bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered peripheral immune profiles in treatment-resistant depression: response to ketamine and prediction of treatment outcome
Authors: Kiraly D D , Horn S R , Van Dam N T , Costi S , Schwartz J , Kim-Schulze S , Patel M , Hodes G E , Russo S J , Merad M , Iosifescu D V , Charney D S , Murrough J W 
Published: March 2017

AbstractA subset of patients with depression have elevated levels of inflammatory cytokines, and some studies demonstrate interaction between inflammatory factors and treatment outcome. However, most studies focus on only a narrow subset of factors in a patient sample. In the current study, we analyzed broad immune profiles in blood from patients with treatment-resistant depression (TRD) at baseline and following treatment with the glutamate modulator ketamine. Serum was analyzed from 26 healthy control and 33 actively depressed TRD patients free of antidepressant medication, and matched for age, sex and body mass index. All subjects provided baseline blood samples, and TRD subjects had additional blood draw at 4 and 24 h following intravenous infusion of ketamine (0.5 mg kg−1). Samples underwent multiplex analysis of 41 cytokines, chemokines and growth factors using quantitative immunoassay technology. Our a priori hypothesis was that TRD patients would show elevations in canonical pro-inflammatory cytokines; analyses demonstrated significant elevation of the pro-inflammatory cytokine interleukin-6. Further exploratory analyses revealed significant regulation of four additional soluble factors in patients with TRD. Several cytokines showed transient changes in level after ketamine, but none correlated with treatment response. Low pretreatment levels of fibroblast growth factor 2 were associated with ketamine treatment response. In sum, we found that patients with TRD demonstrate a unique pattern of increased inflammatory mediators, chemokines and colony-stimulating factors, providing support for the immune hypothesis of TRD. These patterns suggest novel treatment targets for the subset of patients with TRD who evidence dysregulated immune functioning.
Diabetes confers in vitro calcific potential on serum which associates with in vivo vascular calcification
Authors: Patidar Ashish , Singh Dhruv K. , Thakur Shori , Winocour Peter , Farrington Ken , Baydoun Anwar R. 
Published: March 2017

Although vascular calcification (VC) is prevalent in Type 2 diabetes mellitus (T2DM), underlying mechanisms remain unclear. Neither is it known whether T2DM confers calcific potential (CP) on serum, enabling it to induce VC outside the disease milieu. We, therefore, investigated the CP of serum from controls and subjects with T2DM with and without in vivo VC. Samples from 20 healthy controls and 44 age- and sex-matched patients with T2DM with modification of diet in renal disease estimated glomerular filtration rate (MDRD-4 eGFR) &gt; 60 ml·min−1 were analysed for CP using rat aortic smooth muscle cells in vitro. CT scans of femoral arteries identified individuals with in vivo calcification. Serum from subjects with T2DM revealed significantly greater CP than controls. This was further enhanced in the presence of in vivo VC. Addition of β-glycerophosphate (β-GP) plus CaCl2 increased the CP of T2DM serum but not of controls. Along with age, CP was an independent predictor of the presence of VC. In receiver operator curve (ROC) analysis, CP was a significant predictor of femoral arterial VC (C-statistic 0.70: P=0.009). The distribution of CP was bimodal around a cutoff of 100 nmoles of Ca2+ protein mg−1, with a higher proportion of Type 2 diabetes subjects with in vivo calcification (T2DM+) sera above the cutoff value. This group also showed elevated levels of osteoprotegerin (OPG) and matrix Gla protein (MGP). Diabetes confers CP on the serum which is enhanced by the presence of in vivo VC. The CP acquired may be dependent on levels of OPG and MGP. These findings may be clinically relevant for early identification of individuals at risk of VC and for informing therapeutic strategies.
Hepatic Encephalopathy in Malaria or Artesunate Toxicity: A Dilemma in Diagnosis
Authors: Baliga Kiran , Keshav Murali , Baliga Santharam , Gopakumar K. 
Published: March 2017

