bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Phosphodiesterases on the Function of Aryl Hydrocarbon Receptor-Interacting Protein (AIP) in the Pituitary Gland and on the Evaluation of AIP Gene Variants
Authors: Hernández-Ramírez Laura C. , Trivellin Giampaolo , Stratakis Constantine A. 
Published: April 2017

AbstractFamilial isolated pituitary adenoma (FIPA) is caused in about 20% of cases by loss-of-function germline mutations in the AIP gene. Patients harboring AIP mutations usually present with somatotropinomas resulting either in gigantism or young-onset acromegaly. AIP encodes for a co-chaperone protein endowed with tumor suppressor properties in somatotroph cells. Among other mechanisms proposed to explain this function, a regulatory effect over the 3′,5′-cyclic adenosine monophosphate (cAMP) signaling pathway seems to play a prominent role. In this setting, the well-known interaction between AIP and 2 different isoforms of phosphodiesterases (PDEs), PDE2A3 and PDE4A5, is of particular interest. While the interaction with over-expressed AIP does not seem to affect PDE2A3 function, the reported effect on PDE4A5 is, in contrast, reduced enzymatic activity. In this review, we explore the possible implications of these molecular interactions for the function of somatotroph cells. In particular, we discuss how both PDEs and AIP could act as negative regulators of the cAMP pathway in the pituitary, probably both by shared and independent mechanisms. Moreover, we describe how the evaluation of the AIP-PDE4A5 interaction has proven to be a useful tool for testing AIP mutations, complementing other in silico, in vitro, and in vivo analyses. Improved assessment of the pathogenicity of AIP mutations is indeed paramount to provide adequate guidance for genetic counseling and clinical screening in AIP mutation carriers, which can lead to prospective diagnosis of pituitary adenomas.
Korea’s Evolving Business–Government Relationship
Authors: Kim Eun Mee 
Published: April 2017

Abstract
South Korea is a country that has achieved economic development despite the obstacles it faced as a war-torn country with few natural resources and little capital. Poverty and lack of democracy, as well as war and conflict, were challenges the country faced in the early 1960s; issues not very different from those many developing countries face in the 21st century. This chapter focuses on the following topics during the most dynamic period in South Korea’s economic development from the 1960s to the 1980s: the developmental state and industrial policies; the role of the private sector; and state–business relations (SBRs).
The chemical computer: molecular information
Authors: Ball Philip 
Published: April 2017

Abstract‘The chemical computer: molecular information’ outlines the ways that molecules can store and transmit information. Genetics is living proof that complex information can be encoded through systems using molecular recognition. Genetic systems have a vast array of copying, proof–reading and editing tools available to them to prevent errors when replicating, transcribing and translating data (although occasional errors — mutations — are essential for evolutionary progress). These tools can be commandeered by scientists to manipulate the genome. Moore's law states that computer power will double every two years. New technologies, such as genetic and molecular computers, are needed to ensure this law holds true.
The water molecule and its interactions
Authors: Finney John 
Published: April 2017

Abstract
‘The water molecule and its interactions’ discusses the structural and electrical properties of the water molecule. A water molecule is made up of two hydrogen atoms connected by covalent bonds to one oxygen atom. Water molecules interact with each other through a type of interaction called hydrogen bonding. A tetrahedral arrangement of four water molecules around a central one is the key to understanding water. It helps to explain the structure of water in its various states, its properties, and how it interacts with other kinds of molecules, allowing exploration of the properties and behaviour of the wide range of chemical, physical, and biological systems in which water is involved.
What is military strategy?
Authors: Echevarria Antulio J. 
Published: April 2017

Abstract
Military strategy is the practice of reducing an adversary’s physical capacity and willingness to fight, and continuing to do so until one’s aim is achieved. It takes place in wartime and peacetime and may involve using force, directly or indirectly, as a threat. Military strategy is often divided into four components: ends (objectives), ways (courses of action), means (resources), and risk. The practice of military strategy is described along with military power, which is augmented by nine “principles of war”: objective, maneuver, surprise, mass, economy of force, offensive, security, simplicity, and unity of command. A general will likely use combinations of military strategies, linking them into a series of operations or campaigns.
Cyber power and military strategy
Authors: Echevarria Antulio J. 
Published: April 2017

