky Dmitry
Published: February 2019

High-throughput sequencing of fetal DNA is a promising and increasingly common method for the discovery of all (or all coding) genetic variants in the fetus, either as part of prenatal screening or diagnosis, or for genetic diagnosis of spontaneous abortions. In many cases, the fetal DNA (from chorionic villi, amniotic fluid, or abortive tissue) can be contaminated with maternal cells, resulting in the mixture of fetal and maternal DNA. This maternal cell contamination (MCC) undermines the assumption, made by traditional variant callers, that each allele in a heterozygous site is covered, on average, by 50% of the reads, and therefore can lead to erroneous genotype calls. We present a panel of methods for reducing the genotyping error in the presence of MCC. All methods start with the output of GATK HaplotypeCaller on the sequencing data for the (contaminated) fetal sample and both of its parents, and additionally rely on information about the MCC fraction (which itself is readily estimated from the high-throughput sequencing data). The first of these methods uses a Bayesian probabilistic model to correct the fetal genotype calls produced by MCC-unaware HaplotypeCaller. The other two methods “learn” the genotype-correction model from examples. We use simulated contaminated fetal data to train and test the models. Using the test sets, we show that all three methods lead to substantially improved accuracy when compared with the original MCC-unaware HaplotypeCaller calls. We then apply the best-performing method to three chorionic villus samples from spontaneously terminated pregnancies.

Code and training data availability

https://github.com/bazykinlab/ML-maternal-cell-contamination
Cryptococcus neoformansresist to drastic conditions by switching to viable but non-culturable cell phenotype
Authors: Hommel Benjamin , Sturny-Leclère Aude , Volant Stevenn , Veluppillai Nathanael , Duchateau Magalie , Yu Chen-Hsin , Hourdel Véronique , Varet Hugo , Matondo Mariette , Perfect John R , Casadevall Arturo , Dromer Françoise , Alanio Alexandre
Published: February 2019

Metabolically quiescent pathogens can persist in a viable non-replicating state for months or even years. For certain infectious diseases, such as tuberculosis, cryptococcosis, histoplasmosis, latent infection is a corollary of this dormant state, which has the risk for reactivation and clinical disease. During murine cryptococcosis and macrophage uptake, stress and host immunity induce C. neoformans heterogeneity with the generation of a sub-population of yeasts that manifests a phenotype compatible with dormancy (low stress response, latency of growth). In this subpopulation, mitochondrial transcriptional activity is regulated and this phenotype has been considered as a hallmark of quiescence in stem cells. Based on these findings, we worked to reproduce this phenotype in vitro and then standardize the experimental conditions to consistently generate this dormancy inCryptococcus neoformans.

We found that incubation of stationary phase yeasts (STAT) in nutriment limited conditions and hypoxia for 8 days (8D-HYPOx) was able to produced cells that mimic the phenotype obtained in vivo. In these conditions, mortality and/or apoptosis occurred in less than 5% of the yeasts compared to 30-40% of apoptotic or dead yeasts upon incubation in normoxia (8D-NORMOx). Yeasts in 8D-HYPOx harbored a lower stress response, delayed growth and less that 1% of culturability on agar plates, suggesting that these yeasts are viable but non culturable cells (VBNC). These VBNC were able to reactivate in the presence of pantothenic acid, a vitamin that is known to be involved in quorum sensing and a precursor of acetyl-CoA. Global metabolism of 8D-HYPOx cells showed some specific requirements and was globally shut down compared to 8D-NORMOx and STAT conditions. Mitochondrial analyses showed that the mitochondrial masse increased with mitochondria mostly depolarized in 8D-HYPOx compared to 8D-NORMox, with increased expression of mitochondrial genes. Proteomic and transcriptomic analyses of 8D-HYPOx revealed that the number of secreted proteins and transcripts detected also decreased compared to 8D-NORMOx and STAT, and the proteome, secretome and transcriptome harbored specific profiles that are engaged as soon as four days of incubation. Importantly, acetyl-CoA and the fatty acid pathway involving mitochondria are required for the generation and viability maintenance of VBNC.

