bluuebunny/crossref_metadata_2025 huggingface dataset:
Latent periodic process inference from single-cell RNA-seq data
Authors: Liang Shaoheng , Wang Fang , Han Jincheng , Chen Ken
Published: May 2019

Convoluted biological processes underlie the development of multicellular organisms and diseases. Advances in scRNA-seq make it possible to study these processes from cells at various developmental stages. Achieving accurate characterization is challenging, however, particularly for periodic processes, such as cell cycles. To address this, we developed Cyclum, a novel AutoEncoder approach that characterizes circular trajectories in the high-dimensional gene expression space. Cyclum substantially improves the accuracy and robustness of cell-cycle characterization beyond existing approaches. Applying Cyclum to removing cell-cycle effects leads to substantially improved delineations of cell subpopulations, which is useful for establishing various cell atlases and studying tumor heterogeneity. Cyclum is available at https://github.com/KChen-lab/cyclum.
Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
Authors: Fang Li Tai , Zhu Bin , Zhao Yongmei , Chen Wanqiu , Yang Zhaowei , Kerrigan Liz , Langenbach Kurt , Mars Maryellen de , Lu Charles , Idler Kenneth , Jacob Howard , Yu Ying , Ren Luyao , Zheng Yuanting , Jaeger Erich , Schroth Gary , Abaan Ogan D. , Lack Justin , Shen Tsai-Wei , Talsania Keyur , Chen Zhong , Stanbouly Seta , Shetty Jyoti , Tran Bao , Meerzaman Daoud , Nguyen Cu , Petitjean Virginie , Sultan Marc , Cam Margaret , Hung Tiffany , Peters Eric , Kalamegham Rasika , Ebrahim Sahraeian Sayed Mohammad , Mohiyuddin Marghoob , Guo Yunfei , Yao Lijing , Song Lei , Lam Hugo YK , Drabek Jiri , Maestro Roberta , Gasparotto Daniela , Kõks Sulev , Reimann Ene , Scherer Andreas , Nordlund Jessica , Liljedahl Ulrika , Jensen Roderick V , Pirooznia Mehdi , Li Zhipan , Xiao Chunlin , Sherry Stephen , Kusko Rebecca , Moos Malcolm , Donaldson Eric , Tezak Zivana , Ning Baitang , Li Jing , Duerken-Hughes Penelope , Hong Huixiao , Shi Leming , Wang Charles , Xiao Wenming ,   The Somatic Working Group of SEQC-II Consortium
Published: May 2019

We characterized two reference samples for NGS technologies: a human triple-negative breast cancer cell line and a matched normal cell line. Leveraging several whole-genome sequencing (WGS) platforms, multiple sequencing replicates, and orthogonal mutation detection bioinformatics pipelines, we minimized the potential biases from sequencing technologies, assays, and informatics. Thus, our “truth sets” were defined using evidence from 21 repeats of WGS runs with coverages ranging from 50X to 100X (a total of 140 billion reads). These “truth sets” present many relevant variants/mutations including 193 COSMIC mutations and 9,016 germline variants from the ClinVar database, nonsense mutations inBRCA1/2and missense mutations inTP53andFGFR1.Independent validation in three orthogonal experiments demonstrated a successful stress test of the truth set. We expect these reference materials and “truth sets” to facilitate assay development, qualification, validation, and proficiency testing. In addition, our methods can be extended to establish new fully characterized reference samples for the community.
Hepatitis C virus infection is inhibited by a non-canonical antiviral signaling pathway targeted by NS3-NS4A
Authors: Vazquez Christine , Tan Chin Yee , Horner Stacy M.
Published: May 2019

The hepatitis C virus (HCV) NS3-NS4A protease complex is required for viral replication and is the major viral innate immune evasion factor. NS3-NS4A evades antiviral innate immunity by inactivating several proteins, including MAVS, the signaling adaptor for RIG-I and MDA5, and Riplet, an E3 ubiquitin ligase that activates RIG-I. Here, we identified a Tyr-16-Phe (Y16F) change in the NS4A transmembrane domain that prevents NS3-NS4A targeting of Riplet but not MAVS. This Y16F substitution reduces HCV replication in Huh7 cells, but not in Huh-7.5 cells, known to lack RIG-I signaling. Surprisingly, deletion of RIG-I in Huh7 cells did not restore Y16F viral replication. Rather, we found that Huh-7.5 cells lack Riplet expression and that addition of Riplet to these cells reduced HCV Y16F replication. In addition, IRF3 deletion in Huh7 cells was sufficient to restore HCV Y16F replication, and the Y16F protease lacked the ability to prevent IRF3 activation or interferon induction. Taken together, these data reveal that the NS4A Y16 residue regulates a non-canonical Riplet-IRF3-dependent, but RIG-I-MAVS-independent, signaling pathway that limits HCV infection.