Abstract
‘Cyber power and military strategy’ discusses the role of cyber power in reducing a rival power’s physical capacity and willingness to fight. This issue is important for contemporary military strategists because cyber power—the ability to operate within cyberspace with relative security—is comparatively new and has political advantages in that it rarely causes human casualties. The difference between cyber war and cyber power is explained before discussing cyber power’s indispensability to military strategy. It is difficult to imagine any exercise of military force today that would not also involve an attendant use of cyber power.
International differences and standardization
Authors: Nobes Christopher 
Published: April 2017

Abstract
Just how different can accounting numbers be for the same company under different accounting rules? Which countries use International Financial Reporting Standards (IFRS)? In what main ways is US ‘generally accepted accounting principles’ (US GAAP) different from IFRS? How have politics and economics affected accounting? ‘International differences and standardization’ shows how international standardization simplifies the preparation of financial statements covering whole international groups and how it improves the comparability of the accounting information for managers and investors. Differences between US GAAP and IFRS are considered: US GAAP is more detailed than IFRS and tends to be written in terms of rules rather than principles. It also has fewer options.
Molecular signatures that can be transferred across different omics platforms
Authors: Altenbuchinger M , Schwarzfischer P , Rehberg T , Reinders J , Kohler Ch W , Gronwald W , Richter J , Szczepanowski M , Masqué-Soler N , Klapper W , Oefner P J , Spang R 
Published: April 2017

AbstractMotivationMolecular signatures for treatment recommendations are well researched. Still it is challenging to apply them to data generated by different protocols or technical platforms.ResultsWe analyzed paired data for the same tumors (Burkitt lymphoma, diffuse large B-cell lymphoma) and features that had been generated by different experimental protocols and analytical platforms including the nanoString nCounter and Affymetrix Gene Chip transcriptomics as well as the SWATH and SRM proteomics platforms. A statistical model that assumes independent sample and feature effects accounted for 69–94% of technical variability. We analyzed how variability is propagated through linear signatures possibly affecting predictions and treatment recommendations. Linear signatures with feature weights adding to zero were substantially more robust than unbalanced signatures. They yielded consistent predictions across data from different platforms, both for transcriptomics and proteomics data. Similarly stable were their predictions across data from fresh frozen and matching formalin-fixed paraffin-embedded human tumor tissue.Availability and ImplementationThe R-package ‘zeroSum’ can be downloaded at https://github.com/rehbergT/zeroSum. Complete data and R codes necessary to reproduce all our results can be received from the authors upon request.
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields
Authors: Shao Mingfu , Ma Jianzhu , Wang Sheng 
Published: April 2017

Abstract

Motivation
Reconstructing the full-length expressed transcripts (a.k.a. the transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol plays a central role in identifying novel genes and transcripts as well as in studying gene expressions and gene functions. A crucial step in transcript assembly is to accurately determine the splicing junctions and boundaries of the expressed transcripts from the reads alignment. In contrast to the splicing junctions that can be efficiently detected from spliced reads, the problem of identifying boundaries remains open and challenging, due to the fact that the signal related to boundaries is noisy and weak.

Results
We present DeepBound, an effective approach to identify boundaries of expressed transcripts from RNA-seq reads alignment. In its core DeepBound employs deep convolutional neural fields to learn the hidden distributions and patterns of boundaries. To accurately model the transition probabilities and to solve the label-imbalance problem, we novelly incorporate the AUC (area under the curve) score into the optimizing objective function. To address the issue that deep probabilistic graphical models requires large number of labeled training samples, we propose to use simulated RNA-seq datasets to train our model. Through extensive experimental studies on both simulation datasets of two species and biological datasets, we show that DeepBound consistently and significantly outperforms the two existing methods.