All together, these data show that we were able to generate for the first time VBNC phenotype inCryptococcocus neoformans. This VBNC state is associated with a specific metabolism that should be further studied to understand dormancy/quiescence in this yeast.
De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population
Authors: Kessler Michael D. , Loesch Douglas P. , Perry James A. , Heard-Costa Nancy L. , Cade Brian E. , Wang Heming , Daya Michelle , Ziniti John , Datta Soma , Celedón Juan C , Soto-Quiros Manuel E. , Avila Lydiana , Weiss Scott T. , Barnes Kathleen , Redline Susan S. , Vasan Ramachandran S. , Johnson Andrew D. , Mathias Rasika A. , Hernandez Ryan , Wilson James G. , Nickerson Deborah A. , Abecasis Goncalo , Browning Sharon R. , Zoellner Sebastian , O’Connell Jeffrey R. , Mitchell Braxton D. ,   Trans-Omics for Precision Medicine (TOPMed), TOPMed Population Genetics Working Group, O’Connor Timothy D.
Published: February 2019

de novoMutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) program, we directly estimate and analyze DNM counts, rates, and spectra from 1,465 trios across an array of diverse human populations. Using the resulting call set of 86,865 single nucleotide DNMs, we find a significant positive correlation between local recombination rate and local DNM rate, which together can explain up to 35.5% of the genome-wide variation in population level rare genetic variation from 41K unrelated TOPMed samples. While genome-wide heterozygosity does correlate weakly with DNM count, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, interestingly, we do find significantly fewer DNMs in Amish individuals compared with other Europeans, even after accounting for parental age and sequencing center. Specifically, we find significant reductions in the number of T→C mutations in the Amish, which seems to underpin their overall reduction in DNMs. Finally, we calculate near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by non-additive genetic effects and/or the environment, and that a less mutagenic environment may be responsible for the reduced DNM rate in the Amish.

Significance

Here we provide one of the largest and most diverse humande novomutation (DNM) call sets to date, and use it to quantify the genome-wide relationship between local mutation rate and population-level rare genetic variation. While we demonstrate that the human single nucleotide mutation rate is similar across numerous human ancestries and populations, we also discover a reduced mutation rate in the Amish founder population, which shows that mutation rates can shift rapidly. Finally, we find that variation in mutation rates is not heritable, which suggests that the environment may influence mutation rates more significantly than previously realized.
Neural System Identification with Cortical Information Flow
Authors: Ambrogioni L. , Seeliger K. , Güçlü U. , van Gerven M. A. J.
Published: February 2019

Cortical information flow (CIF) is a new framework for system identification in neuroscience. CIF models represent neural systems as coupled brain regions that each embody neural computations. These brain regions are coupled to observed data specific to that region. Neural computations are estimated via stochastic gradient descent. We show using a large-scale fMRI dataset that, in this manner, we can estimate models that learn meaningful neural computations. Our framework is general in the sense that it can be used in conjunction with any (combination of) neural recording techniques. It is also scalable, providing neuroscientists with a principled approach to make sense of the high-dimensional neural datasets.
Gene pathogenicity prediction of Mendelian diseases via the Random Forest algorithm
Authors: He Sijie , Chen Weiwei , Liu Hankui , Li Shengting , Lei Dongzhu , Dang Xiao , Chen Yulan , Zhang Xiuqing , Zhang Jianguo
Published: February 2019

The study of Mendelian diseases and the identification of their causative genes are of great significance in the field of genetics. The evaluation of the pathogenicity of genes and the total number of Mendelian disease genes are both important questions worth studying. However, very few studies have addressed these issues to date, so we attempt to answer them in this study.

We calculated gene pathogenicity prediction (GPP) score by a machine learning approach (random forest algorithm) to evaluate the pathogenicity of genes. When we applied the GPP score to the testing gene set, we obtained accuracy of 80%, recall of 93% and area under the curve (AUC) of 0.87. Our results estimated that a total of 10,399 protein-coding genes were Mendelian disease genes. Furthermore, we found the GPP score was positively correlated with the severity of disease.

Our results indicate that GPP score may provide a robust and reliable guideline to predict the pathogenicity of protein-coding genes. To our knowledge, this is the first trial to estimate the total number of Mendelian disease genes.
Comparative study of GenePOC GBS LB Assay and GeneXpert GBS LB Assay for the detection of Group BStreptococcusin prenatal screening samples
Authors: Choera Tsokyi , Jung-Hynes Brittney , Chen Derrick J.
Published: February 2019

