bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations
Authors: Kojima Yasuhiro , Matsumoto Hirotaka , Kiryu Hisanori 
Published: June 2019

Abstract

Motivation
Evolve and resequence (E&R) experiments show promise in capturing real-time evolution at genome-wide scales, enabling the assessment of allele frequency changes SNPs in evolving populations and thus the estimation of population genetic parameters in the Wright–Fisher model (WF) that quantify the selection on SNPs. Currently, these analyses face two key difficulties: the numerous SNPs in E&R data and the frequent unreliability of estimates. Hence, a methodology for efficiently estimating WF parameters is needed to understand the evolutionary processes that shape genomes.

Results
We developed a novel method for estimating WF parameters (EMWER), by applying an expectation maximization algorithm to the Kolmogorov forward equation associated with the WF model diffusion approximation. EMWER was used to infer the effective population size, selection coefficients and dominance parameters from E&R data. Of the methods examined, EMWER was the most efficient method for selection strength estimation in multi-core computing environments, estimating both selection and dominance with accurate confidence intervals. We applied EMWER to E&R data from experimental Drosophila populations adapting to thermally fluctuating environments and found a common selection affecting allele frequency of many SNPs within the cosmopolitan In(3R)P inversion. Furthermore, this application indicated that many of beneficial alleles in this experiment are dominant.

Availability and implementation
Our C++ implementation of ‘EMWER’ is available at https://github.com/kojikoji/EMWER.

Supplementary information
Supplementary data are available at Bioinformatics online.
DepLogo: visualizing sequence dependencies in R
Authors: Grau Jan , Nettling Martin , Keilwagen Jens 
Published: June 2019

AbstractSummaryStatistical dependencies are present in a variety of sequence data, but are not discernible from traditional sequence logos. Here, we present the R package DepLogo for visualizing inter-position dependencies in aligned sequence data as dependency logos. Dependency logos make dependency structures, which correspond to regular co-occurrences of symbols at dependent positions, visually perceptible. To this end, sequences are partitioned based on their symbols at highly dependent positions as measured by mutual information, and each partition obtains its own visual representation. We illustrate the utility of the DepLogo package in several use cases generating dependency logos from DNA, RNA and protein sequences.Availability and implementationThe DepLogo R package is available from CRAN and its source code is available at https://github.com/Jstacs/DepLogo.Supplementary informationSupplementary data are available at Bioinformatics online.
The Chemosensory Pleasure Scale: A New Assessment for Measuring Hedonic Smell and Taste Capacities
Authors: Zhao Jiu-Bo , Wang Yi-Le , Ma Qian-Wen , Zhao Jing-Bo , Zhang Xiao-Yuan , Zou Lai-Quan 
Published: June 2019

Abstract
Anhedonia, or the inability to experience pleasure, is a key clinical feature of many mental disorders such as depression and schizophrenia. Although various valid measurements of anhedonia and pleasure experience exist, no scales exist that quantify smell and taste pleasure experiences. The Chemosensory Pleasure Scale (CPS) was therefore designed to assess the hedonic capacity for smell and taste pleasure. We examined the reliability and validity of the CPS in our study. First, we conducted exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) to identify and examine the structure of the CPS. Second, the CPS’s validity and test-retest stability were investigated. The CPS was correlated with other measurements of anhedonia and pleasure experience. Furthermore, the empirical validity of CPS was also examined in our study. The results indicated that the CPS is a reliable and valid measure for assessing an individual’s hedonic capacity for smell and taste pleasure in nonclinical samples. Further application of the CPS for various populations is also discussed herein, especially for patients with mental disorders such as depression, schizophrenia, and autism.
Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution
Authors: Phillips Anna J , Dornburg Alex , Zapfe Katerina L , Anderson Frank E , James Samuel W , Erséus Christer , Moriarty Lemmon Emily , Lemmon Alan R , Williams Bronwyn W 
Published: June 2019

Abstract
Leeches (Hirudinida) comprise a charismatic, yet often maligned group of worms. Despite their ecological, economic, and medical importance, a general consensus on the phylogenetic relationships of major hirudinidan lineages is lacking. This absence of a consistent, robust phylogeny of early-diverging lineages has hindered our understanding of the underlying processes that enabled evolutionary diversification of this clade. Here, we used an anchored hybrid enrichment-based phylogenomic approach, capturing hundreds of loci to investigate phylogenetic relationships among major hirudinidan lineages and their closest living relatives. We recovered Branchiobdellida as sister to a clade that includes all major lineages of hirudinidans and Acanthobdella, casting doubt on the utility of Acanthobdella as a “missing link” between hirudinidans and the clitellate group formerly known as Oligochaeta. Further, our results corroborate the reciprocal monophyly of jawed and proboscis-bearing leeches. Our phylogenomic resolution of early-diverging leeches provides a useful framework for illuminating the evolution of key adaptations and host–symbiont associations that have allowed leeches to colonize a wide diversity of habitats worldwide.
Vegetable Gardens versus Cash Crops: Science and Political Economy in the Agricultural and Horticultural Society of India, 1820–40
Authors: Tavolacci Laura 
Published: June 2019

Abstract
The goal of the Agricultural and Horticultural Society of India (founded in 1820) was to create a science for the cultivation of plants in India and use this science to increase agricultural production. This article tracks the ideas of this society in its early decades as it created a highly contested and changing discourse regarding agriculture in India. As the society was based in Calcutta, it had Bengali members who appropriated and modified these ideas according to their own social circumstances. In the first decade of its life, many members envisioned the project of ‘agricultural improvement’ as increasing the production of food and medicine for local consumption as well as agricultural commodities for export. Yet beginning in 1829, this mixed agri-horticultural vision began to change. British members complained that local gardening activities were not remunerative and so the society should focus more on agriculture for export. As a result, agriculture began to be more clearly defined as the large-scale production of commodities for export, separate from the science of horticulture, which concerned growing fruits and vegetables for local consumption. Horticulture increasingly became the lesser science and the society’s focus went towards agriculture for export. Many Bengali members remained more interested in the activities associated with horticulture, proceeding to develop an agri-horticultural knowledge which appropriated new ideas about gardening promoted by the society and combined them in new ways with gardening knowledge from other North Indian networks. This episode reveals the complex world of knowledge about plant cultivation even as the British created an English-language discourse of global capitalist agriculture.
“Beyond Primary Sequence”—Proteomic Data Reveal Complex Toxins in Cnidarian Venoms
Authors: Jaimes-Becerra Adrian , Gacesa Ranko , Doonan Liam B , Hartigan Ashlie , Marques Antonio C , Okamura Beth , Long Paul F 
Published: June 2019

Abstract
Venomous animals can deploy toxins for both predation and defense. These dual functions of toxins might be expected to promote the evolution of new venoms and alteration of their composition. Cnidarians are the most ancient venomous animals but our present understanding of their venom diversity is compromised by poor taxon sampling. New proteomic data were therefore generated to characterize toxins in venoms of a staurozoan, a hydrozoan, and an anthozoan. We then used a novel clustering approach to compare venom diversity in cnidarians to other venomous animals. Comparison of the presence or absence of 32 toxin protein families indicated venom composition did not vary widely among the 11 cnidarian species studied. Unsupervised clustering of toxin peptide sequences suggested that toxin composition of cnidarian venoms is just as complex as that in many venomous bilaterians, including marine snakes. The adaptive significance of maintaining a complex and relatively invariant venom remains unclear. Future study of cnidarian venom diversity, venom variation with nematocyst types and in different body regions are required to better understand venom evolution.
Multi-dimensional Taylor network modelling and optimal control of SISO nonlinear systems for tracking by output feedback
Authors: Sun Qi-Ming , Yan Hong-Sen 
Published: June 2019

Abstract
In this paper, a multi-dimensional Taylor network (MTN) output feedback tracking control of nonlinear single-input single-output (SISO) systems in discrete-time form is studied. To date, neural networks are generally used to identify unknown nonlinear systems. However, the neuron of neural networks includes the exponential function, which contributes to the complexity of calculation, making the neural network control unable to meet the real-time requirements. In order to identify the controlled object whose model is unknown, the MTN, which requires only addition and multiplication, is utilized for successful real-time control of the SISO nonlinear system based on only its output feedback. Lyapunov analysis proves that output signals in the closed-loop system remain bounded and the tracking error converges to an arbitrarily small neighbourhood around the origin. In contrast to the back propagation (BP) neural network self-adaption reconstitution controller, the edge of the scheme is that the MTN optimal controller promises desirable response speed, robustness and real-time control.
Estimating Uncertainty in Wisconsin’s Evidential Breath Alcohol Measurements
Authors: Brockley-Drinkman Diane , Barkholtz Heather M 
Published: June 2019

Abstract
Breath alcohol measurement accuracy and precision quantification is a critical component of impaired driving prosecution and is required for laboratory accreditation. The Chemical Testing Section of Wisconsin’s Department of Transportation conducted a bottom-up study to quantify uncertainty of breath alcohol measurements conducted on Intoximeter’s EC/IR II instrument. After an exercise in combined uncertainty source identification, individual input values were either reported from National Institute of Standards and Technology traceable reference materials or quantified using instrument data from 2014 to 2018. From input values, an expanded uncertainty value of 4.58 × 10-3 g/210L was found that encompasses all identified sources with a 95% confidence interval.
Mating Behavior and Reproductive Biology of Emerald Ash Borer (Coleoptera: Buprestidae) and Two of Its Native Congeners, the Twolined Chestnut Borer and the Bronze Birch Borer
Authors: Rutledge Claire E , Keena Melody A 
Published: June 2019

Abstract
We studied the mating behavior and reproductive biology of three members of the genus Agrilus: the bronze birch borer, Agrilus anxius Gory; the twolined chestnut borer, Agrilus bilineatus (Weber); and the emerald ash borer, Agrilus planipennis Fairmaire. All three species share a highly stereotyped mating behavior. However, the copulation duration of A. planipennis was 90% longer than that of its two congeners. Female reproductive tracts of the three species were anatomically similar, as were the spermatophores. Within the spermatophores, sperm were single in A. anxius and A. bilineatus, while in A. planipennis, sperm were bundled in groups of approximately 20 in a hyaline sheath. We found that field-caught A. anxius and A. bilineatus had higher rates of female insemination than A. planipennis. In additional studies with A. planipennis and A. anxius, we found that mating duration was related to mating success, and fecundity for A. planipennis, but not for A. anxius. For both A. planipennis and A. anxius, the spermatophore was passed to the female toward the end of the copulatory period. Sperm were found in the spermatheca immediately after copulation ended in A. planipennis and 30 min after copulation ended in A. anxius. We present possible explanations for these differences.
Institutions and the Location of Oil Exploration
Authors: Cust James , Harding Torfinn 
Published: June 2019

AbstractWe provide evidence that institutions have a strong influence over where oil and gas exploration takes place. We utilise a global data set on the location of exploration wells and national borders. This allows for a regression discontinuity design with the identifying assumption that the position of borders was determined independently of geology. In order to break potential simultaneity between borders, institutions, and activities in the oil sector, we focus on drilling that occurred after the formation of borders and institutions. Our sample covers 88 countries over the 1966–2010 period. At borders, we estimate more than twice as much drilling on the side with better institutional quality. Subsample analyses reveal effects of institutions on exploration drilling in both developing and high income countries, as well as across three types of operating companies. We find that the supermajor international oil companies are particularly sensitive to institutional quality in developing countries. Our findings are consistent with the view that institutions shape both exploration companies’ incentives to invest in drilling and host countries’ supply of drilling opportunities.
The Problem of Chronic Refugee Communities: Applying Complexity Theory to the Situation Along the Thai–Myanmar Border
Authors: Poocharoen Ora-Orn , Straussman Jeffrey D , Guinn David E 
Published: June 2019

Abstract
Intractable long-term or chronic refugee communities present serious challenges to common refugee-management strategies. We argue that they are best understood and managed by using adaptive techniques drawn from complexity theory. To illustrate this strategy, we use the refugee communities situated along the Thai–Myanmar border as a case study. The article outlines the key elements of complexity theory, the complexity lens, for use in analysis of the problem. It then applies the complexity lens to the case study: identifying and describing the actors and networks that compose the complex system of the Thai–My refugees (the complex system) and the dynamic developments within that community over time (dynamic development). Based on this analysis, the article utilizes the complexity lens to evaluate the policy options commonly offered for the management of this ongoing refugee situation.
Giant ovarian cystadenocarcinoma in an adult patient, a rare finding in modern times
Authors: Molina Gabriel Alejandro , Izurieta Alison Nicole , Moyon Miguel Angel , Aguayo William G , Moyon Fernando X , Tufiño Jorge F , Guzman Lenin J , Parra Ruben Alejandro 
Published: June 2019

Abstract
Ovarian cancer (OC) is one of the most commonly diagnosed cancers among women. Regretfully due to its a broad spectrum of clinical behavior and challenging diagnosis most cases are diagnosed at a late stage. On rare occasions, these tumors can grow to massive sizes if left untreated, worsening the prognosis of the patient. Thanks to the advancement of medicine and diagnostic techniques, these rare cases are less frequent. Timely detection and surgery could avoid all these potentially troublesome scenarios. We report the case of a 64-year-old female with a giant 13 kg high-grade papillary serous ovarian cystadenocarcinoma, the tumor grew during a four year period and was adequately treated with surgery and is under close follow up with the oncologist. To our knowledge, this is the first case of a giant ovarian cystadenocarcinoma ever reported in Ecuador.
Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria
Authors: Kotrys Anna V , Cysewski Dominik , Czarnomska Sylwia D , Pietras Zbigniew , Borowski Lukasz S , Dziembowski Andrzej , Szczesny Roman J 
Published: June 2019

AbstractMaintenance of mitochondrial gene expression is crucial for cellular homeostasis. Stress conditions may lead to a temporary reduction of mitochondrial genome copy number, raising the risk of insufficient expression of mitochondrial encoded genes. Little is known how compensatory mechanisms operate to maintain proper mitochondrial transcripts levels upon disturbed transcription and which proteins are involved in them. Here we performed a quantitative proteomic screen to search for proteins that sustain expression of mtDNA under stress conditions. Analysis of stress-induced changes of the human mitochondrial proteome led to the identification of several proteins with poorly defined functions among which we focused on C6orf203, which we named MTRES1 (Mitochondrial Transcription Rescue Factor 1). We found that the level of MTRES1 is elevated in cells under stress and we show that this upregulation of MTRES1 prevents mitochondrial transcript loss under perturbed mitochondrial gene expression. This protective effect depends on the RNA binding activity of MTRES1. Functional analysis revealed that MTRES1 associates with mitochondrial RNA polymerase POLRMT and acts by increasing mitochondrial transcription, without changing the stability of mitochondrial RNAs. We propose that MTRES1 is an example of a protein that protects the cell from mitochondrial RNA loss during stress.
The Current Practice of Making and Applying International Agreements in Japan
Authors: Mori Tadaatsu 
Published: June 2019

Abstract
This chapter describes the treaty-making practice in Japan, with a focus on explaining the mechanism for striking the balance between democratic control and effective management of foreign affairs. The chapter first outlines the structure of Japan’s Constitution regarding the responsibility for managing foreign affairs and the authority for concluding treaties and other international agreements. The chapter further introduces the process of concluding treaties step by step—from examination by the Cabinet Legislation Bureau to the Diet approval. The “Ohira Principles,” elaborated by Foreign Minister Masayoshi Ohira in 1974, specified three categories of treaties for the Diet approval. The chapter points out that the formula was extremely well crafted, although it has been challenged by the growing need for effective management over a wide range of issues in foreign affairs. In the course of discussion, the chapter takes up examples such as an Exchange of Notes of ODA projects, the 1997 “Guidelines for Japan-U.S. Defense Cooperation,” the Guam International Agreement, and the Japan-U.S. SOFA and Supplementary Agreement on the Environment, the Japan-U.S. ACSA. The chapter also describes how the current Diet approval process proceeds, by referring to existing practices such as the “thirty-day rule” and bundling of multiple treaties, and then briefly covers the domestic legal effect of treaties, including bills for implementing treaties as well as “self-executing” treaties. The chapter concludes that the Japanese treaty-making practice will continue to face a question of how to strike the right balance between producing necessary treaties and other international agreements in a timely manner while also maintaining a sufficient level of democratic control by the Diet.
Five Conceptions of the Function of Foreign Relations Law
Authors: McLachlan Campbell 
Published: June 2019

Abstract
The comparative study of foreign relations law must first grapple with a conundrum: outside the United States, the field enjoys no wide currency or commonly accepted scope, yet the set of problems with which it is concerned arise at an interface with which all states must engage: between international law and national constitutional law. This chapter argues that the essential point of departure for effective comparative analysis is to adopt a functional approach, identifying what functions foreign relations law performs. In doing so, it identifies five different conceptions of the function of foreign relations law that shape the way in which jurists have approached the field. These conceptions are: (1) exclusionary: to separate the international from the national, taking the exercise of foreign relations out of the purview of national law; (2) internationalist: to mediate the inward reception of international law into the domestic legal system; (3) constitutional: to distribute the exercise of the foreign relations law between the organs of government; (4) diplomatic: to facilitate the diplomatic relations of the state with other states; and (5) allocative: to allocate jurisdiction and applicable law in matters concerning the exercise or enforcement of the public power of states. The chapter critically assesses the persuasive power and the potential shortcomings of each of these conceptions. Using the example of domestic cases engaging peremptory norms, it shows how the allocative approach helps to give a better explanation of when and why domestic courts intervene to enforce or apply such rules.
International Immunities in U.S. Law
Authors: Stewart David P. 
Published: June 2019

Abstract
This chapter describes domestic U.S. law governing the immunities of foreign states and governments, foreign heads of state and governments, diplomatic and consular officials, other official visitors, and international organizations from the jurisdiction of U.S. courts. A major focus is the Foreign Sovereign Immunities Act of 1976, which provides specific exceptions to immunity for a foreign state’s commercial activities, noncommercial torts, arbitral agreements and awards, expropriations of foreign property, and acts of state-sponsored terrorism (among others). As the chapter notes, these statutory exceptions have been the subject of extensive judicial interpretation. Similarly, the immunities of foreign officials (including accredited diplomats and consular officers, heads of state and government, and visiting officials of lesser rank) have evolved over time. The chapter also addresses the immunities of international organizations and their officers and employees located in the United States, as well as the representatives of member states to those organizations. As an aspect of foreign relations law, these issues frequently assume significant political as well as legal importance. Moreover, while they are common to many legal systems, national laws often differ in their specific approaches; accordingly, the chapter notes several areas of comparative interest. The chapter concludes with a brief assessment of future developments in U.S. law.