Availability and implementation
DeepBound is freely available at https://github.com/realbigws/DeepBound.
Trade-offs between forage fish fisheries and their predators in the California Current
Authors: Koehn Laura E , Essington Timothy E , Marshall Kristin N , Sydeman William J , Szoboszlai Amber I , Thayer Julie A 
Published: April 2017

AbstractForage fish generate economic benefits through directed fisheries, but also generate benefits through their role as prey to other valued species (large piscivorous fish, seabirds, and marine mammals). Previous evaluations of the ecosystem consequences of forage fish fisheries used models with coarse taxonomic resolution of forage fish and their predators. Here, we quantify trade-offs between forage fish fisheries and predator fisheries, and between forage fish fisheries and species of conservation interest in the California Current, using a taxonomically detailed foodweb model and a generalized equilibrium model. We propagated uncertainty in trade-offs to forage fish fishing based on uncertainty in foodweb model parameterization and uncertainty in predator–prey functional relationships in the generalized equilibrium model. The model predicted loss in catch of some higher trophic level fisheries [mainly salmon (Oncorhynchus sp.) and halibut (Paralichthys californicus)] from fishing sardine (Sardinops sagax), anchovy (Engraulis mordax), herring (Clupea pallasii), or aggregated forage fish, but the lost economic revenue from predators never exceeded the economic benefit from additional forage fish catch. Predicted reductions in biomass of seabirds and marine mammals were sufficiently large that, depending on the value of these nonmarket species, consideration of nonmarket predators could tip the balance of trade-offs toward conservation of forage fish and away from harvest. This work highlights specific predators [brown pelicans (Pelecanus occidentalis), marbled murrelets (Brachyramphus marmoratus), multiple other seabirds, sea lions (Zalophus californianus and Eumetopias jubatus), baleen whales (Mysticeti)] that are potentially sensitive to specific forage fish fisheries in the California Current.
Noninvasive RCM for Differentiation of Melanotic Macules From Melanocytic Lesions—Blinded Evaluation of a Series of 42 Pigmented Macules
Authors: Laimer Martin , Arzberger Edith , Kirchner Clara-Anna , Prodinger Christine , Hofmann-Wellenhof Rainer , Ahlgrimm-Siess Verena 
Published: April 2017

BACKGROUND
Differentiation of melanotic macules from melanocytic lesions, most importantly of melanoma, is a common problem on clinical-dermoscopic examination.

OBJECTIVE
To assess the value of noninvasive reflectance confocal microscopy (RCM) in the differential diagnosis of melanotic macules and melanocytic lesions.

PATIENTS AND METHODS
Reflectance confocal microscopy images of 42 pigmented macules on mucocutaneous junctions of genitalia and lips, including 31 melanotic macules, 6 nevi, and 5 melanomas, were retrospectively and independently assessed in a blinded manner by one expert observer and 2 less experienced observers together.

RESULTS
The authors differentiated 3 subtypes of melanotic macules; 2 subtypes (“solar lentigo type” and regular subtype of “dendritic type” melanotic macules) could be classified with confidence as benign by all RCM investigators, comprising 64% of melanotic macules. The third subtype (irregular subtype of “dendritic type” melanotic macules; 36%) displaying RCM features overlapping with melanoma was difficult to differentiate and should be biopsied not to miss a melanoma. The RCM differentiation between melanotic macules and nevi was easily performed.

CONCLUSION
RCM has the potential to increase the diagnostic accuracy in the noninvasive differentiation of pigmented macules on mucocutaneous junctions.
PARAPAPILLARY GAMMA AND DELTA ZONES IN HIGH MYOPIA
Authors: Jonas Jost B. , Fang Yuxin , Weber Pascal , Ohno-Matsui Kyoko 
Published: April 2017

Purpose:
To examine parapapillary zones gamma and delta in highly myopic eyes.

Methods:
The retrospective observational study included patients attending the Tokyo high myopia clinics. Fundus photographs were morphometrically examined.