AbstractMalaria remains an overwhelming problem with around 214 million cases reported worldwide each year. It remains a major health problem in the tropical developing countries and India accounts for 70% of the total malaria incidence in the Southeast Asia region. Even though, artesunate, a novel drug used in the treatment of chloroquine-resistant cases of Plasmodium falciparum infection causes transient transaminitis (elevation of alanine and aspartate transaminases), hepatitis and hepatic encephalopathy are very rare. We encountered a child with falciparum malaria, who accidently ingested artesunate tablets (16 mg/kg) and developed hepatic encephalopathy with clinical and biochemical improvement in a matter of 4 to 5 days. There are only a few reports of children with malaria developing hepatic encephalopathy, with or without coinfection with hepatotropic viruses. Also, there are no reports of hepatic encephalopathy secondary to artesunate overdose, creating a dilemma in diagnosis and management.
BORC/kinesin-1 ensemble drives polarized transport of lysosomes into the axon
Authors: Farías Ginny G. , Guardia Carlos M. , De Pace Raffaella , Britt Dylan J. , Bonifacino Juan S. 
Published: March 2017

SignificanceLysosomes are found in all neuronal domains, including the soma, axon, and dendrites. How neurons are transported in these domains, however, remains poorly understood. In the present study, we show that a protein ensemble comprising BORC, Arl8, SKIP, and kinesin-1 specifically drives lysosome transport into the axon and not the dendrites. We also show that this mechanism of axonal lysosome transport is essential for maintenance of growth-cone dynamics and turnover of autophagosomes in the distal axon. These findings imply that transport of lysosomes into the axon and the dendrites occurs by different mechanisms, and demonstrate that BORC-regulated lysosome transport is critical for axonal functions.
Prion protein dynamics before aggregation
Authors: Srivastava Kinshuk Raj , Lapidus Lisa J. 
Published: March 2017

Significance
The prion protein aggregates and causes neurodegenerative diseases in many mammalian species. The aggregated protein is transmissible to other organisms and species. Aggregation is believed to originate in cellular endosomes at low pH. We have measured reconfiguration of unfolded prion of two species under a variety of conditions and found a wide range of rates. At low pH the reconfiguration rate for hamster prion is in the middle of the measured range, but increases when an aggregation inhibitor is added. These results agree with a model in which aggregation is fastest when reconfiguration is about the same rate as bimolecular association, and suggest a new approach to finding drugs for prion diseases in which reconfiguration is altered to prevent aggregation.
Effectiveness of UNAIDS targets and HIV vaccination across 127 countries
Authors: Medlock Jan , Pandey Abhishek , Parpia Alyssa S. , Tang Amber , Skrip Laura A. , Galvani Alison P. 
Published: March 2017

Significance
Despite extraordinary advances in the treatment of HIV, the global pandemic has yet to be reversed. We developed a mathematical model for 127 countries to evaluate Joint United Nations Program on HIV/AIDS (UNAIDS) targets for expanding diagnosis and treatment of the infected, and partially efficacious HIV vaccination. Under the current levels of diagnosis and treatment, we estimated 49 million new HIV cases globally from 2015 to 2035. Achieving the ambitious UNAIDS target is predicted to avert 25 million of these new infections, with an additional 6.3 million averted by the 2020 introduction of a 50%-efficacy vaccine. Our study provides country-specific impacts of a partially effective HIV vaccine and demonstrates its importance to the elimination of HIV transmission globally.
Ultrathin dendrimer–graphene oxide composite film for stable cycling lithium–sulfur batteries
Authors: Liu Wen , Jiang Jianbing , Yang Ke R. , Mi Yingying , Kumaravadivel Piranavan , Zhong Yiren , Fan Qi , Weng Zhe , Wu Zishan , Cha Judy J. , Zhou Henghui , Batista Victor S. , Brudvig Gary W. , Wang Hailiang 
Published: March 2017

