bluuebunny/crossref_metadata_2025_split huggingface dataset:
IZAPA'S INDUSTRIAL HINTERLAND: THE EASTERN SOCONUSCO MANGROVE ZONE DURING ARCHAIC AND FORMATIVE TIMES
Authors: Neff Hector , Burger Paul H. , Culleton Brendan J. , Kennett Douglas J. , Jones John G. 
Published: December 2018

AbstractArchaeological survey and excavations in the mangrove-estuary zone south of Izapa have generated an understanding of how the environment and human exploitation patterns changed during the Archaic and Formative periods. Archaic-period archaeological remains are not present, but the sedimentary record shows that Archaic people were clearing the coastal-plain forest for agricultural purposes. This activity augmented delivery of sediments to the littoral zone, which expanded the mangrove forest and created a productive environment that could be colonized by Early Formative villagers by around 1600 calb.c.Population growth during the Early Formative created conditions that favored emergence of specialized pyro-industries, especially salt production, by around 1000 calb.c.Production intensity increased thereafter, especially during the Late Formative period, coincident with the apogee of Izapa. Salt production became more episodic during the Terminal Formative period, when interior populations were declining to a nadir after cala.d.250.
Why We Should Defend Gene Editing as Eugenics
Authors: AGAR NICHOLAS 
Published: December 2018

Abstract:This paper considers the relevance of the concept of “eugenics,”—a term associated with some of the most egregious crimes of the twentieth century—to the possibility of editing human genomes. The author identifies some uses of gene editing as eugenics but proposes that this identification does not suffice to condemn them. He proposes that we should distinguish between “morally wrong” practices, which should be condemned, and “morally problematic” practices that call for solutions, and he suggests that eugenic uses of gene editing fall into this latter category. Although when we choose the characteristics of future people we are engaging in morally dangerous acts, some interventions in human heredity should nevertheless be acknowledged as morally good. These morally good eugenic interventions include some uses of preimplantation genetic diagnosis. The author argues that we should think about eugenic interventions in the same way that we think about morally problematic interventions in public health. When we recognize some uses of gene editing as eugenics, we make the dangers of selecting or modifying human genetic material explicit.
Gene Doping—in Animals? Ethical Issues at the Intersection of Animal Use, Gene Editing, and Sports Ethics
Authors: NEUHAUS CAROLYN P. , PARENT BRENDAN 
Published: December 2018

Abstract:Gene editors such as CRISPR could be used to create stronger, faster, or more resilient nonhuman animals. This is of keen interest to people who breed, train, race, and profit off the millions of animals used in sport that contribute billions of dollars to legal and illegal economies across the globe. People have tried for millennia to perfect sport animals; CRISPR proposes to do in one generation what might have taken decades previously. Moreover, gene editing may facilitate enhancing animals’ capacities beyond their typical limits. This paper describes the state of animal use and engineering for sport, examines the moral status of animals, and analyzes current and future ethical issues at the intersection of animal use, gene editing, and sports. We argue that animal sport enthusiasts and animal welfarists alike should be concerned about the inevitable use of CRISPR in sport animals. Though in principle CRISPR could be used to improve sport animals’ well-being, we think it is unlikely in practice to do so.
Genome Editing for Involuntary Moral Enhancement
Authors: RAKIĆ VOJIN 
Published: December 2018

Abstract:During the previous years, voluntary moral bioenhancement (VMBE) has been contrasted to compulsory moral bioenhancement (CMBE). In this paper a third possible type of moral bioenhancement is discussed: genome editing for moral enhancement of the unborn that is neither voluntary nor compulsory, but involuntary. Involuntary moral bioenhancement (IMBE) might engineer people who will be more moral than they otherwise would have been. The possibilities of genome editing aimed at moral enhancement of our offspring is assessed. It is argued that genome editing might have the potential to engineer our offspring in three domains: to be more empathetic, to be less violently aggressive, and to have a higher potential for complex moral reflection. Genome editing is discussed in these three domains, and a proposal made that a combination of VMBE and IMBE might be the best option humans have to become better.
Continued Access to Investigational Medicinal Products for Clinical Trial Participants—An Industry Approach
Authors: KELMAN ARIELLA , KANG ANNA , CRAWFORD BRIAN 
Published: December 2018

