bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphine decreases the pro-angiogenic interaction between breast cancer cells and macrophages in vitro
Authors: Khabbazi Samira , Nassar Zeyad D. , Goumon Yannick , Parat Marie-Odile 
Published: August 2016

AbstractInteractions between the various cell types that constitute a solid tumour are essential to the biology of the tumour. We evaluated the effect of morphine on the proangiogenic interaction taking place between macrophages and breast cancer cells in vitro. The conditioned medium (CM) from breast cancer cells co-cultured with macrophages elicited endothelial cell proliferation and tube formation. This effect was inhibited if the co-culture occurred in the presence of morphine. The CM from breast cancer cells or macrophages grown individually, whether or not prepared in the presence of morphine, was ineffective in stimulating EC proliferation or tube formation. Using a mouse antibody array, we identified several angiogenesis-regulating factors differentially expressed in the CM of co-cultured cells prepared in the presence or absence of morphine, amongst which interleukin (IL)-6, tumour necrosis factor (TNF)-α and vascular endothelial growth factor (VEGF)-A. VEGF was induced in both cell types by the co-culture and this was prevented by morphine in a non-naloxone reversible fashion. The effect of CM from co-cultured cells on endothelial tube formation, but not proliferation, was prevented by anti-VEGF neutralizing antibody. Our results indicate that morphine prevents, in part via modulating VEGF-A expression, the pro-angiogenic interaction between macrophages and breast cancer cells.
First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L.
Authors: Zhen Shoumin , Deng Xiong , Wang Jian , Zhu Gengrui , Cao Hui , Yuan Linlin , Yan Yueming 
Published: August 2016

AbstractProtein acetylation and succinylation are the most crucial protein post-translational modifications (PTMs) involved in the regulation of plant growth and development. In this study, we present the first lysine-acetylation and lysine-succinylation proteome analysis of seedling leaves in Brachypodium distachyon L (Bd). Using high accuracy nano LC-MS/MS combined with affinity purification, we identified a total of 636 lysine-acetylated sites in 353 proteins and 605 lysine-succinylated sites in 262 proteins. These proteins participated in many biology processes, with various molecular functions. In particular, 119 proteins and 115 sites were found to be both acetylated and succinylated, simultaneously. Among the 353 acetylated proteins, 148 had acetylation orthologs in Oryza sativa L., Arabidopsis thaliana, Synechocystis sp. PCC 6803, and Glycine max L. Among the 262 succinylated proteins, 170 of them were found to have homologous proteins in Oryza sativa L., Escherichia coli, Sacchayromyces cerevisiae, or Homo sapiens. Motif-X analysis of the acetylated and succinylated sites identified two new acetylated motifs (K---K and K-I-K) and twelve significantly enriched succinylated motifs for the first time, which could serve as possible binding loci for future studies in plants. Our comprehensive dataset provides a promising starting point for further functional analysis of acetylation and succinylation in Bd and other plant species.
A fluorescent acrylamide-type monomer bearing an environment-sensitive methoxybenzocoumarin structure for the development of functional polymeric sensors
Authors: Uchiyama Seiichi , Remón Patricia , Pischel Uwe , Kawamoto Kyoko , Gota Chie 
Published: August 2016

Abstract
A new fluorescent acrylamide-type monomer bearing a hydrogen bonding- and polarity-sensitive benzocoumarin fluorophore was synthesized. The absorption spectra, fluorescence spectra, and fluorescence lifetime of a model compound were measured in ten solvents with different hydrogen-bonding abilities and polarities to investigate the sensitivity of the fluorophore to the surrounding environment. These spectroscopic studies demonstrated that the fluorophore emits stronger fluorescence in more protic, polar environments. A fluorescent polymeric thermometer was prepared from N-isopropylacrylamide and the new fluorescent monomer, and it showed good functionality in aqueous solution (e.g., high sensitivity to temperature changes and high chemical stability), indicating the applicability of the herein developed fluorescent monomer for use in functional sensors.
60 GHz 5‐bit digital controlled phase shifter in a digital 40 nm CMOS technology without ultra‐thick metals
Authors: Gao H. , Ying K. , Matters‐Kammerer M.K. , Harpe P. , Wang B. , Liu B. , Serdijn W.A. , Baltus P.G.M. 
Published: August 2016

A 5‐bit digital controlled switch‐type passive phase shifter realised in a 40 nm digital CMOS technology without ultra‐thick metals for the 60 GHz Industrial, Scientific and Medical (ISM) band is presented. A patterned shielding with electromagnetic bandgap structure and a stacked metals method to increase the on‐chip inductor quality factor are proposed. To reduce the insertion loss from the transistors, the transistor switches are implemented with a body–source connection. For all 32 states, the minimum phase error is 1.5°, and the maximum phase error is 6.8°. The measured insertion loss is −20.9 ± 1 dB including pad loss at 60 GHz and the return loss is >10 dB over 57–64 GHz. The total chip size is 0.24 mm2 with 0 mW DC power consumption.
Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells
Authors: Moreno Alberto , Carrington Jamie T. , Albergante Luca , Al Mamun Mohammed , Haagensen Emma J. , Komseli Eirini-Stavroula , Gorgoulis Vassilis G. , Newman Timothy J. , Blow J. Julian 
Published: August 2016

Significance
We provide evidence that in organisms with gigabase-sized genomes, such as humans, one or more stretches of DNA typically remain unreplicated when cells enter mitosis and are segregated to daughter cells via structures called ultrafine anaphase bridges. p53-binding protein 1 (53BP1) accumulates at the subsequent DNA structures inherited by each daughter cell in the following G1 phase to facilitate resolution in S phase. We show that the abundance of these structures match theoretical predictions for the number of unreplicated DNA segments when the number of replication origins is artificially increased or decreased. We show that 53BP1 preferentially binds to chromosomal regions with low numbers of replication origins. This work challenges the prevailing view of how genome stability is maintained in proliferating cells.
Network pharmacology of JAK inhibitors
Authors: Moodley Devapregasan , Yoshida Hideyuki , Mostafavi Sara , Asinovski Natasha , Ortiz-Lopez Adriana , Symanowicz Peter , Telliez Jean-Baptiste , Hegen Martin , Clark James D. , Mathis Diane , Benoist Christophe 
Published: August 2016

SignificanceJAK kinase inhibitors (JAKis) have advanced options for treatment of autoimmune diseases. Because JAKs are signaling hubs for several cytokine receptors, JAKis’ overall impact on the immune system and how they actually improve diseases like rheumatoid arthritis remain poorly understood. Combined immunophenotyping and genomic profiling revealed broad JAKi effects on the immunogenomic network, irrespective of inhibitor fine specificity, with effects on population homeostasis and coregulated gene-expression networks, particularly in innate immunocytes. Persistent repression by JAKis of IFN signature genes lasted beyond drug clearance and correlated with changes in the structure of the underlying chromatin, with direct implications for practical use of the drugs. Further JAKi development may need to take into account their broad network and epigenomic effects.
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets
Authors: Lu Jing , Carlson Heather A. 
Published: August 2016

Motivation: What if you could explain complex chemistry in a simple tree and share that data online with your collaborators? Computational biology often incorporates diverse chemical data to probe a biological question, but the existing tools for chemical data are ill-suited for the very large datasets inherent to bioinformatics. Furthermore, existing visualization methods often require an expert chemist to interpret the patterns. Biologists need an interactive tool for visualizing chemical information in an intuitive, accessible way that facilitates its integration into today’s team-based biological research.
Results: ChemTreeMap is an interactive, bioinformatics tool designed to explore chemical space and mine the relationships between chemical structure, molecular properties, and biological activity. ChemTreeMap synergistically combines extended connectivity fingerprints and a neighbor-joining algorithm to produce a hierarchical tree with branch lengths proportional to molecular similarity. Compound properties are shown by leaf color, size and outline to yield a user-defined visualization of the tree. Two representative analyses are included to demonstrate ChemTreeMap’s capabilities and utility: assessing dataset overlap and mining structure–activity relationships.
Availability and Implementation: The examples from this paper may be accessed at http://ajing.github.io/ChemTreeMap/. Code for the server and client are available in the Supplementary Information, at the aforementioned github site, and on Docker Hub (https://hub.docker.com) with the nametag ajing/chemtreemap.
Contact: carlsonh@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Multivariate Welch t-test on distances
Authors: Alekseyenko Alexander V. 
Published: August 2016

Motivation: Permutational non-Euclidean analysis of variance, PERMANOVA, is routinely used in exploratory analysis of multivariate datasets to draw conclusions about the significance of patterns visualized through dimension reduction. This method recognizes that pairwise distance matrix between observations is sufficient to compute within and between group sums of squares necessary to form the (pseudo) F statistic. Moreover, not only Euclidean, but arbitrary distances can be used. This method, however, suffers from loss of power and type I error inflation in the presence of heteroscedasticity and sample size imbalances.
Results: We develop a solution in the form of a distance-based Welch t-test, TW2, for two sample potentially unbalanced and heteroscedastic data. We demonstrate empirically the desirable type I error and power characteristics of the new test. We compare the performance of PERMANOVA and TW2 in reanalysis of two existing microbiome datasets, where the methodology has originated.
Availability and Implementation: The source code for methods and analysis of this article is available at https://github.com/alekseyenko/Tw2. Further guidance on application of these methods can be obtained from the author.
Contact: alekseye@musc.edu
Official American Thoracic Society/Centers for Disease Control and
Prevention/Infectious Diseases Society of America Clinical Practice Guidelines: Treatment
of Drug-Susceptible Tuberculosis
Authors: Nahid Payam , Dorman Susan E. , Alipanah Narges , Barry Pennan M. , Brozek Jan L. , Cattamanchi Adithya , Chaisson Lelia H. , Chaisson Richard E. , Daley Charles L. , Grzemska Malgosia , Higashi Julie M. , Ho Christine S. , Hopewell Philip C. , Keshavjee Salmaan A. , Lienhardt Christian , Menzies Richard , Merrifield Cynthia , Narita Masahiro , O'Brien Rick , Peloquin Charles A. , Raftery Ann , Saukkonen Jussi , Schaaf H. Simon , Sotgiu Giovanni , Starke Jeffrey R. , Migliori Giovanni Battista , Vernon Andrew 
Published: August 2016