Significance
The promise of lithium–sulfur batteries for future electric transportation and stationary energy storage is being limited by their poor cycling stability. Previous approaches to improvement often involve incorporating additional components with significant dead weight or volume in battery structures. We develop an ultrathin functionalized dendrimer–graphene oxide composite film which can be applied to virtually any sulfur cathode to alleviate capacity fading over battery cycling without compromising the energy or power density of the entire battery. The design provides a new strategy for confining lithium polysulfide intermediates and thus stabilizing lithium–sulfur batteries. It also brings a suitable platform for elucidating the underlying materials and surface chemistry.
Ena/VASP proteins regulate activated T-cell trafficking by promoting diapedesis during transendothelial migration
Authors: Estin Miriam L. , Thompson Scott B. , Traxinger Brianna , Fisher Marlie H. , Friedman Rachel S. , Jacobelli Jordan 
Published: March 2017

SignificanceT-cell trafficking is essential for the function of the adaptive immune system, and regulation of T-cell entry into tissues can be an effective therapy in diseases such as autoimmunity. However, the mechanisms regulating T-cell migration and trafficking are poorly understood. We have identified a key role for Ena/VASP (vasodilator-stimulated phosphoprotein) family cytoskeletal effectors selectively in activated T-cell trafficking to secondary lymphoid organs and to peripheral sites of inflammation. Ena/VASP deficiency in T cells causes a defect in α4 integrin function, which impairs transendothelial migration. Our work suggests that further studies of the Ena/VASP pathway in T cells could identify therapeutically useful ways to more selectively modulate α4 integrin activity and activated T-cell trafficking.
Practice, Practice, Practice
Authors: Miller Kiri 
Published: March 2017

Abstract
This chapter analyzes dance games as transmission systems, assessing their capacity to notate, transmit, and archive embodied repertoires that are typically taught in face-to-face, body-to-body contexts. Dance games ask players to sight-read unfamiliar choreography in real time, mirroring the screen dancer as the routine unfolds. They imply that choreography can work like streaming audio or video—passing straight into a player’s proprioceptive system—and challenge players to cultivate techniques of anticipation to minimize “kinesthetic lag.” The games teach these techniques using hybrid notation systems, modular choreography tied to musical structure, and patterned repetition that integrates technical training into a repertoire of works. Close readings of Dance Central’s version of “Crank That” and Just Dance’s version of “Apache (Jump On It)” show how this technical pedagogy dovetails with the games’ remediation of existing song-and-dance repertoires to reinforce racialized models of dance authenticity.
Choreographic Labor, FTFO
Authors: Miller Kiri 
Published: March 2017

Abstract
This chapter focuses on choreographic labor, highlighting the perspectives of game choreographers. These creative workers function as cultural intermediaries between the game industry and various dance cultures; their embodied and affective labor position them as representatives of “real dance.” The technical constraints imposed by motion-capture and animation processes impact the nature of creative labor in dance game production. Choreographers have pushed against those constraints to assert their own creative agency and affirm particular dance values. This chapter also addresses issues of ownership—in terms of choreographic copyright, cultural heritage, and cultural appropriation—and shows how dance games reflect choreographers’ experiences as teachers, students, competitors, and producers of creative content in an era of precarious labor.
Sex and Salvation in the Vergilian Cento of the Fourth Century
Authors: Pollmann Karla 
Published: March 2017

Abstract
In a cento, a writer uses fragments from texts of canonical authors (Genette’s hypotext) taken out of their original context to create a new work (Genette’s hypertext), which one could call ‘literary patchwork’. This chapter argues innovatively to differentiate between the predominantly parodical aim of pagan centos and the predominantly exegetical aim of Christian centos, and illustrates the implications and consequences of this assumption by analysing the centos of the fourth-century writers Ausonius and Proba. While both poets are adhering to a classicism that sees Vergil as indispensable for conveying a culturally convincing message, they manage to exploit the authority and embedded polysemy of the hypotext for diametrically opposed messages. Thus the chapter programmatically demonstrates that the literary genre of the cento, instead of being wrongly accused of epigonality, is a highly original and complex literary form.
Entanglement spectroscopy and its application to the quantum Hall effects
Authors: Regnault Nicolas 
Published: March 2017