Group B Streptococcal (GBS) infections in the United States are a leading cause of meningitis and sepsis in newborns. The CDC, therefore recommends GBS screening for all pregnant women at 35–37 weeks of gestation and administration of intrapartum prophylaxis (in those that tested positive) as an effective means of controlling disease transmission. Several FDA approved molecular diagnostic tests are available for rapid and accurate detection of GBS in antepartum women. In this study, we report a clinical comparison of the Xpert GBS LB assay and a novel FDA-cleared test, GenePOC GBS LB assay. A total of 250 vaginal-rectal swabs from women undergoing prenatal screening were submitted to the University of Wisconsin’s clinical microbiology laboratory for GBS testing. We found 96.8% of samples were concordant between the two tests, while 3.2% were discordant with higher sensitivity observed for the GenePOC GBS LB assay, and higher specificity for the GeneXpert GBS LB assay.
KAP1 is an antiparallel dimer with a natively functional asymmetry
Authors: Fonti Giulia , Marcaida Maria J. , Bryan Louise C. , Traeger Sylvain , Kalantzi Alexandra S. , Helleboid Pierre-Yves J.L. , Demurtas Davide , Tully Mark D. , Grudinin Sergei , Trono Didier , Fierz Beat , Peraro Matteo Dal
Published: February 2019

KAP1 (KRAB-domain associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 SUMO ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering diffraction data, integrative modeling and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with a native asymmetry at the C-terminal domain. This conformation supports our finding that the RING domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.
Mechanics of DNA Replication and Transcription Guide the Asymmetric Distribution of RNAPol2 and Nucleosomes on Replicated Daughter Genomes
Authors: Ziane Rahima , Camasses Alain , Radman-Livaja Marta
Published: February 2019

Eukaryotic DNA replication occurs in the context of chromatin. Chromatin in its capacity as a transcription regulator, is also thought to have a role in the epigenetic transmission of transcription states from one cell generation to the next. It is still unclear how chromatin structure survives the disruptions of nucleosomal architecture during genomic replication or if chromatin features are indeed instructive of the transcription state of the underlying gene. We have therefore developed a method for measuring chromatin structure dynamics after replication – ChIP -NChAP (Chromatin Immuno-Precipitation - Nascent Chromatin Avidin Pulldown) - which we used to monitor the distribution of RNAPol2 and new and old H3 histones on newly-replicated daughter genomes in S. Cerevisiae. The strand specificity of our sequencing libraries allowed us to uncover the inherently asymmetric distribution of RNAPol2, H3K56ac (a mark of new histones), and H3K4me3 and H3K36me3 (“active transcription marks” used as proxies for old histones) on daughter chromatids. We find a difference in the timing of lagging and leading strand replication on the order of minutes at a majority of yeast genes. Nucleosomes and RNAPol2 preferentially bind to either the leading or the lagging strand gene copy depending on which one replicated first and RNAPol2 then shifts to the sister copy after its synthesis has completed. Our results suggest that active transcription states are inherited simultaneously and independently of their underlying active chromatin states through the recycling of the transcription machinery and old histones, respectively. We find that “active” histone marks do not instruct the cell to reestablish the same active transcription state at its underlying genes. We propose that rather than being a consequence of chromatin state inheritance transcription actually contributes to the reestablishment of chromatin states on both replicated gene copies. Our findings are consistent with a two-step model of chromatin assembly and RNAPol2 binding to nascent DNA that is based on local differences in replication timing between the lagging and leading strand. The model describes how chromatin and transcription states are first restored on one and then the other replicated gene copy, thus ensuring that after division each cell will have “inherited” a gene copy with identical gene expression and chromatin states.
Calcium-dependent protein kinase 5 links calcium-signaling withSARD1-dependent immune memory in systemic acquired resistance
Authors: Guerra Tiziana , Schilling Silke , Sylvester Fabian-Philipp , Conrads Benjamin , Romeis Tina
Published: February 2019

- Systemic acquired resistance (SAR) prepares infected plants for faster and stronger defense activation upon subsequent attacks. SAR requires an information relay from primary infection to distal tissue and the initiation and maintenance of a self-maintaining phytohormone salicylic acid (SA)-defense loop.

- In spatial and temporal resolution we show that calcium-dependent protein kinase CPK5 contributes to immunity and SAR. In local basal resistance CPK5 functions upstream of SA-synthesis, -perception, and -signaling. In systemic tissue, enhanced CPK5 signaling leads to an accumulation of SAR marker genes including transcription factorSystemic Acquired Resistance Deficient 1(SARD1).

- Plants of enhanced CPK5-, but not CPK6-, signaling display a ‘super-priming’ phenotype of enhanced resistance toward a secondary bacterial infection. Insard1background, CPK5-mediated basal resistance is still mounted but systemic ‘super-priming’ is lost.

- The biochemical analysis determines CPK5 half maximal kinase activity for calcium K50 [Ca2+] to ∼100 nM close to the cytoplasmic resting level. This low activation threshold uniquely qualifies CPK5 to decode subtle changes in calcium prerequisite to immune signal relay and to onset and maintenance of priming at later time points in distal tissue. Our data explain why CPK5 functions as a hub in basal and systemic plant immunity.