Importance

The HCV NS3-NS4A protease complex facilitates viral replication by cleaving and inactivating the antiviral innate immune signaling proteins MAVS and Riplet, which are essential for RIG-I activation. NS3-NS4A therefore prevents IRF3 activation and interferon induction during HCV infection. Here, we uncover an amino acid residue within the NS4A transmembrane domain that is essential for inactivation of Riplet, but does not affect MAVS cleavage by NS3-NS4A. Our study reveals that Riplet is involved in a RIG-I- and MAVS-independent signaling pathway that activates IRF3 and that this pathway is normally inactivated by NS3-NS4A during HCV infection. Our study selectively uncouples these distinct regulatory mechanisms within NS3-NS4A and defines a new role for Riplet in the antiviral response to HCV. As Riplet is known to be inhibited by other RNA viruses, such as such influenza A virus, this innate immune signaling pathway may also be important in controlling other RNA virus infections.
Charge and hydrophobicity are key features in sequence-trained machine learning models for predicting the biophysical properties of clinical-stage antibodies
Authors: Hebditch Max , Warwicker Jim
Published: May 2019

Abstract

Improved understanding of properties that mediate protein solubility and resistance to aggregation are important for developing biopharmaceuticals, and more generally in biotechnology and synthetic biology. Recent acquisition of large datasets for antibody biophysical properties enables the search for predictive models. In this report, machine learning methods are used to derive models for 12 biophysical properties. A physicochemical perspective is maintained in analysing the models, leading to the observation that models cluster largely according to charge (cross-interaction measurements) and hydrophobicity (self-interaction methods). These two properties also overlap in some cases, for example in a new interpretation of variation in hydrophobic interaction chromatography. Since the models are developed from differences of antibody variable loops, the next stage is to extend models to more diverse protein sets.

Availability

The web application for the sequence based algorithms are available on the protein-sol webserver, at https://protein-sol.manchester.ac.uk/abpred, with models and virtualisation software available at https://protein-sol.manchester.ac.uk/software.
Overexpression of osmosensitive Ca2+-activated channel TMEM63B promotes migration in HEK293T cells
Authors: Marques Marta C. , Albuquerque Inês S. , Vaz Sandra H. , Bernardes Gonçalo J. L.
Published: May 2019

The recent discovery of the osmosensitive calcium (Ca2+) channel OSCA has revealed the potential mechanism by which plant cells sense diverse stimuli. Osmosensory transporters and mechanosensitive channels can detect and respond to osmotic shifts that play an important role in active cell homeostasis. TMEM63 family of proteins are described as the closest homologues of OSCAs. Here, we characterize TMEM63B, a mammalian homologue of OSCAs, recently classified as mechanosensitive. In HEK293T cells TMEM63B localizes to the plasma membrane and is associated to F-actin. This Ca2+-activated channel specifically induces Ca2+ influx across the membrane in response to extracellular Ca2+ concentration and hyperosmolarity. In addition, overexpression of TMEM63B in HEK293T cells significantly enhanced cell migration and wound healing. The link between Ca2+ osmosensitivity and cell migration might help to establish TMEM63B’s pathogenesis, for example in cancer in which it is frequently overexpressed.
Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling
Authors: Girma Gezahegn , Natsume Satoshi , Carluccio Anna Vittoria , Takagi Hiroki , Matsumura Hideo , Uemura Aiko , Muranaka Satoru , Takagi Hiroko , Stavolone Livia , Gedil Melaku , Spillane Charles , Terauchi Ryohei , Tamiru Muluneh
Published: May 2019

Dioecy (distinct male and female individuals) combined with scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata). SuperSAGE analysis generated a total of 20,236 unique tags, of which 13,901 were represented by a minimum of 10 tags. Of these, 88 tags were significantly differentially expressed in male, female and monoecious plants. Of the 88 differentially expressed SuperSAGE tags, 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of four candidate genes. Our findings suggest that mechanisms of flowering and sex determination are likely conserved in Dioscorea. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two years, revealing that over 85% of the accessions are either male or non-flowering, and that less than 15% are female, while monoecious plants are rare. Intensity of flowering appeared to be a function of sex, with male plants flowering more abundantly than female ones. Candidate genes identified in this study can be targeted with the aim to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve the efficiency of yam breeding.
Using distant supervision to augment manually annotated data for relation extraction
Authors: Su Peng , Li Gang , Wu Cathy , Vijay-Shanker K.
Published: May 2019

Significant progress has been made in applying deep learning on natural language processing tasks recently. However, deep learning models typically require a large amount of annotated training data while often only small labeled datasets are available for many natural language processing tasks in biomedical literature. Building large-size datasets for deep learning is expensive since it involves considerable human effort and usually requires domain expertise in specialized fields. In this work, we consider augmenting manually annotated data with large amounts of data using distant supervision. However, data obtained by distant supervision is often noisy, we first apply some heuristics to remove some of the incorrect annotations. Then using methods inspired from transfer learning, we show that the resulting models outperform models trained on the original manually annotated sets.
A Circuit Model of Auditory Cortex
Authors: Park Youngmin , Geffen Maria N.
Published: May 2019

The mammalian sensory cortex is composed of multiple types of inhibitory and excitatory neurons, which form sophisticated microcircuits for processing and transmitting sensory information. Despite rapid progress in understanding the function of distinct neuronal populations, the parameters of connectivity that are required for the function of these microcircuits remain unknown. Recent studies found that two most common inhibitory interneurons, parvalbumin- (PV) and somatostatin-(SST) positive interneurons control sound-evoked responses, temporal adaptation and network dynamics in the auditory cortex (AC). These studies can inform our understanding of parameters for the connectivity of excitatory-inhibitory cortical circuits. Specifically, we asked whether a common microcircuit can account for the disparate effects found in studies by different groups. By starting with a cortical rate model, we find that a simple current-compensating mechanism accounts for the experimental findings from multiple groups. They key mechanisms are two-fold. First, PVs compensate for reduced SST activity when thalamic inputs are strong with less compensation when thalamic inputs are weak. Second, SSTs are generally disinhibited by reduced PV activity regardless of thalamic input strength. These roles are augmented by plastic synapses. These differential roles reproduce the differential effects of PVs and SSTs in stimulus-specific adaptation, forward suppression and tuning-curve adaptation, as well as the influence of PVs on feedforward functional connectivity in the circuit. This circuit exhibits a balance of inhibitory and excitatory currents that persists on stimulation. This approach brings together multiple findings from different laboratories and identifies a circuit that can be used in future studies of upstream and downstream sensory processing.

Significance Statement

The mammalian auditory cortex is composed of multiple types of inhibitory and excitatory neurons, which form sophisticated microcircuits for processing and transmitting sensory information. Distinct inhibitory neuron subtypes play distinct functions in auditory processing, but it remains unknown what simple set of underlying mechanisms is responsible for inhibitory cortical function. Here, we built minimal rate and spiking models and identified a specific set of synaptic mechanisms that could best reproduce the broad set of experimental results in the auditory cortex. The simplicity of our model provides an understanding of inhibitory cortical processing at the circuit level, which explains results from different laboratories, and provides for a novel computational framework for future studies of cortical function.
A metabolic pathway for glucosinolate activation by the human gut symbiontBacteroides thetaiotaomicron
Authors: Liou Catherine S. , Sirk Shannon J. , Diaz Camil A.C. , Klein Andrew P. , Fischer Curt R. , Higginbottom Steven K. , Sonnenburg Justin L. , Sattely Elizabeth S.
Published: May 2019

Diet is the largest source of plant-derived metabolites that influence human health. The gut microbiota can metabolize these molecules, altering their biological function. However, little is known about the gut bacterial pathways that process plant-derived molecules. Glucosinolates are well-known metabolites in brassica vegetables and metabolic precursors to cancer-preventive isothiocyanates. Here, we identify a genetic and biochemical basis for isothiocyanate formation byBacteroides thetaiotaomicron,a prominent gut commensal species. Using a genome-wide transposon insertion screen, we identified an operon required for glucosinolate metabolism inB. thetaiotaomicron.Expression of BT2159-BT2156 in a non-metabolizing relative,Bacteroides fragilis, resulted in gain of glucosinolate metabolism. We show that isothiocyanate formation requires the action of BT2158 and either BT2156 or BT2157in vitro. Monocolonization of mice with mutantBtΔ2157showed reduced isothiocyanate production in the gastrointestinal tract. These data provide insight into the mechanisms by which a common gut bacterium processes an important dietary nutrient.
Comparative analysis of the Accelerated Aged seed transcriptome profiles of maize CSSLs (I178 and X178)
Authors: Li Li , Wang Feng , Li Xuhui , Peng Yixuan , Zhang Hongwei , Hey Stefan , Wang Guoying , Wang Jianhua , Gu Riliang
Published: May 2019

Seed longevity is one of the most essential characters of seed quality. Two Chromosome segment substitution lines (CSSL) I178 and X178 with significant difference on seed longevity were subjected to transcriptome sequencing before (0d-AA) and after five days of accelerated ageing (5d-AA) treatments. Compared to the non-accelerated ageing treatment (0d-AA), 286 and 220 differential expressed genes (DEGs) were identified in I178 and X178, respectively Among those, 98 DEGs were detected in both I178 and X178 after 5d-AA, Enriched GO terms included cellular components of cell part, intracellular part, organelle and membrane etc., including carbohydrate derivative catabolic process, carbohydrate synthesis, sugar isomerase (SIS) family protein etc. Transcriptome analysis of I178 and X178 showed that Alternative splicing (AS) occurs in 63.6% of the expressed genes in all samples. Only 381 genes specifically occurred AS in I178 and X178 after 5d-AA, mostly enriched in nucleotide and nucleoside binding. Combined with the reported QTL mapping result, the DEG and the AS information, 13 DEGs in the mapping intervals and 7 AS-DEGs were potential candidates may directly or indirectly associated to seed ageing.
Encountering relatable information in experiential learning spaces
Authors: Miller Faye Q.
Published: May 2019

Purpose

The purpose of this paper is to provide an emerging framework for university libraries’ research and reference services, which aims to strengthen partnerships between research information specialists and early career researchers (ECRs).

Design/methodology/approach

The conceptual model used in this paper was originally developed from a constructivist grounded theory study, analyzing data from a sample of ECRs across multiple disciplines at two universities and contextualized by a review of recent research into ECRs’ information experiences, and researcher–librarian partnerships in experiential learning spaces within and beyond libraries.

Findings

This paper provides a review of the literature on one aspect of the knowledge ecosystem model relevant to research information specialists: tangible forms of information such as texts, tools, humans, cultures and environments encountered during informal learning experiences in six spaces: professional development programs, formal coursework, events, community, home and social media.

Research limitations/implications

This paper is a catalyst for discussions and research into how research information specialists can facilitate access to the forms of information and learning experienced by ECRs, and what research information specialists can do with tangible information to respond to ECRs needs for experiential learning.

Practical implications

As the previous study found that ECRs perceived their knowledge as vital resources toward their research career progression, it would be useful for research information specialists to understand and design services paying attention to the importance of ECRs’ initial encounters with tangible information to create the knowledge they need.

Social implications

Working toward improved engagement and partnership through increased awareness and understanding of informed learning experiences between ECRs, their mentors and other developers and research librarians/information specialists can result in higher quality development and communication of new research, which can impact on society’s innovation and advancement.

Originality/value

The new integrative framework presented in this paper can assist in terms of identifying what informs ECRs professional development toward strengthening ECR and librarian/information specialist partnerships.
System dynamics modeling with fuzzy logic application to mitigate the bullwhip effect in supply chains
Authors: Poornikoo Mehdi , Qureshi Muhammad Azeem
Published: May 2019

Purpose

A plethora of studies focused on the cause and solutions for the bullwhip effect, and consequently many have successfully experimented to dampen the effect. However, the feasibility of such studies and the actual contribution for supply chain performance are yet up for debate. This paper aims to fill this gap by providing a holistic system-based perspective and proposes a fuzzy logic decision-making implementation for a single-product, three-echelon and multi-period supply chain system to mitigate such effect.

Design/methodology/approach

This study uses system dynamics (SD) as the central modeling method for which Vensim® is used as a tool for hybrid simulation. Further, the authors used MATLAB for undertaking fuzzy logic modeling and constructing a fuzzy inference system that is later on incorporated into SD model for interaction with the main supply chain structure.

Findings

This research illustrated the usefulness of fuzzy estimations based on experts’ linguistically and logically defined parameters instead of relying merely on the traditional demand forecasting based on time series. Despite the increased complexity of the calculations and structure of the fuzzy model, the bullwhip effect has been considerably decreased resulting in an improved supply chain performance.

Practical implications

This dynamic modeling approach is not only useful in supply chain management but also the model developed for this study can be integrated into a corporate financial planning model. Further, this model enables optimization for an automated system in a company, where decision-makers can adjust the fuzzy variables according to various situations and inventory policies.

Originality/value

This study presents a systemic approach to deal with uncertainty and vagueness in dynamic models, which might be a major cause in generating the bullwhip effect. For this purpose, the combination between fuzzy set theory and system dynamics is a significant step forward.
A cyber-systemic learning action approach towards selected students’ competencies development
Authors: Štrukelj Tjaša , Zlatanović Dejana , Nikolić Jelena , Sternad Zabukovšek Simona
Published: May 2019

Purpose

The purpose of this paper is to prove that it is possible and necessary that higher education institutions develop appropriate competencies of students during the learning process as required by the practice if teachers use the systemic approach and cybernetics knowledge. The authors especially research the importance of competence entrepreneurship and how to stimulate entrepreneurship by developing competencies of creativity, teamwork and communication.

Design/methodology/approach

Based on systems theory, transversal competencies entrepreneurship, creativity, teamwork and communication, as well as their interdependence, were requisitely holistic selected. In the selection of diverse contemporary learning methods, the authors started from an action research approach that implies learning by doing, i.e. participation of students. With the use of statistical methods, the authors showed that a cyber-systemic requisite holistic learning action approach based on interdependence of teacher and students learning process results in innovation of researched transversal competencies.

Findings

Based on two quantitative and qualitative researches of 96 students’ competencies, the authors found out that when using contemporary learning methods, the desired results can be achieved. In described learning process everyone involved gained: both the teacher and the students.

Research limitations/implications

The survey does not include verifying the usefulness of developed competencies in practice. Also, the study only covers the findings of the research study of one academic year.

Practical implications

The research is important for the practice of higher education, as it demonstrates that the teacher is with a targeted focus on the selected viewpoints able to effectively improve students’ competencies.

Social implications

If higher education’s institutions take a strategic decision to target improvement of the transversal competencies of students, they will be easier and faster to employ, and practice will get more relevant employees. The economy will be more efficient and effective.

Originality/value

According to the authors’ knowledge, no research measures the development of selected transversal competencies using the contemporary learning methods, based on cyber-systemic learning action approach. The authors found out that the methods used have influenced the final results, which show that all measured students’ transversal competencies have improved.
Trade books’ evolving depictions of Thomas Jefferson, America’s third president
Authors: Bickford John H. , Lindsay Megan , Hendrickson Ryan C.
Published: May 2019

Purpose

History-based trade books are an essential classroom option for social studies and English teachers. Professional organizations in history, social studies, English, reading and literature promote these engaging, age-appropriate secondary sources. Research suggests that misrepresentations appear often within history-based curricula, yet the majority of empirical studies have been completed on textbooks. The purpose of this paper is to examine the historical representation of Thomas Jefferson within trade books.

Design/methodology/approach

The data sample included trade books targeting various ages to make comparisons within and between grade ranges; the authors selected books published in distinctly different years to examine how Jefferson’s historical representation changed over time. The mixed methods content analysis used both open coding and axial coding.

Findings

Findings included sanitized versions of slavery at Monticello and omissions of his relationship with Sally Hemings. Date of publication, particularly those published after 1999 as new scientific evidence emerged linking Hemings and Jefferson, and intended audience shaped patterns of representation about Jefferson’s privileged social position, authorship of the Declaration of Independence, political philosophy and involvement in the American Revolution, to mention a few. Heroification, a common historical misrepresentation, did not appear.

Research limitations/implications

Limitations included: uneven portions of the data pool as children’s and young adult trade books were not common in early and mid-twentieth century; organization of books by grade range is problematic due to inexact nature of ranking narratives’ complexity; and definitive conclusions cannot emerge from a single study. Future research should consider how trade books represent other historical figures, particularly slave-owning American presidents.

Practical implications

Practical suggestions, such as how to address misrepresentations using primary sources, are offered.

Originality/value

Thomas Jefferson, undoubtedly an impactful American, is frequently included in elementary, middle level and high school curriculum. The authors examined Jefferson’s historical representation within trade books.
Moderating role of innovation culture in the relationship between organizational learning and innovation performance
Authors: Ghasemzadeh Peivand , Nazari Jamal A. , Farzaneh Mandana , Mehralian Gholamhossein
Published: May 2019

Purpose

Different studies have analyzed the relationship between organizational learning (OL) and innovation performance (IP). However, the question of how innovation culture (IC) affects the relationship between OL and IP remains unexplored. This study aims to examine the impact of IC on the relationship between OL and various dimensions of IP, including product, process and objective innovation.

Design/methodology/approach

A research model was developed and performed based on the relevant literature in the field of OL, IC and IP. The hypotheses are tested with the data collected from companies operating in an intensive knowledge-based industry.

Findings

Based on the results of 625 questionnaires completed by pharmaceutical companies, OL activities and IC can result in product and process innovation. However, this relationship was not supported for the objective innovation. Furthermore, in terms of the moderating role of IC in the relationship between OL and IP dimensions, the results were significant.

Practical implications

The findings help to gain a better understanding of how organizational commitment by creating a culture for innovation can help to maximize the benefits of continuous OL in product and process innovation.

Originality/value

Considering the three aspects of IP, it is the first survey of the contribution of OL in firms’ IP with considering the moderating role of IC. The proposed model would enrich the relevant literature and provide us with better understanding how OL contributes to the IP.
Environmental regulations and their effect on innovation and competitiveness in tourism in Barbados, Guyana and Jamaica
Authors: Huntley Lewis Eritha Olinda
Published: May 2019

Purpose

This paper aims to explore the need for innovation in Caribbean tourism with stringent (mandatory) environmental regulations as the key driver of the process. It draws examples from three destinations, Barbados, Guyana and Jamaica.

Design/methodology/approach

This assessment entailed a review of the literature on the key issues. Theories on innovation, regulations and competitiveness were examined in brief. The paper also presents an overview of Caribbean tourism to provide context. Of note is the dearth of information on the drivers of innovation and its effect on the Caribbean tourism industry which was a major limitation of this assessment.

Findings

The main implication of this review is that it attempts to highlight the need for discourse on the effective use of environmental regulations to influence the behaviour of industry operatives towards achieving sustainable tourism. Within the context of climate change and the threat that this poses to Caribbean tourism, there is the critical need for this discourse. Consideration is also given to the value stringency of regulation since it is theorised that, if applied correctly, this may be the impetus to drive businesses to innovate to be competitive.

Originality/value

This is a novel approach to the management of the tourism industry which has shown a preference for self-regulation. Given the proposed outcome, the paper advocates mandatory, stringent regulations since self-regulation is a choice left solely to the industry operatives.
Earning the “Write to Speak”: Sell‐Side Analysts and Their Struggle to Be Heard
Authors: Spence Crawford , Aleksanyan Mark , Millo Yuval , Imam Shahed , Abhayawansa Subhash
Published: May 2019

This paper explores the ways in which sell‐side (SS) financial analysts seek to position themselves advantageously within the wider field of investment advice in spite of widespread skepticism over the value that their forecasts and recommendations add to investment decisions. The field of investment advice has been characterized in recent years by a number of regulatory and technological changes that have forced SS analysts to reconstitute the ways in which they influence the investment decisions of buy‐side (BS) actors. Faced with existential threats, SS analysts have responded to the disruptive impact of technology and regulation by struggling hard to ensure that their services are still valued by fund managers. Key to this ongoing process is the recalibration of professional expertise, which previous research has alluded to but not explored in detail. Central to the persistence of SS analysts in processes of investment decision making are activities revolving around the production and use of analyst reports which, our findings indicate, are less valuable for their informational content than their role as “relational devices,” ascribing legitimacy to SS analysts and earning them an entry ticket to more substantive, value‐adding interactions with companies and BS actors. We also show that economic considerations in the area of investment advice are influenced by social ties, the motivations of various actors in the field, and their relative position vis‐à‐vis other actors. More generally, we contribute to the literature on professional projects by showing how professional groups are constantly engaged in attempts to reposition themselves in the social space, but that field‐level changes can restrict the outcomes of these strategies to mitigation rather than advancement for the professionals concerned.
How Getting the Facts Right Can Fuel Partisan‐Motivated Reasoning
Authors: Bisgaard Martin
Published: May 2019

Scholars often evaluate citizens' democratic competence by focusing on their ability to get relevant facts right. In this article, I show why this approach can yield misleading conclusions about citizen competence. I argue that although citizens with strong partisan loyalties might be forced to accept the same facts, they find alternative ways to rationalize reality. One such way, I show, is through the selective attribution of credit and blame. With four randomized experiments, conducted in diverse national settings and containing closed‐ as well as open‐ended questions, I find that as partisans correctly updated economic beliefs to reflect new facts, they conversely attributed responsibility in a highly selective fashion. Although partisans might acknowledge the same facts, they are apt in seizing on and producing attributional arguments that fit their preferred worldviews.
A study of temperature control in different designs of emergency drug transport bags
Authors: Dingley J. , Thatcher N. , Williams D.
Published: May 2019

We investigated whether low melting point phase‐change waxes could be incorporated into emergency drug transport bags to attenuate the known temperature extremes their contents can be exposed to. We exposed two custom‐made hollow‐walled drug containers placed within a pair of drug transport bags to three day/night cycles including periods of direct radiant sunlight. The wall cavities of one contained air, whereas those of the other contained a paraffin wax (melting point of 44–46 °C) with a high latent heat of fusion (until fully melted, its temperature does not increase further). We collected 25,920 temperature datasets at six locations. We found that 97.8% and 84.7% of ampoule temperatures within the wax and air cavity containers, respectively, were within a target range of 15–40 °C over the study duration (Levene statistic W = 4279.1; Levene's test for equality of variance, p < 0.001). Ampoule temperatures in the wax cavity container only exceeded 40 °C for 1.7% of the time. Even when they did so, their temperature was attenuated to 40.3 °C, despite an ambient air temperature of > 40 °C for 6.4% of the time (peak 46.9 °C) and a bag surface temperature of > 40 °C for 17.2% of the time (peak 64.4 °C). In contrast, the ampoule temperature in the air cavity container exceeded 40 °C for 17.1% of the time (peak 54.1 °C). The latent heat of fusion of phase‐change materials may be exploited in the design of drug transport bags to mitigate any temperature changes in the drugs stored within them.
Orchestrating the antioxidant defenses in the epididymis
Authors: O'Flaherty C.
Published: May 2019

Background

During the post‐testicular maturation that occurs in the epididymis, spermatozoa need to face biochemical and morphological changes that may make them vulnerable to oxidative damage. During spermatogenesis and the epididymal maturation, the spermatozoon acquires antioxidant enzymes needed to face possible increases of reactive oxygen species (ROS) produced by its own aerobic metabolism but also due toROSproduced in high quantities by abnormal spermatozoa.

Objectives

Provide an up‐to‐date review of the enzymatic antioxidant system in the epididymis.

Material and methods

A thorough literature review was performed for papers concerning the players of the antioxidant defenses in the epididymis.

Results

The antioxidant system in the epididymis is composed by superoxide dismutases, catalase, glutathione peroxidases, peroxiredoxins, glutathione‐S‐transferases, thioredoxins and thioredoxin reductase. They work together to maintain low levels ofROSduring the epididymal maturation. Knockout models revealed that the absence of one of the enzyme impact sperm quality affecting a variety of proteins involved in motility, the ability to fertilize oocyte, and promotes oxidative damage to the spermDNA.

Discussion and conclusions

These findings suggest that each enzyme is playing a specific role, and in most of the cases, no compensatory mechanisms are put in place when one enzyme is absent. This review highlights the different antioxidant enzymes in the epididymis and their role during maturation of the spermatozoon.
Open Population Maximum Likelihood Spatial Capture-Recapture
Authors: Glennie Richard , Borchers David L. , Murchie Matthew , Harmsen Bart J. , Foster Rebecca J.
Published: May 2019

Open population capture-recapture models are widely used to estimate population demographics and abundance over time. Bayesian methods exist to incorporate open population modeling with spatial capture-recapture (SCR), allowing for estimation of the effective area sampled and population density. Here, open population SCR is formulated as a hidden Markov model (HMM), allowing inference by maximum likelihood for both Cormack-Jolly-Seber and Jolly-Seber models, with and without activity center movement. The method is applied to a 12-year survey of male jaguars (Panthera onca) in the Cockscomb Basin Wildlife Sanctuary, Belize, to estimate survival probability and population abundance over time. For this application, inference is shown to be biased when assuming activity centers are fixed over time, while including a model for activity center movement provides negligible bias and nominal confidence interval coverage, as demonstrated by a simulation study. The HMM approach is compared with Bayesian data augmentation and closed population models for this application. The method is substantially more computationally efficient than the Bayesian approach and provides a lower root-mean-square error in predicting population density compared to closed population models.
‘Fake News’ in urology: evaluating the accuracy of articles shared on social media in genitourinary malignancies
Authors: Alsyouf Muhannad , Stokes Phillip , Hur Dan , Amasyali Akin , Ruckle Herbert , Hu Brian
Published: May 2019

Objectives

To evaluate the accuracy of the most popular articles on social media platforms pertaining to genitourinary malignancies, and to identify the prevalence of misinformation available to patients.

Materials and Methods

The 10 most shared articles on popular social media platforms (Facebook, Twitter, Pinterest, and Reddit) were identified for prostate cancer, bladder cancer, kidney cancer, testis cancer, and PSA testing using a social media analysis tool (August 2017 and August 2018). Articles were reviewed for accuracy by comparing the article information against available scientific research and consensus data. They were classified as accurate, misleading or inaccurate. The Mann–Whitney U‐test was used for statistical comparison.

Results

Articles pertaining to prostate cancer were the most shared across all social media platforms (399 000 shares), followed by articles pertaining to kidney cancer (115 000), bladder cancer (17 894), PSA testing (8827) and testicular cancer (7045). The prevalence of inaccurate or misleading articles was high: prostate cancer, 7/10 articles; kidney, 3/10 articles; bladder, 2/10 articles; testis, 2/10 articles; and PSA testing, 1/10 articles. There was a significantly higher average number of shares for inaccurate (54 000 shares; P < 0.01) and misleading articles (7040 shares; P < 0.01) than for accurate articles (1900 shares). Inaccurate articles were 28 times more likely to be shared than factual articles.

Conclusion

Misleading or inaccurate information on genitourinary malignancies is commonly shared on social media. This study highlights the importance of directing patients to appropriate cancer resources and potentially argues for oversight by the medical and technology communities.
Hydrogen sulfide and dermatological diseases
Authors: Coavoy‐Sánchez Silvia A. , Costa Soraia K. P. , Muscará Marcelo N.
Published: May 2019

Skin diseases constitute a major health problem affecting a high proportion of the population every day and have different aetiologies that include inflammation, infections, and tumours. Hydrogen sulfide (H2S) is a gaseous signalling molecule recognized as a gasotransmitter together with NO and carbon monoxide. Under physiological conditions, H2S is produced in the skin by enzymic pathways and plays a physiological role in a variety of functions, such as vasodilatation, cell proliferation, apoptosis, and inflammation. Alterations of H2S production are implicated in a variety of dermatological diseases, such as psoriasis, melanoma, and other dermatoses. On the other hand, H2S‐releasing‐based therapies based on H2S donor compounds are being developed to treat some of these situations. In this review, we provide an up‐to‐date overview of the role of H2S in the normal skin and its clinical and pathological significance, as well as the therapeutic potential of different H2S donors for treatment of skin diseases.

Linked Articles

This article is part of a themed section on Hydrogen Sulfide in Biology & Medicine. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.4/issuetoc
Infants’ intentionally communicative vocalizations elicit responses from caregivers and are the best predictors of the transition to language: A longitudinal investigation of infants’ vocalizations, gestures and word production
Authors: Donnellan Ed , Bannard Colin , McGillion Michelle L. , Slocombe Katie E. , Matthews Danielle
Published: May 2019

What aspects of infants’ prelinguistic communication are most valuable for learning to speak, and why? We test whether early vocalizations and gestures drive the transition to word use because, in addition to indicating motoric readiness, they (a) are early instances of intentional communication and (b) elicit verbal responses from caregivers. In study 1, 11 month olds (N = 134) were observed to coordinate vocalizations and gestures with gaze to their caregiver's face at above chance rates, indicating that they are plausibly intentionally communicative. Study 2 tested whether those infant communicative acts that were gaze‐coordinated best predicted later expressive vocabulary. We report a novel procedure for predicting vocabulary via multi‐model inference over a comprehensive set of infant behaviours produced at 11 and 12 months (n = 58). This makes it possible to establish the relative predictive value of different behaviours that are hierarchically organized by level of granularity. Gaze‐coordinated vocalizations were the most valuable predictors of expressive vocabulary size up to 24 months. Study 3 established that caregivers were more likely to respond to gaze‐coordinated behaviours. Moreover, the dyadic combination of infant gaze‐coordinated vocalization and caregiver response was by far the best predictor of later vocabulary size. We conclude that practice with prelinguistic intentional communication facilitates the leap to symbol use. Learning is optimized when caregivers respond to intentional vocalizations with appropriate language.
Evaluating seasonal patterns of female aggression: Case study in a cavity‐nesting bird with intense female–female competition
Authors: Bentz Alexandra B. , Philippi Kelsey J. , Rosvall Kimberly A.
Published: May 2019

Seasonal plasticity in aggression is likely to be shaped by the contexts in which aggression is beneficial, as well as the constraints inherent in its underlying mechanisms. In males, seasonal plasticity in testosterone (T) secretion is thought to underlie seasonal plasticity in conspecific aggression, but it is less clear how and why female aggression may vary across different breeding stages. Here, we integrate functional and mechanistic perspectives to begin to explore seasonal patterns of conspecific aggression in female tree swallows (Tachycineta bicolor), a songbird with intense female–female competition and T‐mediated aggression. Female tree swallows elevate T levels during early breeding stages, coinciding with competition for nest boxes, after which time T levels are roughly halved. However, females need to defend ownership of their nesting territory throughout the breeding season, suggesting it may be adaptive to maintain aggressive capabilities, despite low T levels. We performed simulated territorial intrusions using 3D‐printed decoys of female tree swallows to determine how their aggressive response to a simulated intrusion changes across the breeding season. First, we found that 3D‐printed decoys produce data comparable to stage‐matched studies using live decoys, providing researchers with a new, more economical method of decoy construction. Further, female aggressiveness remained relatively high through incubation, a period of time when T levels are quite low, suggesting that other mechanisms may regulate conspecific female aggression during parental periods. By showing that seasonal patterns of female aggression do not mirror the established patterns of T levels in this highly competitive bird, our findings provide a unique glimpse into how behavioural mechanisms and functions may interact across breeding stages to regulate plasticity.
Hegel And Schelling on the Path of Aristotelian Ascent
Authors: Rogers Chandler D.
Published: May 2019

This essay argues that Schelling's late transition from Negative to Positive Philosophy constitutes a pointed inversion of the path of systematic ascent mapped by Hegel for the first time in the Phenomenology's Preface, which itself establishes Hegel's development out of and beyond Schelling's early philosophy; that a key notion to inspire the Hegelian vision articulated in the Preface returns to cap off the critique implicit in Schelling's late inversion, where this notion emerges from their divergent readings of Aristotle's Metaphysics; and finally, that while Hegel's theorization of the end of all philosophizing represents his innovative enlargement from within the framework he finds in Aristotle, Schelling's vision of this same end facilitates the crisis of reason which opens unto revelation, and so is akin to the vision which carries Aquinas beyond Aristotle, albeit in Schelling's post‐Spinozist mode of thought.
Low‐temperature thermochronological database of bedrock in the Japanese Islands
Authors: Sueoka Shigeru , Tagami Takahiro
Published: May 2019

To provide better access to thermochronological data and understand the long‐term denudation history of the Japanese Islands, we compiled a low‐temperature thermochronological dataset of fission‐track (FT) and (U–Th–Sm)/He (He) ages for apatite and zircon in bedrocks. These thermochronometric ages are compiled from 90 literature sources and 1,096 localities, and include 418 apatite FT ages, 851 zircon FT ages, 42 apatite He ages, and 30 zircon He ages. Many FT ages have been reported previously; however, the number of He ages is limited in the Japanese Islands. The compiled data are spatially biased; for instance, more data are reported for the Chubu and Kinki districts and the Pacific coast of the Shikoku Island, whereas less data were available for the Tohoku and Chugoku districts. For better understanding arc‐scale uplift‐denudation history, further thermochronological research in the lesser‐studied regions and more He thermochronometric measurements are desired. This compilation will be updated and provided on the website of the Fission‐Track Research Group in Japan (http://ftrgj.org/index.html).