Abstract
Entanglement spectroscopy has stimulated an extensive range of studies. The entanglement spectrum is the spectrum of the reduced density matrix when the system is partitioned into two. For many quantum systems, when computed from the bulk ground-state wavefunction, it gives access to the physics of edge excitations. It is thus a valuable tool to diagnose topological ordering. These lecture notes provide an overview of entanglement spectroscopy, mostly in the context of the fractional quantum Hall effect. The basic concepts are introduced through the example of quantum spin chains. The connection with entanglement entropy and the matrix product state representation is discussed. The entanglement spectrum can be computed for non-interacting topological phases, revealing edge excitation from the ground state. Application to fractional quantum Hall phases shows how much information is encoded within the ground state and how different partitions probe different types of excitations. Application to fractional Chern insulators is discussed.
Transport of Dirac surface states
Authors: Carpentier D. 
Published: March 2017

AbstractThe occurrence of robust states at the surface of three-dimensional topological insulators is their most salient feature. Indeed, it is their existence in ARPES experiments that is used as a signature of the topological property of the bulk bands. These surface states turn out to be described by a relativistic two-dimensional Dirac equation at low energy. These lecture notes focus on the transport properties of these Dirac surface states. While transport may not be the ideal probe of the existence of Dirac-like electronic excitations, it remains a tool of choice in condensed matter. These notes survey some of the transport properties of Dirac excitations and the techniques appropriate to their studies. For the sake of pedagogy, the focus is on the simplest transport properties, neglecting in particular transport in hybrid structures with superconductors.
Spin textures in quantum Hall systems
Authors: Douçot Benoît 
Published: March 2017

Abstract
The subject of these lecture notes combines several different manifestations of topology in a condensed matter system. The most classical of these is through the notion of texture. By this is meant any non-singular and topologically non-trivial spatial configuration of some relevant order parameter. The goal of these notes is to provide a theory-oriented introduction to the physics of textures in quantum Hall ferromagnets. They do not attempt to provide a comprehensive review of this very rich subject, and many important aspects are not mentioned, but instead they focus on recent advances in this field.
Out-of-equilibrium behaviour in topologically ordered systems on a lattice: fractionalized excitations and kinematic constraints
Authors: Castelnovo Claudio 
Published: March 2017

Abstract
These lecture notes deal with aspects of out-of-equilibrium behaviour in topologically ordered systems, broadly interpreted as systems that do not develop a local order parameter at low temperature (e.g. symmetry breaking) and yet exhibit non-trivial global properties. The specific cases of classical spin ice and the quantum toric code are discussed. Within classical systems, it is found that substantial progress can be made in understanding the dynamics through effective modelling of the vacuum and its emergent excitations. However, at the quantum level, modelling is limited to that of leading energy barriers and asymptotic behavior, although it turns out that an intriguing parallel can be drawn between the toric code Hamiltonian and a class of lattice systems known as kinetically constrained models.
Local Transformation
Authors: Beck Ulrik 
Published: March 2017

Abstract
This chapter documents the local transformation of rural Vietnamese communes in twelve different provinces from 2006 to 2014. Two key areas are considered, namely occupational and agricultural choice and provision of public goods. While many areas showed improvements and steady structural transformation into other activities supporting agriculture, the level and the speed of transformation process varied between different geographical regions and, on some indicators, it appears that some communes are not currently reaping the benefits of the high levels of economic growth. While communes report fewer problems in 2014 than in 2006, there has been a marked increase in the number of communes who feel climate change is a problem. Commune administrators expect this to increase even more going forward.
Labour and Migration
Authors: Narciso Gaia 
Published: March 2017