Results:
The study population included 600 eyes (304 individuals) with a mean age of 62.7 ± 14.3 years (range: 13–90 years) and mean axial length of 29.6 ± 2.2 mm (range: 23.2–35.4 mm). In multivariate analysis (regression coefficient r2:0.90), larger horizontal gamma zone diameter was correlated with wider delta zone diameter (P < 0.001; standardized regression coefficient beta: 0.81), higher ratio of vertical-to-horizontal disk diameter (P < 0.001; beta: 0.10), shorter fovea–outer gamma zone border distance (P < 0.001; beta: −0.19), longer disk–fovea distance (P < 0.001; beta: 0.18), and higher count of chorioretinal atrophic lesions (P < 0.001; beta: 0.07). Longer horizontal delta zone width was correlated with longer horizontal gamma zone diameter (P < 0.001; beta: 1.00), longer horizontal disk diameter (P < 0.001; beta: 0.15), shorter disk–fovea distance (P < 0.001; beta: −0.19), longer fovea–outer gamma zone border distance (P < 0.001; beta: 0.19), and smaller diameter of the largest chorioretinal lesion (P = 0.03; beta: −0.04). Longer width of both zones together was associated with longer horizontal disk diameter (P < 0.001; beta: 0.31), higher ratio of vertical-to-horizontal disk diameter (P = 0.001; beta: 0.18), longer disk–fovea distance (P < 0.001; beta: 0.19), shorter fovea–outer gamma zone border distance (P < 0.001; beta: −0.18), higher number of chorioretinal lesions (P < 0.001; beta: 0.30), and longer vertical distance between the superior and inferior temporal arterial arcade (P = 0.001; beta: 0.13).

Conclusion:
Larger gamma and delta zones were correlated with larger optic disk and more marked vertical optic disk rotation, longer disk–fovea distance, higher number of chorioretinal lesions, and longer temporal vascular arcade diameter. Parapapillary gamma and delta zones may develop before chorioretinal lesions develop and enlarge.
Neuropathic pain after chronic nerve constriction may not correlate with chloride dysregulation in mouse trigeminal nucleus caudalis neurons
Authors: Castro Alberto , Li Ying , Raver Charles , Chandra Ramesh , Masri Radi , Lobo Mary K. , Keller Asaf 
Published: April 2017

Abstract
Changes in chloride reversal potential in rat spinal cord neurons have previously been associated with persistent pain in nerve injury and inflammation models. These changes correlate with a decrease in the expression of the potassium chloride transporter, KCC2, and with increases in neuronal excitability. Here, we test the hypothesis that similar changes occur in mice with neuropathic pain induced by chronic constriction injury of the trigeminal infraorbital nerve (CCI-ION). This model allows us to distinguish an acute pain phase (3-5 days after injury) from a persistent pain phase (12-14 days after CCI-ION). Chronic constriction injury of the trigeminal infraorbital nerve induced significant decreases in mechanical pain thresholds in both the acute and persistent phases. To estimate GABAA reversal potentials in neurons from trigeminal nucleus caudalis, we obtained perforated patch recordings in vitro. GABAA reversal potential decreased by 8% during the acute phase in unidentified neurons, but not in GABAergic interneurons. However, at 12 to 14 days after CCI-ION, GABAA reversal potential recovered to normal values. Quantitative real-time polymerase chain reaction analysis revealed no significant changes, at either 3 to 5 days or 12 to 14 days after CCI-ION, in either KCC2 or NKCC1. These findings suggest that CCI-ION in mice results in transient and modest changes in chloride reversal potentials, and that these changes may not persist during the late phase. This suggests that, in the mouse model of CCI-ION, chloride dysregulation may not have a prominent role in the central mechanisms leading to the maintenance of chronic pain.
Development and Psychometric Evaluation of the Professional Practice Work Environment Inventory
Authors: Ives Erickson Jeanette , Duffy Mary E. , Ditomassi Marianne , Jones Dorothy 
Published: April 2017

OBJECTIVE
The purpose is to examine the psychometric properties of the professional practice work environment inventory (PPWEI).