Abstract:In the conduct of clinical trials for pharmaceutical research, access to investigational medicines following clinical trials is often necessary for the continued health and well-being of the trial participants; it is an ethical obligation under some circumstances, as outlined in the Declaration of Helsinki 2013 Article 34. This obligation becomes particularly important in lower-income countries, where access to medical care may be limited. Although there is agreement among global research and bioethics communities that continued access should be provided with prospectively defined parameters and procedures, the process is complex, as many responsible parties and complicated logistics are involved. Roche Pharmaceuticals developed and publicly posted the company’s policy regarding continued access to investigational medicines in 2013. This article provides insights on the policy, including the parameters that determine when continued access is and is not considered to be appropriate, along with an example from an active clinical development program. It also describes how multiple stakeholders, including those in academia, industry, government, and patient advocacy, have worked together to assess approaches to continued access. Continued access plans should be transparent and agreed to by research participants, investigators, and governments prior to the study and reassessed based on clinical trial evidence of safety and efficacy and availability of adequate treatments, along with relevant international laws and customs. Conducting responsible continued access programs requires close partnerships with investigators, health authorities, and third-party research partners.
Healthy Volunteers for Clinical Trials in Resource-Poor Settings: National Registries Can Address Ethical and Safety Concerns
Authors: BOMPART FRANCOIS 
Published: December 2018

Abstract:Healthy volunteers (HVs) who participate in clinical trials are a vulnerable group that deserves specific protection. We assessed the number and types of studies that involve HVs around the world and outline the methodological barriers to their analysis. We found that tens of thousands of HVs are involved every year in clinical trials in a large variety of countries and that the overwhelming majority of studies are not “first-in-human” but pharmacokinetic studies. The two cornerstones for both ethical and safe participation of HVs in clinical trials are properly obtained informed consent and a minimization of exposure to risk, in particular by avoiding concealed participation in multiple trials. To minimize the risk of exploitation of HVs and their exposure to risk, we propose ways to ensure genuine informed consent, and advocate setting up national healthy volunteer registries as established in France and the U.K.
Advance Directives and Code Status Information Exchange: A Consensus Proposal for a Minimum Set of Attributes
Authors: LEHMANN CHRISTOPH U. , PETERSEN CAROLYN , BHATIA HARESH , BERNER ETA S. , GOODMAN KENNETH W. 
Published: December 2018

Abstract:Documentation of code status and advance directives for end-of-life (EOL) care improves care and quality of life, decreases cost of care, and increases the likelihood of an experience desired by the patient and his/her family. However, the use of advance directives and code status remains low and only a few organizations maintain code status in electronic form. Members of the American Medical Informatics Association’s Ethics Committee identified a need for a patient’s EOL care wishes to be documented correctly and communicated easily through the electronic health record (EHR) using a minimum data set for the storage and exchange of code status information. After conducting an environmental scan that produced multiple resources, Ethics Committee members used multiple conference calls and a shared document to arrive at consensus on the proposed minimum data set. Ethics Committee members developed a minimum required data set with links to the HL7 C_CDA Advance Directives Module. Data categories include information on the organization obtaining the code status information, the patient, any supporting documentation, and finally the desired code status information including mandatory, optional, and conditional elements. The “minimum set of attributes” to exchange advance directive / code status data described in this manuscript enables communication of patient wishes across multiple providers and health care settings. The data elements described serve as a starting point for a dialog among informatics professionals, physicians experienced in EOL care, and EHR vendors, with the goal of developing standards for incorporating this functionality into the EHR systems.
Cardiac Networks United: an integrated paediatric and congenital cardiovascular research and improvement network
Authors: Gaies Michael , Anderson Jeffrey , Kipps Alaina , Lorts Angela , Madsen Nicolas , Marino Bradley , Costello John M. , Brown David , Jacobs Jeffrey P. , Kasnic David , Lihn Stacey , Lannon Carole , Margolis Peter , Pearson Gail D. , Kaltman Jonathan , Charpie John R. , Redington Andrew N. , Pasquali Sara K. ,   on behalf of the Cardiac Networks United Executive Committee and Advisory Board
Published: December 2018