Abstract
This chapter provides an overview of the characteristics of households with a migrant away, and analyses the effects of migration in Viet Nam, on the basis of the VARHS conducted in 2012 and 2014. The data reveal significant movements of household members, both intra- and inter-province. Differences are uncovered between sending and non-sending households: households with a migrant are wealthier than non-sending households, as measured by food expenditure. The analysis shows that migration acts as a shock-coping mechanism, especially in the presence of natural shocks. Remittance-recipient households seem to react better to natural shocks, as the remittance flows counterbalance the need for borrowing.
Social and Political Capital
Authors: Markussen Thomas 
Published: March 2017

Abstract
This chapter exploits five waves of VARHS to investigate issues of social and political capital in rural Viet Nam. The chapter analyses membership of the Communist Party, ‘mass organizations’ (MOs) (Farmers’ Union, Women’s Union, etc.) and other voluntary organizations (such as sports clubs, cultural groups, etc.), trust, and the significance of family ties in economic transactions (e.g. the share of land tenants who are relatives of their landlord). The chapter also presents fixed effects regressions, exploring the effects of social and political capital on household income. The results indicate positive returns to Communist Party membership, trust, and access to informal insurance.
SynergyFinder: a web application for analyzing drug combination dose–response matrix data
Authors: Ianevski Aleksandr , He Liye , Aittokallio Tero , Tang Jing 
Published: March 2017

Abstract
Summary: Rational design of drug combinations has become a promising strategy to tackle the drug sensitivity and resistance problem in cancer treatment. To systematically evaluate the pre-clinical significance of pairwise drug combinations, functional screening assays that probe combination effects in a dose–response matrix assay are commonly used. To facilitate the analysis of such drug combination experiments, we implemented a web application that uses key functions of R-package SynergyFinder, and provides not only the flexibility of using multiple synergy scoring models, but also a user-friendly interface for visualizing the drug combination landscapes in an interactive manner.
Availability and Implementation: The SynergyFinder web application is freely accessible at https://synergyfinder.fimm.fi; The R-package and its source-code are freely available at http://bioconductor.org/packages/release/bioc/html/synergyfinder.html.
Creating a Culture of Collaboration: A Brief History of Academic Neurosurgery in Washington, DC
Authors: Siu Alan , Neal Christopher J , Syed Hasan R , Felbaum Daniel R , Nair M Nathan , McGrail Kevin M , Caputy Anthony J , Shields Donald C 
Published: March 2017

Abstract
Clinical neurosurgery has been practiced in the US capital for just over 100 years. As former residents and fellows of Drs. Harvey Cushing and Walter Dandy moved to the region, hospitals at Georgetown and George Washington Universities became early adopters of this new surgical discipline. Later academic neurosurgery programs were established at the National Institutes of Health, Walter Reed Medical Center, and Children's National Medical Center. Neurosurgical pioneers at these institutions developed new technologies and diagnostic procedures which continue to inform our current practice. In addition, continued collaboration between the multiple training sites in Washington, DC has uniquely enriched our residents’ training experience.
GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data
Authors: Beagrie Robert A. , Schueler Markus 
Published: March 2017

AbstractGenome Architecture Mapping (GAM) is a recently developed method for mapping chromatin interactions genome-wide. GAM is based on sequencing genomic DNA extracted from thin cryosections of cell nuclei. As a new approach, GAM datasets require specialized analytical tools and approaches. Here we present GAMtools, a pipeline for analysing GAM datasets. GAMtools covers the automated mapping of raw next-generation sequencing data generated by GAM, detection of genomic regions present in each nuclear slice, calculation of quality control metrics, generation of inferred proximity matrices, plotting of heatmaps and detection of genomic features for which chromatin interactions are enriched/depleted.