BACKGROUND
Derived from the Professional Practice Environment (PPE) and the Revised PPE scales, the PPWEI was designed to measure 8 components of the PPE that can be used to assist nurse administrators in decision-making.

METHODS
A psychometric evaluation was undertaken with 874 nurses who were providing direct care to patients at the Massachusetts General Hospital and who provided no missing data on the newly developed 72-item PPWEI.

RESULTS
Cronbach’s α internal consistency reliability of the total score was .93, with 61 items having factor loadings more than .50, the factor loading cutoff used to define the component subscales. Principal component analyses with varimax rotation and Kaiser normalization demonstrated 8 components, explaining 64.6% of variance. Cronbach’s α reliability coefficients of the PPWEI subscales ranged from .82 to .93.

CONCLUSION
The multidimensional PPWEI is a psychometrically sound measure of several components of the PPE in the acute care setting and sufficiently reliable and valid for use as independent subscales in healthcare research.
Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectorsAedes aegyptiandAedes albopictus
Authors: Palatini Umberto , Miesen Pascal , Carballar-Lejarazu Rebeca , Ometto Lino , Rizzo Ettore , Tu Zhijian , van Rij Ronald , Bonizzoni Mariangela 
Published: April 2017

ABSTRACTBackgroundArthropod-borne viruses (arboviruses) transmitted by mosquito vectors cause many important emerging or resurging infectious diseases in humans including dengue, chikungunya and Zika. Understanding the co-evolutionary processes among viruses and vectors is essential for the development of novel transmission-blocking strategies. Arboviruses form episomal viral DNA fragments upon infection of mosquito cells and adults. Additionally, sequences from insect-specific viruses and arboviruses have been found integrated into mosquito genomes.ResultsWe used a bioinformatic approach to analyze the presence, abundance, distribution, and transcriptional activity of integrations from 425 non-retroviral viruses, including 133 arboviruses, across the presently available 22 mosquito genome sequences. Large differences in abundance and types of viral integrations were observed in mosquito species from the same region. Viral integrations are unexpectedly abundant in the arboviral vector speciesAedes aegyptiandAe. albopictus, but are ∼10-fold less abundant in all other mosquitoes analysed. Additionally, viral integrations are enriched in piRNA clusters of both theAe. aegyptiandAe. albopictusgenomes and, accordingly, they express piRNAs, but not siRNAs.ConclusionsDifferences in number of viral integrations in the genomes of mosquito species from the same geographic area support the conclusion that integrations of viral sequences is not dependent on viral exposure, but that lineage-specific interactions exits. Viral integrations are abundant inAe. aegyptiandAe. albopictus, and represent a thus far unappreciated component of their genomes. Additionally, the genome locations of viral integrations and their production of piRNAs indicate a functional link between viral integrations and the piRNA pathway. These results greatly expand the breadth and complexity of small RNA-mediated regulation and suggest a role for viral integrations in antiviral defense in these two mosquito species.
Beyond the Linear Genome: Comprehensive Determination of the Endogenous Circular Elements inC. elegansand Human Genomes via an Unbiased Genomic-Biophysical Method
Authors: Shoura Massa J. , Gabdank Idan , Hansen Loren , Merker Jason , Gotlib Jason , Levene Stephen D. , Fire Andrew Z. 
Published: April 2017

AbstractInvestigations aimed at defining the 3-D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. High-throughput sequencing has only recently made extensive genomic mapping of eccDNA sequences possible and had yet to be applied using a rigorous approach that distinguishes ascertainment bias from true enrichment. Here, we define eccDNA distribution, utilizing a set of unbiased topology-dependent approaches for enrichment and characterization. We use parallel biophysical, enzymatic, and informatic approaches to obtain a comprehensive profiling of eccDNA inC. elegansand in three human cell types, where eccDNAs were previously uncharacterized. We also provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture in which endogenous genomic DNA circles are present in normal physiological DNA metabolism, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples.