bluuebunny/crossref_metadata_2025 huggingface dataset:
First Aid and Voluntarism in England, 1945–85
Authors: Ramsden Stefan , Cresswell Rosemary
Published: November 2018

First aid was the focus of growing voluntary activity in the post-war decades. Despite the advent of the National Health Service in 1948, increased numbers of people volunteered to learn, teach, and administer first aid as concern about health and safety infiltrated new activities and arenas. In this article we use the example of the Voluntary Aid Societies (VAS, focusing in particular on St John Ambulance) to highlight continuities and change in the relationship between state and voluntary sector in health and welfare provision during the four decades after 1945. Though the state assumed vastly expanded health and welfare responsibilities after the war, the continuing vitality of the VAS suggests cultural continuities that the post-war welfare state did not eradicate. The article therefore builds on the insights of historians who argue that volunteering remained a vital component of British society across the later twentieth century, and that the state and voluntary sector were not mutually exclusive.
Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains
Authors: Phan My V T , Ngo Tri Tue , Hong Anh Pham , Baker Stephen , Kellam Paul , Cotten Matthew
Published: November 2018

The Coronaviridae family of viruses encompasses a group of pathogens with a zoonotic potential as observed from previous outbreaks of the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Accordingly, it seems important to identify and document the coronaviruses in animal reservoirs, many of which are uncharacterized and potentially missed by more standard diagnostic assays. A combination of sensitive deep sequencing technology and computational algorithms is essential for virus surveillance, especially for characterizing novel- or distantly related virus strains. Here, we explore the use of profile Hidden Markov Model-defined Pfam protein domains (Pfam domains) encoded by new sequences as a Coronaviridae sequence classification tool. The encoded domains are used first in a triage to identify potential Coronaviridae sequences and then processed using a Random Forest method to classify the sequences to the Coronaviridae genus level. The application of this algorithm on Coronaviridae genomes assembled from agnostic deep sequencing data from surveillance of bats and rats in Dong Thap province (Vietnam) identified thirty-four Alphacoronavirus and eleven Betacoronavirus genomes. This collection of bat and rat coronaviruses genomes provided essential information on the local diversity of coronaviruses and substantially expanded the number of coronavirus full genomes available from bat and rats and may facilitate further molecular studies on this group of viruses.
The Spillovers of Employment Guarantee Programs on Child Labor and Education
Authors: Li Tianshu , Sekhri Sheetal
Published: November 2018

Many developing countries use employment guarantee programs to combat poverty. This study examines the consequences of such employment guarantee programs for the human capital accumulation of children. It exploits the phased roll-out of India’s flagship Mahatma Gandhi National Rural Employment Guarantee Scheme (MGNREGA) to study the effects on enrollment in schools and child labor. Introduction of MGNREGA results in lower relative school enrollment in treated districts. It also finds that the drop in enrollment is driven by primary school children. Children in higher grades are just as likely to attend school under MGNREGA, but their school performance deteriorates. Using nationally representative employment data, the study finds evidence indicating an increase in child labor highlighting the unintentional perverse effects of the employment guarantee schemes for human capital.
Reconfiguring a One-Way Street: A Position Paper on Why and How to Improve Equity in Global Physician Training
Authors: Hudspeth James C. , Rabin Tracy L. , Dreifuss Bradley A. , Schaaf Mylo , Lipnick Michael S. , Russ Christiana M. , Autry Amy (Meg) , Pitt Michael B. , Rowthorn Virginia
Published: November 2018

Large numbers of U.S. physicians and medical trainees engage in hands-on clinical global health experiences abroad, where they gain skills working across cultures with limited resources. Increasingly, these experiences are becoming bidirectional, with providers from low- and middle-income countries traveling to experience health care in the United States, yet the same hands-on experiences afforded stateside physicians are rarely available for foreign medical graduates or postgraduate trainees when they arrive. These physicians are typically limited to observership experiences where they cannot interact with patients in most U.S. institutions. In this article, the authors discuss this inequity in global medical education, highlighting the shortcomings of the observership training model and the legal and regulatory barriers prohibiting foreign physicians from engaging in short-term clinical training experiences. They provide concrete recommendations on regulatory modifications that would allow meaningful short-term clinical training experiences for foreign medical graduates, including the creation of a new visa category, the designation of a specific temporary licensure category by state medical boards, and guidance for U.S. host institutions supporting such experiences. By proposing this framework, the authors hope to improve equity in global health partnerships via improved access to meaningful and productive educational experiences, particularly for foreign medical graduates with commitment to using their new knowledge and training upon return to their home countries.
Teaching Critical Thinking: A Case for Instruction in Cognitive Biases to Reduce Diagnostic Errors and Improve Patient Safety
Authors: Royce Celeste S. , Hayes Margaret M. , Schwartzstein Richard M.
Published: November 2018

Diagnostic errors contribute to as many as 70% of medical errors. Prevention of diagnostic errors is more complex than building safety checks into health care systems; it requires an understanding of critical thinking, of clinical reasoning, and of the cognitive processes through which diagnoses are made. When a diagnostic error is recognized, it is imperative to identify where and how the mistake in clinical reasoning occurred. Cognitive biases may contribute to errors in clinical reasoning. By understanding how physicians make clinical decisions, and examining how errors due to cognitive biases occur, cognitive bias awareness training and debiasing strategies may be developed to decrease diagnostic errors and patient harm. Studies of the impact of teaching critical thinking skills have mixed results but are limited by methodological problems.

This Perspective explores the role of clinical reasoning and cognitive bias in diagnostic error, as well as the effect of instruction in metacognitive skills on improvement of diagnostic accuracy for both learners and practitioners. Recent literature questioning whether teaching critical thinking skills increases diagnostic accuracy is critically examined, as are studies suggesting that metacognitive practices result in better patient care and outcomes. Instruction in metacognition, reflective practice, and cognitive bias awareness may help learners move toward adaptive expertise and help clinicians improve diagnostic accuracy. The authors argue that explicit instruction in metacognition in medical education, including awareness of cognitive biases, has the potential to reduce diagnostic errors and thus improve patient safety.
The number and localization of CD68+ and CD163+ macrophages in different stages of cutaneous melanoma
Authors: Salmi Satu , Siiskonen Hanna , Sironen Reijo , Tyynelä-Korhonen Kristiina , Hirschovits-Gerz Benjamin , Valkonen Mari , Auvinen Päivi , Pasonen-Seppänen Sanna
Published: November 2018

The role of tumor-associated macrophages (TAMs) in cutaneous melanoma is controversial. TAMs include immunogenic and immunosuppressive subtypes, and have distinct functions according to their microanatomical localization. Our aim was to investigate TAMs in benign, premalignant, and malignant melanocytic lesions to determine possible associations with tumor progression and clinicopathological characteristics. In total, 184 tissue samples, including benign and dysplastic nevi, in-situ melanomas, superficial (Breslow’s depth <1 mm), and deep (Breslow’s depth >4 mm) invasive melanomas and lymph node metastases, were analyzed for macrophage content. Samples were stained immunohistochemically for CD68 and CD163, representing all TAMs and M2-macrophages, respectively. Macrophages were counted by hotspot analysis, and assessed semiquantitatively from the tumor cell nests and stromal component of malignant cases. CD68+ and CD163+ TAMs were more abundant in invasive melanomas compared with benign nevi. The proportion of TAMs in the tumor nests was higher in deep melanomas and lymph node metastases compared with superficially invasive melanomas. High amounts of CD68+ macrophages in tumor cell nests were associated with recurrence, whereas low CD163+ macrophage proportion in tumor stroma was associated with recurrence and in primary melanomas also with poor overall survival. TAMs seem to promote tumor progression in cutaneous melanoma. In particular, CD68+ TAMs and their abundance in tumor nests were associated with poor prognostic factors. However, the correlation of low stromal CD163+ TAM proportion with a poor prognosis indicates that the role of TAMs depends on their subtype and microanatomical localization.
Differential cross-tolerance to the effects of nicotinic acetylcholine receptor drugs in C57BL/6J mice following chronic varenicline
Authors: de Moura Fernando B. , McMahon Lance R.
Published: November 2018

Varenicline is a smoking cessation pharmacotherapy with a presumed mechanism of action of partial efficacy at the α4β2 nicotinic acetylcholine receptor (nAChR); however, the extent to which daily varenicline use leads to changes in nAChR sensitivity is unclear. This study examined the consequences of daily varenicline treatment on disruptions in operant responding (i.e. rate-decreasing effects) and hypothermia induced by administration of nicotine, epibatidine, cytisine, and cocaine in C57BL/6J mice. Furthermore, mecamylamine was used to assess the involvement of nAChRs in the effects of varenicline. Mice were trained under a fixed ratio 20 of milk reinforcement, and rectal temperatures were measured after 30 min following drug-administration. Varenicline, nicotine, epibatidine, and cytisine produced dose-dependent decreases in response rate and rectal temperature. Chronic varenicline (30 mg/kg) engendered tolerance to varenicline, but more cross-tolerance to nicotine, for both disruptions in operant responding and hypothermia. Cross-tolerance only developed to the hypothermic effects of epibatidine, and no cross-tolerance developed to any effects of cytisine and cocaine. In varenicline-tolerant mice, mecamylamine did not antagonize the effects of varenicline. The varying magnitudes of tolerance and cross-tolerance among effects and drugs are indicative of a nonuniform nAChR pharmacology in vivo.
Abortion through telemedicine
Authors: Fok Wing Kay , Mark Alice
Published: November 2018

Purpose of review

Medical abortion offers a well tolerated and effective method to terminate early pregnancy, but remains underutilized in the United States. Over the last decade, ‘telemedicine’ has been studied as an option for medical abortion to improve access when patients and providers are not together. A number of studies have explored various practice models and their feasibility as an alternative to in-person service provision.

Recent findings

A direct-to-clinic model of telemedicine medical abortion has similar efficacy with no increased risk of significant adverse events when compared with in-person abortion. A direct-to-consumer model is currently being studied in the United States. International models of direct-to-consumer medical abortion have shown promising results.

The introduction of telemedicine into abortion care has been met with early success. Currently, there are limitations to the reach of telemedicine because of specific restrictions on mifepristone in the United States as well as laws that specifically prohibit telemedicine for abortion. If these barriers are removed, telemedicine can potentially increase abortion access.
The Endogenous Opioid System: Role and Dysfunction Caused by Opioid Therapy
Authors: TOUBIA TAREK , KHALIFE TAREK
Published: November 2018

The endogenous opioid system is comprised of a wide array of receptors and ligands that are present throughout the central and peripheral nervous system, the gastrointestinal tract, and the immune system. This explains the multitude of physiological functions it is responsible for including analgesia, mood regulation, and modulation of the stress response. It also plays a pivotal role in modulating the brain’s reward center with behavioral and social implications on mood disorders and addiction. Exogenous opioid therapy hijacks the endogenous system and alters its functions contributing to an imbalance that is responsible for the pathogenesis of several disease states.
Short Peripheral Catheter Quality and Economics
Authors: Jones Randall K.
Published: November 2018

Peripheral intravenous therapy is an established therapy with known complications and failures. The burden of the cost of unsuccessful short peripheral catheter (SPC) placement and maintenance is not always clearly identified. This often-obscured cost of poor quality needs to be defined and addressed. The scope of the problem is defined here, and a metric that can be applied to measure the magnitude of the problem and identify targets for focused improvement initiatives that would improve the quality of infusion therapy using SPCs is proposed.
Does the Use of an Infusion Pump for Red Blood Cells Increase Hemolysis?
Authors: Centrella-Nigro Andrea , Scarano Joseph , Ramraj Nadine
Published: November 2018

Transfusions of red blood cells (RBCs) are frequently administered for a variety of clinical conditions. The use of an infusion pump has become common practice in nursing. Lack of evidence regarding hemolysis associated with transfusing older RBCs using an infusion pump led one 361-bed acute care suburban medical center to maintain its nursing policy to infuse all blood products by gravity. A combined simulated and clinical study was conducted with 25 units of RBCs. No significant hemolysis was demonstrated as measured by hemolysis index and serum potassium levels. As a result of this study, the nursing policy at the medical center was changed.
PD-1 Expression in HIV-Specific CD8+ T cells Before Antiretroviral Therapy Is Associated With HIV Persistence
Authors: Ghiglione Yanina , Trifone César , Salido Jimena , Rhodes Ajantha , Ruiz María Julia , Polo María Laura , Salomón Horacio , Laufer Natalia , Sued Omar , Lewin Sharon R. , Turk Gabriela
Published: November 2018

Background:

The persistence of latently infected T cells remains the principal barrier to HIV cure. Understanding how the early immune responses shape persistence of HIV on antiretroviral therapy (ART) will be fundamental for potential eradication. Here, we aimed to determine the relationship between CD8+ T-cell function and phenotype before therapy and HIV persistence on ART.

Methods:

Blood samples from 29 individuals enrolled during primary HIV infection (at baseline and every 3 months up to 2 years post-ART initiation) were obtained. HIV-specific T-cell function and expression of the activation markers were evaluated before ART by flow cytometry. Cell-associated HIV DNA and unspliced (US)-RNA were quantified in purified CD4+ T cells by real-time polymerase chain reaction. Data were analyzed using nonparametric statistics.

Results:

Elevated immune activation, dominance of monofunctional CD8+ T cells, and skewed distribution of memory profile were observed before ART. After ART initiation, HIV DNA and US-RNA levels rapidly diminished, reaching a plateau by 30 weeks after ART. The proportion of baseline HIV-specific effector memory and terminal effector CD8+ T cells directly correlated with HIV DNA levels at 1 year after ART. A strong positive correlation was observed between the proportion of bulk and HIV-specific PD-1High CD8+ T cells measured before ART and HIV DNA at 1 year after ART.

Conclusions:

A higher proportion of terminally differentiated CD8+ T cells and increased PD1 expression were associated with HIV persistence on ART after treatment of primary infection. Thus, the quality of the early CD8+ T-cell immune response may serve as a predictor of HIV persistence on ART.
Axillary Chest Wall Hibernoma With Intrathoracic Extension Presenting as Thoracic Outlet Syndrome
Authors: Klinkenberg Theo J. , Wolf Rienhart F.E. , Bouma Wobbe , Suurmeijer Albert J.H. , Mariani Massimo A.
Published: November 2018

Hibernomas are rare benign soft tissue tumors derived from brown fat. This case report describes an axillary hibernoma with intrathoracic extension, presenting as a thoracic outlet syndrome. A multimodality imaging series illustrates the classic radiologic features of hibernoma as well as its highly unusual pattern of growth. The latter resulted in TOS with vascular displacement and osseous remodeling, features that are generally absent in lipomatous masses. Detailed preoperative imaging allowed to plan a single surgical procedure in which an extrathoracic axillary approach was combined with intrathoracic video-assisted thoracic surgery.
Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini
Authors: Toczydlowska-Socha Diana , Zielinska Magdalena M. , Kurkowska Malgorzata , Astha  , Almeida Catarina F. , Stefaniak Filip , Purta Elzbieta , Bujnicki Janusz M.
Published: November 2018

The 5′-cap structure, characteristic for RNA polymerase II-transcribed RNAs, plays important roles in RNA metabolism. In humans, RNA cap formation includes post-transcriptional modification of the first transcribed nucleotide by RNA cap1 methyltransferase (CMTr1). Here, we report that CMTr1 activity is hindered towards RNA substrates with highly structured 5′ termini. We found that CMTr1 binds ATP-dependent RNA DHX15 helicase and that this interaction, mediated by the G-patch domain of CMTr1, has an advantageous effect on CMTr1 activity towards highly structured RNA substrates. The effect of DHX15 helicase activity is consistent with the strength of the secondary structure that has to be removed for CMTr1 to access the 5′-terminal residues in a single-stranded conformation. This is, to our knowledge, the first demonstration of the involvement of DHX15 in post-transcriptional RNA modification, and the first example of a molecular process in which DHX15 directly affects the activity of another enzyme. Our findings suggest a new mechanism underlying the regulatory role of DHX15 in the RNA capping process. RNAs with highly structured 5′ termini constitute a significant fraction of the human transcriptome. Hence, CMTr1–DHX15 cooperation is likely to be important for the metabolism of RNA polymerase II-transcribed RNAs.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
RNA uridylation and decay in plants
Authors: de Almeida Caroline , Scheer Hélène , Gobert Anthony , Fileccia Veronica , Martinelli Federico , Zuber Hélène , Gagliardi Dominique
Published: November 2018

RNA uridylation consists of the untemplated addition of uridines at the 3′ extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algaeChlamydomonas reinhardtiiand the flowering plantArabidopsis thaliana. Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include microRNAs (miRNAs), small interfering silencing RNAs (siRNAs), ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) and mRNA fragments generated during post-transcriptional gene silencing. Viral RNAs can also get uridylated during plant infection. We describe here the evolutionary history of plant TUTases and we summarize the diverse molecular functions of uridylation during RNA degradation processes in plants. We also outline key points of future research.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
RNA polyadenylation and its consequences in prokaryotes
Authors: Hajnsdorf Eliane , Kaberdin Vladimir R.
Published: November 2018

Post-transcriptional addition of poly(A) tails to the 3′ end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered inEscherichia colimore than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 thatE. colipoly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin–antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
mRNAs biotinylated within the 5′ cap and protected against decapping: new tools to capture RNA–protein complexes
Authors: Bednarek Sylwia , Madan Vanesa , Sikorski Pawel J. , Bartenschlager Ralf , Kowalska Joanna , Jemielity Jacek
Published: November 2018

The 5′-terminus of eukaryotic mRNAs comprises a 7-methylguanosine cap linked to the first transcribed nucleotide via a 5′-5′ triphosphate bond. This cap structure facilitates numerous interactions with molecules participating in mRNA processing, turnover and RNA translation. Here, we report the synthesis and biochemical properties of a set of biotin-labelled cap analogues modified within the triphosphate bridge and increasing mRNA stability while retaining biological activity. Successful co-transcriptional incorporation of the cap analogues allowed for the quantification of cap-dependent translation efficiency, capping efficiency and the susceptibility to decapping by Dcp2. The utility of such cap-biotinylated RNAs as molecular tool was demonstrated by ultraviolet-cross-linking and affinity capture of protein–RNA complexes. In conclusion, RNAs labelled with biotin via the 5′ cap structure can be applied to a variety of biological experiments based on biotin–avidin interaction or by means of biotin-specific antibodies, including protein affinity purification, pull-down assays,
in vivo
visualization, cellular delivery and many others.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
The multitasking polyA tail: nuclear RNA maturation, degradation and export
Authors: Tudek Agnieszka , Lloret-Llinares Marta , Jensen Torben Heick
Published: November 2018

A polyA (pA) tail is an essential modification added to the 3′ ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast
Saccharomyces cerevisiae
, human cells and, when relevant, the fission yeast
Schizosaccharomyces pombe
. Polyadenylation mediated by the
S. cerevisiae
Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3′-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in
S. pombe
and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
Role of oligouridylation in normal metabolism and regulated degradation of mammalian histone mRNAs
Authors: Meaux Stacie A. , Holmquist Christopher E. , Marzluff William F.
Published: November 2018

Metazoan replication-dependent histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Histone mRNAs are present in large amounts only in S-phase cells, and their levels are coordinately regulated with the rate of DNA replication. In mammals, the stemloop at the 3′ end of histone mRNA is bound to stemloop binding protein, a protein required for both synthesis and degradation of histone mRNA, and an exonuclease, 3′hExo (ERI1). Histone mRNAs are rapidly degraded when DNA synthesis is inhibited in S-phase cells and at the end of S-phase. Upf1 is also required for rapid degradation of histone mRNA as is the S-phase checkpoint. We report that Smg1 is required for histone mRNA degradation when DNA replication is inhibited, suggesting it is the PI-like kinase that activates Upf1 for histone mRNA degradation. We also show that some mutant Upf1 proteins are recruited to histone mRNAs when DNA replication is inhibited and act as dominant negative factors in histone mRNA degradation. We report that the pathway of rapid histone mRNA degradation when DNA replication is inhibited in S-phase cells that are activating the S-phase checkpoint is similar to the pathway of rapid degradation of histone mRNA at the end of S-phase.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
The role of 3′ end uridylation in RNA metabolism and cellular physiology
Authors: Zigáčková Dagmar , Vaňáčová Štěpánka
Published: November 2018

Most eukaryotic RNAs are posttranscriptionally modified. The majority of modifications promote RNA maturation, others may regulate function and stability. The 3′ terminal non-templated oligouridylation is a widespread modification affecting many cellular RNAs at some stage of their life cycle. It has diverse roles in RNA metabolism. The most prevalent is the regulation of stability and quality control. On the cellular and organismal level, it plays a critical role in a number of pathways, such as cell cycle regulation, cell death, development or viral infection. Defects in uridylation have been linked to several diseases. This review summarizes the current knowledge about the role of the 3′ terminal oligo(U)-tailing in biology of various RNAs in eukaryotes and describes key factors involved in these pathways.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
A comprehensive analysis of single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer
Authors: Zhang Peng , Yang Mingran , Zhang Yiding , Xiao Shuai , Lai Xinxing , Tan Aidi , Li Shao
Published: November 2018

Intestinal-type gastric cancer is preceded by premalignant lesions including chronic atrophic gastritis (CAG) and intestinal metaplasia (IM), which are characterized as changes in cell types. In this study, for the first time, we systematically constructed a single-cell atlas for a total of 31,164 high-quality cells from gastric mucosa biopsies of patients spanning a cascade of gastric premalignant lesions and early gastric cancer (EGC) using single-cell RNA sequencing (scRNA-seq). Based on the atlas, we construct a network underlying the changes of cellular and molecular characteristics of gastric epithelial cells across different lesions. We found the conversion of gland mucous cells (GMCs) toward a more intestinal-like stem cell phenotype during metaplasia, and identified OR51E1 as a novel marker for early-malignant enteroendocrine cells. We also found that HES6 might mark a goblet cell subset that precede morphologically identifiable goblet cells in IM mucosa, potentially aiding the identification of metaplasia at the early stage. Finally, we identified a panel of EGC-related specific signature, with clinical implications for the precise diagnosis of EGC. Our study offers unparalleled insights into the human gastric cellulome in premalignant and early-malignant lesions and provides an important data resource that will facilitate studies in gastritis-induced tumourigenesis and gastric cell biology.

Significance Statement

Understanding cellular characteristics in gastric premalignant and malignant lesions would help us better understand the gastric cancer (GC) pathogenesis. In this paper, for the first time, we systematically constructed a single-cell transcriptome network of human premalignant gastric mucosa and early GC (EGC) and derived novel findings from it. We identified OR51E1 as a novel marker for early-malignant enteroendocrine cells and a panel of genes as the EGC-specific signature, with clinical implications for the precise diagnosis of EGC. We also found HES6 might mark a goblet cell subset that precede morphologically identifiable goblet cells in IM mucosa, potentially aiding the identification of metaplasia at the early stage. Our study provided an unprecedented data resource that will facilitate studies underlying gastritis-induced tumorigenesis.
Multifaceted influence of pre-mitotic cytotoxicity of primed CD8 T cells on immunity and infection
Authors: Dandamudi Durga Bhavani , Blair David A , Arifa Raquel Duque do Nascimento , Lafaille Juan J , Dustin Michael L , Mayya Viveka
Published: November 2018

Granzyme B mRNA is expressed in primed CD8 T cells within 12 hours, but the consequences of this for the immune response are unknown. We observed that substantial portion of the naïve CD8 T cell repertoire expressed granzyme B and became pre-mitotic cytotoxic cells (PMCs) immediately in response toListeria monocytogenesorLymphocytic choriomeningitis virusinfections. The surprising breadth arose from sufficiency of low potency peptide-MHC to induce granzyme B expression in the context of infection. PMCs killed antigen bearing dendritic cells (DCs) in a granzyme B-dependent but largely perforinindependent fashion between 1-2 days post infection. This terminated antigen presentation at 3 days and resulted in reduced clonal expansion. As additional consequences, we highlight that PMCs reduced the burden of DC-borne infectious agents, but also opened a window of vulnerability for secondary infection. Thus, PMCs serve antigen-specific, regulatory and host defence functions, that are innate-like in scale, at the onset of the adaptive immune response.
DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data
Authors: Xue Albert Y. , Yu Angela M , Lucks Julius B. , Bagheri Neda
Published: November 2018

Motivation

RNA molecules can undergo complex structural dynamics, especially during transcription, which influence their biological functions. Recently developed high-throughput chemical probing experiments study RNA cotranscriptional folding to generate nucleotide-resolution ‘reactivities’ for each length of a growing nascent RNA and reflect structural dynamics. However, the manual annotation and qualitative interpretation of reactivity across these large datasets can be nuanced, laborious, and difficult for new practitioners. We developed a quantitative and systematic approach to automatically detect RNA folding events from these datasets to reduce human bias/error, standardize event discovery, and generate hypotheses about RNA folding trajectories for further analysis and experimental validation.

Results

Detection ofUnknownEvents withTunableThresholds (DUETT) identifies RNA structural transitions in cotranscriptional RNA chemical probing datasets. DUETT employs a feedback control-inspired method and a linear regression approach and relies on interpretable and independently tunable parameter thresholds to match qualitative user expectations with quantitatively identified folding events. We validate the approach by identifying known RNA structural transitions within the cotranscriptional folding pathways of theEscherichia colisignal recognition particle (SRP) RNA and theBacillus cereus crcBfluoride riboswitch. We identify previously overlooked features of these datasets such as heightened reactivity patterns in the SRP RNA about 12 nucleotide lengths before base pair rearrangement. We then apply a sensitivity analysis to identify tradeoffs when choosing parameter thresholds. Finally, we show that DUETT is tunable across a wide range of contexts, enabling flexible application to study broad classes of RNA folding mechanisms.

Availability

https://github.com/BagheriLab/DUETT

Contact

jblucks@northwestern.edu,n-bagheri@northwestern.edu
Long Non-Coding RNA LncKdm2b Regulates Cortical Neuronal Differentiation by Cis-Activating Kdm2b
Authors: Li Wei , Shen Wenchen , Zhang Bo , Tian Kuan , Li Yamu , Mu Lili , Luo Zhiyuan , Zhong Xiaoling , Wu Xudong , Liu Ying , Zhou Yan
Published: November 2018

The mechanisms underlying spatial and temporal control of cortical neurogenesis of the brain are largely elusive. Long non-coding RNAs (lncRNAs) have emerged as essential cell fate regulators. Here we found LncKdm2b (also known as Kancr), a lncRNA divergently transcribed from a bidirectional promoter of Kdm2b, is transiently expressed during early differentiation of cortical projection neurons. Interestingly, Kdm2b’s transcription is positively regulated in cis by LncKdm2b, which has intrinsic-activating function and facilitates a permissive chromatin environment at the Kdm2b’s promoter by associating with hnRNPAB. Lineage tracing experiments and phenotypic analyses indicated LncKdm2b and Kdm2b are crucial in proper differentiation and migration of cortical projection neurons. Moreover, KDM2B exerts its role relying on its leucine-rich repeats (LRR) but independent of its PRC1-related function. These observations unveiled a lncRNA-dependent machinery in regulating cortical neuronal differentiation.
Berberine chloride ameliorated PI3K/Akt-p/SIRT-1/PTEN signaling pathway in insulin resistance syndrome-induced rats
Authors: El-Zeftawy Marwa , Ghareeb Doaa , Saad Rasha , Mahmoud Salma , Elguindy Nihal , El-Sayed Mohammed
Published: November 2018

Insulin resistance is one of dangerous factors as it leads to numerous metabolic disorders such as non-insulin dependent diabetes mellitus. It affects most tissues mainly adipose tissue, liver and muscle. Nowadays, berberine has several medical applications against diseases. The current study was carried out to identify the effect of berberine chloride (BER-chloride) on phosphatidyl inositol-3-kinase/ phosphorylated protein kinase B/ sirtuin type 1/ phosphatase and tension homologue (PI3K/Akt-p/SIRT-1/PTEN) pathway during insulin resistance phenomena. Insulin resistance model was performed in experimental rats by using high fat diet. Plasma glucose, serum insulin, lipid profiles, hepatic oxidative stress markers were estimated. Serum transaminases activities and kidney function tests were determined. Further, hepatic PI3K, AKt-p, SIRT-1; PTEN levels were assayed. The concentration of adiponectin in serum, hepatic tissue and white adipose tissue was determined. Moreover, fold change in hepatic insulin, insulin receptor and retinol binding protein-4 (RBP4) at molecular level was performed. Histopathological study of white adipose tissue was also determined. The results showed increase the rats’ body weights, blood glucose, homeostatic model assessment, glycated hemoglobin, insulin and lipid profiles levels in group of rats fed on high fat diet for eight weeks and this elevation was decreased after administration of BER-chloride for two weeks. Further, BER-chloride administration exhibited improvement of oxidative stress parameters, PI3K, AKt-p, SIRT-1 and PTEN. This was associated with down-regulation of RBP4. According to these data we conclude that, BER-chloride mediated several insulin signaling pathways that could be of therapeutic significance to insulin resistance.
Cellular response to small molecules that selectively stall protein synthesis by the ribosome
Authors: Liaud Nadège , Horlbeck Max A. , Gilbert Luke A. , Gjoni Ketrin , Weissman Jonathan S. , Cate Jamie H. D.
Published: November 2018

Identifying small molecules that inhibit protein synthesis by selectively stalling the ribosome constitutes a new strategy for therapeutic development. Compounds that inhibit the translation of PCSK9, a major regulator of low-density lipoprotein cholesterol, have been identified that reduce LDL cholesterol in preclinical models and that affect the translation of only a few off-target proteins. Although some of these compounds hold potential for future therapeutic development, it is not known how they impact the physiology of cells or ribosome quality control pathways. Here we used a genome-wide CRISPRi screen to identify proteins and pathways that modulate cell growth in the presence of high doses of a selective PCSK9 translational inhibitor, PF-06378503 (PF8503). The two most potent genetic modifiers of cell fitness in the presence of PF8503, the ubiquitin binding protein ASCC2 and helicase ASCC3, bind to the ribosome and protect cells from toxic effects of high concentrations of the compound. Surprisingly, translation quality control proteins Pelota (PELO) and HBS1L sensitize cells to PF8503 treatment. In genetic interaction experiments, ASCC3 acts together with ASCC2, and functions downstream of HBS1L. Taken together, these results identify new connections between ribosome quality control pathways, and provide new insights into the selectivity of compounds that stall human translation that will aid the development of next-generation selective translation stalling compounds to treat disease.
Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation
Authors: Vidad Ashley R. , Macaspac Stephen , Ng Ho-Leung
Published: November 2018

G-protein coupled receptors (GPCRs) are the largest protein family of drug targets. Detailed mechanisms of binding are unknown for many important GPCR-ligand pairs due to the difficulties of GPCR recombinant expression, biochemistry, and crystallography. We describe our new method, ConDock, for predicting ligand binding sites in GPCRs using combined information from surface conservation and docking starting from crystal structures or homology models. We demonstrate the effectiveness of ConDock on well-characterized GPCRs such as the β2 adrenergic and A2A adenosine receptors. We also demonstrate that ConDock successfully predicts ligand binding sites from high-quality homology models. Finally, we apply ConDock to predict ligand binding sites on a structurally uncharacterized GPCR, GPER. GPER is the G-protein coupled estrogen receptor, with four known ligands: estradiol, G1, G15, and tamoxifen. ConDock predicts that all four ligands bind to the same location on GPER, centered on L119, H307, and N310; this site is deeper in the receptor cleft than predicted by previous studies. We compare the sites predicted by ConDock and traditional methods that utilize information from surface geometry, surface conservation, and ligand chemical interactions. Incorporating sequence conservation information in ConDock overcomes errors introduced from physics-based scoring functions and homology modeling.
A thermodynamic chemical reaction network drove autocatalytic prebiotic peptides formation
Authors: Bao Peng , He Yu-Qin , Li Guo-Xiang , Zhang Hui-En , Xiao Ke-Qing
Published: November 2018

The chemical reaction networks (CRNs), which led to the transition on early Earth from geochemistry to biochemistry remain unknown. We show that under mild hydrothermal circumstances, a thermodynamic chemical reaction network including sulfite/sulfate coupled with anaerobic ammonium oxidation (Sammox), might have driven prebiotic peptides synthesis. Peptides comprise 14 proteinogenic amino acids, endowed Sammox-driven CRNs with autocatalysis. The peptides exhibit both forward and reverse catalysis, with the opposite catalytic impact in sulfite- and sulfate-fueled Sammox-driven CRNs, respectively, at both a variable temperature range and a fixed temperature, resulting in seesaw-like catalytic properties. The ratio of sulfite to sulfate switches the catalytic orientation of peptides, resulting in Sammox-driven CRNs that has both anabolic and catabolic reactions at all times. Furthermore, peptides produced from sulfite-fueled Sammox-driven CRNs could catalyze both sulfite-fueled Sammox and Anammox (nitrite reduction coupled with anaerobic ammonium oxidation) reactions. We propose that Sammox-driven CRNs were critical in the creation of life and that Anammox microorganisms that have both Sammox functions are direct descendants of Sammox-driven CRNs.
The Brain-Derived Neurotrophic Factor Val66Met Genotype Does Not Influence the Grey or White Matter Structures Underlying Recognition Memory
Authors: McKay Nicole S. , Moreau David. , Henare Dion T. , Kirk Ian J.
Published: November 2018

A single nucleotide polymorphism (SNP) in the gene coding for brain-derived neurotrophic factor (BDNF) has previously been associated with a reduction in recognition memory performance. While previous findings have highlighted that this SNP contributes to recognition memory, little is known about its influence on subprocesses of recognition, familiarity and recollection. Previous research has reported reduced hippocampal volume and decreased fractional anisotropy in carriers of the Met allele across a range of white matter tracts, including those networks that may support recognition memory. Here, in a sample of 61 healthy young adults, we used a source memory task to measure accuracy on each recognition subprocess, in order to determine whether the Val66Met SNP (rs6265) influences these equally. Additionally, we compared grey matter volume between these groups for structures that underpin familiarity and recollection separately. Finally, we used probabilistic tractography to reconstruct tracts that subserve each of these two recognition systems. Behaviourally, we found group differences on the familiarity measure, but not on recollection. However, we did not find any group difference on grey- or white-matter structures. Together, these results suggest a functional influence of the Val66Met SNP that is independent of coarse structural changes, and nuance previous research highlighting the relationship between BDNF, brain structure, and behaviour.
Destin: toolkit for single-cell analysis of chromatin accessibility
Authors: Urrutia Eugene , Chen Li , Zhou Haibo , Jiang Yuchao
Published: November 2018

Single-cell assay of transposase-accessible chromatin followed by sequencing (scATAC-seq) is an emerging new technology for the study of gene regulation with single-cell resolution. The data from scATAC-seq are unique sparse, binary, and highly variable even within the same cell type. As such, neither methods developed for bulk ATAC-seq nor single-cell RNA-seq data are appropriate. Here, we present Destin, a bioinformatic and statistical framework for comprehensive scATAC-seq data analysis. Destin performs cell-type clustering via weighted principle component analysis, weighting accessible chromatin regions by existing genomic annotations and publicly available regulomic data sets. The weights and additional tuning parameters are determined via model-based likelihood. We evaluated the performance of Destin using downsampled bulk ATAC-seq data of purified samples and scATAC-seq data from seven diverse experiments. Compared to existing methods, Destin was shown to outperform across all data sets and platforms. For demonstration, we further applied Destin to 2,088 adult mouse forebrain cells and identified cell type-specific association of previously reported schizophrenia GWAS loci.

Availability

Destin toolkit is freely available as an R package at https://github.com/urrutiag/destin.

Contact

yuchaoj@email.unc.edu.
On the adaptive behavior of head-fixed flies navigating in two-dimensional, visual virtual reality
Authors: Haberkern Hannah , Basnak Melanie A. , Ahanonu Biafra , Schauder David , Cohen Jeremy D. , Bolstad Mark , Bruns Christopher , Jayaraman Vivek
Published: November 2018

A navigating animal’s sensory experience is shaped not just by its surroundings, but by its movements within them, which in turn are influenced by its past experiences. Studying the intertwined roles of sensation, experience and directed action in navigation has been made easier by the development of virtual reality (VR) environments for head-fixed animals, which allow for quantitative measurements of behavior in well-controlled sensory conditions. VR has long featured in studies ofDrosophila melanogaster, but these experiments have typically relied on one-dimensional (1D) VR, effectively allowing the fly to change only its heading in a visual scene, and not its position. Here we explore how flies navigate in a two-dimensional (2D) visual VR environment that more closely resembles their experience during free behavior. We show that flies’ interaction with landmarks in 2D environments cannot be automatically derived from their behavior in simpler 1D environments. Using a novel paradigm, we then demonstrate that flies in 2D VR adapt their behavior in a visual environment in response to optogenetically delivered appetitive and aversive stimuli. Much like free-walking flies after encounters with food, head-fixed flies respond to optogenetic activation of sugar-sensing neurons by initiating a local search behavior. Finally, by pairing optogenetic activation of heat-sensing cells to the flies’ presence near visual landmarks of specific shapes, we elicit selective learned avoidance of landmarks associated with aversive “virtual heat”. These head-fixed paradigms set the stage for an interrogation of fly brain circuitry underlying flexible navigation in complex visual environments.