AbstractOptimising short- and long-term outcomes for children and patients with CHD depends on continued scientific discovery and translation to clinical improvements in a coordinated effort by multiple stakeholders. Several challenges remain for clinicians, researchers, administrators, patients, and families seeking continuous scientific and clinical advancements in the field. We describe a new integrated research and improvement network – Cardiac Networks United – that seeks to build upon the experience and success achieved to-date to create a new infrastructure for research and quality improvement that will serve the needs of the paediatric and congenital heart community in the future. Existing gaps in data integration and barriers to improvement are described, along with the mission and vision, organisational structure, and early objectives of Cardiac Networks United. Finally, representatives of key stakeholder groups – heart centre executives, research leaders, learning health system experts, and parent advocates – offer their perspectives on the need for this new collaborative effort.
A General Framework for Global Retrievals of Trace Gases From IASI: Application to Methanol, Formic Acid, and PAN
Authors: Franco B. , Clarisse L. , Stavrakou T. , Müller J.‐F , Van Damme M. , Whitburn S. , Hadji‐Lazaro J. , Hurtmans D. , Taraborrelli D. , Clerbaux C. , Coheur P.‐F 
Published: December 2018

AbstractRetrieving concentrations of minor atmospheric trace gases from satellite observations is challenging due to their weak spectral signature. Here we present a new version of the ANNI (Artificial Neural Network for Infrared Atmospheric Sounding Interferometer, IASI) retrieval framework, which relies on a hyperspectral range index (HRI) for the quantification of the gas spectral signature and on an artificial feedforward neural network to convert the HRI into a gas total column. We detail the different steps of the retrieval method, especially where they differ from previous work, and apply the retrieval to three important volatile organic compounds: methanol (CH3OH), formic acid (HCOOH), and peroxyacetyl nitrate (PAN). The comparison of the retrieved columns with those from an optimal estimation inversion retrieval shows an overall excellent agreement: differences occur mainly when the sensitivity to the target gas is low and are consistent with the conceptual differences between the two approaches. We present retrieval examples over selected regions, comparison with previously developed products, and the global seasonal distributions including the first global distributions of PAN on a daily basis. The ANNI retrieval has been carried out on the whole time series of IASI observations (2007–2018), so that currently over 10 years of twice‐daily global CH3OH, HCOOH, and PAN total column distributions have been produced. This unique data set opens avenues for tackling important questions related to sources, transport, and transformation of volatile organic compounds in the global atmosphere.
Groundwater‐River Water Exchange Enhances Growing Season Evapotranspiration and Carbon Uptake in a Semiarid Riparian Ecosystem
Authors: Missik Justine E. C. , Liu Heping , Gao Zhongming , Huang Maoyi , Chen Xingyuan , Arntzen Evan , Mcfarland Douglas P. , Ren Huiying , Titzler P. Scott , Thomle Jonathan N. , Goldman Amy 
Published: December 2018

AbstractSemiarid ecosystems play a critical role in determining the interannual variability of the global terrestrial carbon sink. Water availability is a critical driver of productivity in semiarid ecosystems, which often alternate between carbon sink/source functioning during wet/dry years. In this study, we investigate how groundwater availability resulting from groundwater‐river water exchange influences net ecosystem exchange of CO2 (NEE), evapotranspiration (ET), and the surface energy balance at two semiarid ecosystems along the Columbia River in central Washington, USA. We examined 1 year of eddy covariance measurements from an upland sagebrush ecosystem primarily fed by rainfall without groundwater access and a riparian grassland ecosystem with groundwater access during the dry season due to lateral groundwater‐river water exchange. The two sites had distinct seasonal patterns of NEE and ET, driven by differences in water availability. While NEE at the upland sagebrush site was strongly constrained by water availability during the dry months, access to groundwater allowed the riparian site to maintain high NEE magnitude and ET during the same dry months. The riparian site had larger annual gross primary productivity than the upland site (612 vs. 424 gC/m2), which was offset by higher ecosystem respiration (558 vs. 363 gC/m2). Thus, the magnitude of the annual NEE at the upland site was larger than that at the riparian site (−62 vs. −54 gC/m2). Our results demonstrate that groundwater access determined by connectivity between groundwater and surface water can be a critical driver of carbon uptake and ET in semiarid ecosystems.
Are Slope Streaks Indicative of Global‐Scale Aqueous Processes on Contemporary Mars?
Authors: Bhardwaj Anshuman , Sam Lydia , Martín‐Torres F. Javier , Zorzano María‐Paz 
Published: December 2018

AbstractSlope streaks are prevalent and intriguing dark albedo surface features on contemporary Mars. Slope streaks are readily observed in the equatorial and subequatorial dusty regolith regions with low thermal inertia. They gradually fade over decadal timescales. The proposed mechanisms for their formation vary widely based on several physicochemical and geomorphological explanations. The scientific community is divided in proposing both dry and wet mechanisms for the formation of slope streaks. Here we perform a systematic evaluation of the literature for these wet and dry mechanisms. We discuss the probable constraints on the various proposed mechanisms and provide perspectives on the plausible process driving global‐scale slope streak formation on contemporary Mars. Although per our understanding, a thorough consideration of the global distribution of slope streaks, their morphology and topography, flow characteristics, physicochemical and atmospheric coincidences, and terrestrial analogies weighs more in favor of several wet mechanisms, we acknowledge that such wet mechanisms cannot explain all the reported morphological and terrain variations of slope streaks. Thus, we suggest that explanations considering both dry and wet processes can more holistically describe all the observed morphological variations among slope streaks. We further acknowledge the constraints on the resolutions of remote sensing data and on our understanding of the Martian mineralogy, climate, and atmosphere and recommend continuous investigations in this direction using future remote sensing acquisitions and simulations. In this regard, finding more wet and dry terrestrial analogs for Martian slope streaks and studying them at high spatiotemporal resolutions can greatly improve our understanding.
Structural Insights into the FtsQ/FtsB/FtsL Complex, a Key Component of the Divisome
Authors: Choi Yuri , Kim Jinwoo , Yoon Hye-Jin , Jin Kyeong Sik , Ryu Sangryeol , Lee Hyung Ho 
Published: December 2018

AbstractBacterial cell division is a fundamental process that results in the physical separation of a mother cell into two daughter cells and involves a set of proteins known as the divisome. Among them, the FtsQ/FtsB/FtsL complex was known as a scaffold protein complex, but its overall structure and exact function is not precisely known. In this study, we have determined the crystal structure of the periplasmic domain of FtsQ in complex with the C-terminal fragment of FtsB, and showed that the C-terminal region of FtsB is a key binding region of FtsQ via mutational analysis in vitro and in vivo. We also obtained the solution structure of the periplasmic FtsQ/FtsB/FtsL complex by small angle X-ray scattering (SAXS), which reveals its structural organization. Interestingly, the SAXS and analytical gel filtration data showed that the FtsQ/FtsB/FtsL complex forms a 2:2:2 heterohexameric assembly in solution with the “Y” shape. Based on the model, the N-terminal directions of FtsQ and the FtsB/FtsL complex should be opposite, suggesting that the Y-shaped FtsQ/FtsB/FtsL complex might fit well into the curved membrane for membrane anchoring.
Expansion of viral variants associated with immune escape and impaired virion secretion in patients with HBV reactivation after resolved infection
Authors: Inuzuka Tadashi , Ueda Yoshihide , Arasawa Soichi , Takeda Haruhiko , Matsumoto Tomonori , Osaki Yukio , Uemoto Shinji , Seno Hiroshi , Marusawa Hiroyuki 
Published: December 2018

AbstractHBV reactivation could be induced under immunosuppressive conditions in patients with resolved infection. This study aimed to clarify the viral factors associated with the pathogenesis of HBV reactivation in association with the immunosuppressive status. Whole HBV genome sequences were determined from the sera of 24 patients with HBV reactivation, including 8 cases under strong immunosuppression mediated by hematopoietic stem cell transplantation (HSCT) and 16 cases without HSCT. Ultra-deep sequencing revealed that the prevalence of genotype B and the ratio of non-synonymous to synonymous evolutionary changes in the surface (S) gene were significantly higher in non-HSCT cases than in patients with HSCT. Those non-synonymous variants included immune escape (6/16 cases) and MHC class II-restricted T-cell epitope variants (6/16 cases). Furthermore, reactivated HBV in 11 of 16 (69%) non-HSCT cases possessed substitutions associated with impaired virion secretion, including E2G, L77R, L98V, T118K, and Q129H in the S region, and M1I/V in the PreS2 region. In conclusion, virologic features of reactivated HBV clones differed depending on the intensity of the immunosuppressive condition. HBV reactivation triggered by immunosuppressive conditions, especially those without HSCT, was characterized by the expansion of variants associated with immune escape, MHC class II-restricted T-cell epitope alterations, and/or impaired virion secretion.
Social and anxiety-like behaviors contribute to nicotine self-administration in adolescent outbred rats
Authors: Wang Tengfei , Han Wenyan , Chitre Apurva S. , Polesskaya Oksana , Solberg Woods Leah C. , Palmer Abraham A. , Chen Hao 
Published: December 2018

AbstractBoth emotional and social traits interact with genetic factors to influence smoking behavior. We previously established a socially acquired nicotine intravenous self-administration model where social learning of a nicotine-associated odor cue reversed conditioned flavor aversion and promoted nicotine intake. In this study, we first phenotyped ~800 adolescent heterogeneous stock rats in open field, novel object interaction, social interaction, elevated plus maze, and marble burying behaviors. These rats were then phenotyped on socially acquired nicotine self-administration. We found 243 significant correlations between different behavioral tests. Principal component regression analysis found that ~10–20% of the variance in nicotine-related measures, such as intake during the first or the last three fixed-ratio sessions, the progressive ratio session, and reinstatement behavior, can be explained by variations in behavioral traits. Factors corresponding to social behavior and anxiety were among the strongest predictors of nicotine intake and reinstatement of nicotine-seeking behavior. We also found many sex differences in behavioral measures. These data indicated that the genetic diversity of this population, in combination with social behaviour and anxiety, are significant contributors to the divergent nicotine self-administration behavior and indicated a high probability of discovering sex-specific genetic mechanisms for nicotine intake in future genome-wide association studies.
Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus)
Authors: Nam Gyu-Hwi , Mishra Anshuman , Gim Jeong-An , Lee Hee-Eun , Jo Ara , Yoon Dahye , Kim Ahran , Kim Woo-Jin , Ahn Kung , Kim Do-Hyung , Kim Suhkmann , Cha Hee-Jae , Choi Yung Hyun , Park Chan-Il , Kim Heui-Soo 
Published: December 2018

AbstractOlive flounder (Paralichthys olivaceus) is one of economically valuable fish species in the East Asia. In comparison with its economic importance, available genomic information of the olive flounder is very limited. The mass mortality caused by variety of pathogens (virus, bacteria and parasites) is main problem in aquaculture industry, including in olive flounder culture. In this study, we carried out transcriptome analysis using the olive flounder gill tissues after infection of three types of pathogens (Virus; Viral hemorrhagic septicemia virus, Bacteria; Streptococcus parauberis, and Parasite; Miamiensis avidus), respectively. As a result, we identified total 12,415 differentially expressed genes (DEG) from viral infection, 1,754 from bacterial infection, and 795 from parasite infection, respectively. To investigate the effects of pathogenic infection on immune response, we analyzed Gene ontology (GO) enrichment analysis with DEGs and sorted immune-related GO terms per three pathogen groups. Especially, we verified various GO terms, and genes in these terms showed down-regulated expression pattern. In addition, we identified 67 common genes (10 up-regulated and 57 down-regulated) present in three pathogen infection groups. Our goals are to provide plenty of genomic knowledge about olive flounder transcripts for further research and report genes, which were changed in their expression after specific pathogen infection.