Abstract
The American Thoracic Society, Centers for Disease Control and Prevention, and Infectious Diseases Society of America jointly sponsored the development of this guideline for the treatment of drug-susceptible tuberculosis, which is also endorsed by the European Respiratory Society and the US National Tuberculosis Controllers Association. Representatives from the American Academy of Pediatrics, the Canadian Thoracic Society, the International Union Against Tuberculosis and Lung Disease, and the World Health Organization also participated in the development of the guideline. This guideline provides recommendations on the clinical and public health management of tuberculosis in children and adults in settings in which mycobacterial cultures, molecular and phenotypic drug susceptibility tests, and radiographic studies, among other diagnostic tools, are available on a routine basis. For all recommendations, literature reviews were performed, followed by discussion by an expert committee according to the Grading of Recommendations, Assessment, Development and Evaluation methodology. Given the public health implications of prompt diagnosis and effective management of tuberculosis, empiric multidrug treatment is initiated in almost all situations in which active tuberculosis is suspected. Additional characteristics such as presence of comorbidities, severity of disease, and response to treatment influence management decisions. Specific recommendations on the use of case management strategies (including directly observed therapy), regimen and dosing selection in adults and children (daily vs intermittent), treatment of tuberculosis in the presence of HIV infection (duration of tuberculosis treatment and timing of initiation of antiretroviral therapy), as well as treatment of extrapulmonary disease (central nervous system, pericardial among other sites) are provided. The development of more potent and better-tolerated drug regimens, optimization of drug exposure for the component drugs, optimal management of tuberculosis in special populations, identification of accurate biomarkers of treatment effect, and the assessment of new strategies for implementing regimens in the field remain key priority areas for research. See the full-text online version of the document for detailed discussion of the management of tuberculosis and recommendations for practice.
The Trade Union Act 2016 and the Failure of Human Rights
Authors: Ewing K.D. , Hendy QC John 
Published: August 2016

Abstract
The Trade Union Bill raised major concerns about freedom of association in particular and its compatibility with a number of treaty obligations, including notably, the European Convention on Human Rights, Article 11. Complaints were made to the International Labour Organisation, and the Parliamentary Joint Committee on Human Rights considered the Bill. This paper seeks to assess the extent to which such human rights considerations influenced the final text which became the Act. Our view is that, although the government made a number of notable concessions, these were informed more by political than by legal considerations. Despite the concessions, human rights concerns still remain. Our secondary aim in this paper is to consider some factors relevant to the possibility of a successful legal challenge based on those concerns. We think such a challenge unlikely for two reasons. Firstly, the concessions removed many of the substantive provisions most susceptible to a human rights challenge. Secondly, whilst the domestic courts have been reluctant to embrace Convention rights in trade union cases, the Strasbourg Court has recently been notably sympathetic to the British Government in Article 11 cases, carving out for this country an apparently protected position on freedom of association issues.
Pediatric Kawasaki Disease and Adult Human Immunodeficiency Virus Kawasaki-Like Syndrome Are Likely the Same Malady
Authors: Johnson Raymond M. , Bergmann Kelly R. , Manaloor John J. , Yu Xiaoqing , Slaven James E. , Kharbanda Anupam B. 
Published: August 2016

AbstractBackground.  Pediatric Kawasaki disease (KD) and human immunodeficiency virus (HIV)+ adult Kawasaki-like syndrome (KLS) are dramatic vasculitides with similar physical findings. Both syndromes include unusual arterial histopathology with immunoglobulin (Ig)A+ plasma cells, and both impressively respond to pooled Ig therapy. Their distinctive presentations, histopathology, and therapeutic response suggest a common etiology. Because blood is in immediate contact with inflamed arteries, we investigated whether KD and KLS share an inflammatory signature in serum.Methods.  A custom multiplex enzyme-linked immunosorbent assay (ELISA) defined the serum cytokine milieu in 2 adults with KLS during acute and convalescent phases, with asymptomatic HIV+ subjects not taking antiretroviral therapy serving as controls. We then prospectively collected serum and plasma samples from children hospitalized with KD, unrelated febrile illnesses, and noninfectious conditions, analyzing them with a custom multiplex ELISA based on the KLS data.Results.  Patients with KLS and KD subjects shared an inflammatory signature including acute-phase reactants reflecting tumor necrosis factor (TNF)-α biologic activity (soluble TNF receptor I/II) and endothelial/smooth muscle chemokines Ccl1 (Th2), Ccl2 (vascular inflammation), and Cxcl11 (plasma cell recruitment). Ccl1 was specifically elevated in KD versus febrile controls, suggesting a unique relationship between Ccl1 and KD/KLS pathogenesis.Conclusions.  This study defines a KD/KLS inflammatory signature mirroring a dysfunctional response likely to a common etiologic agent. The KD/KLS inflammatory signature based on elevated acute-phase reactants and specific endothelial/smooth muscle chemokines was able to identify KD subjects versus febrile controls, and it may serve as a practicable diagnostic test for KD.
Allergy prevention by breastfeeding: possible mechanisms and evidence from human cohorts
Authors: Munblit Daniel , Verhasselt Valérie 
Published: August 2016

Purpose of review
Allergy is a modern disease which does not seem to benefit from breast milk preventive effects. We propose that maternal milk composition has not adapted to the needs of allergy prevention because of the recent and rapid increase of allergy. Modulation of breast milk composition may be the best strategy to counteract allergy development. We will review recent advances in understanding of allergy physiopathology and how breast milk factors may be specifically appropriate to interfere with allergy development in early life.

Recent findings
There is strong evidence both from rodent and human studies that breast milk factors may impact on parameters which are now recognized to be essential for allergy physiopathology: infant gut barrier function, microbiota metabolites production, and oral tolerance induction. Data from human cohorts support the possibility to modify breast milk composition by selected interventions and to impact health outcomes in offspring.

Summary
Nutritional intervention in lactating mothers should endow breast milk with the capacity to combat allergy epidemics in addition to infectious disease.
Preoperative Hypoalgesia After Cold Pressor Test and Aerobic Exercise is Associated With Pain Relief 6 Months After Total Knee Replacement
Authors: Vaegter Henrik B. , Handberg Gitte , Emmeluth Claus , Graven-Nielsen Thomas 
Published: August 2016

Objectives:
Chronic pain after total knee replacement (TKR) is not uncommon. Preoperative impaired conditioning pain modulation (CPM) has been used to predict chronic postoperative pain. Interestingly, exercises reduce pain sensitivity in patients with knee osteoarthritis (KOA). This pilot study investigated the association between exercise-induced hypoalgesia (EIH) and CPM on post-TKR pain relief.

Methods:
Before and 6 months post-TKR, 14 patients with chronic KOA performed the cold pressor test on the nonaffected leg and 2 exercise conditions (bicycling and isometric knee extension), randomized and counterbalanced. Before and during the cold pressor test and after exercises test stimuli were applied to extract the pain sensitivity difference: computer-controlled cuff inflation on the affected lower leg until the participants detected the cuff pain threshold (cPPT) and subsequently the cuff pain tolerance (cPTT) and manual pressure pain thresholds (PPTs) at the legs, arm, and shoulder. Clinical pain intensity (numerical rating scale [NRS]) and psychological distress (questionnaires) were assessed.

Results:
Clinical pain intensity, psychological distress, cPPT, and PPT at the affected leg improved post-TKR compared with pre-TKR (P<0.05). Preoperatively, the CPM and bicycling EIH assessed by the increase in cPTT correlated with reduction in NRS pain scores post-TKR (P<0.05). Improved CPM and EIH responses after TKR were significantly correlated with reduction in NRS pain scores post-TKR (P<0.05).

Discussion:
In KOA patients, hypoalgesia after cold pressor stimulation and aerobic exercise assessed preoperatively by cuff algometry was associated with pain relief 6 months after TKR. EIH as a novel preoperative screening tool should be further investigated in larger studies.
Discourse Strategies and the Production of Prosody by Prelingually Deaf Adolescent Cochlear Implant Users
Authors: Holt Colleen M. , Yuen Ivan , Demuth Katherine 
Published: August 2016

Objectives:
The purpose of this study is to assess the use of discourse strategies and the production of prosody by prelingually deaf adolescent users of cochlear implants (CIs) when participating in a referential communication task. We predict that CI users will issue more directives (DIRs) and make less use of information requests (IRs) in completing the task than their normally hearing (NH) peers. We also predict that in signaling these IRs and DIRs, the CI users will produce F0 rises of lesser magnitude than the NH speakers.

Design:
Eight prelingually deaf adolescent CI users and 8 NH adolescents completed a referential communication task, where participants were required to direct their interlocutor around a map. Participants were aged from 12.0 to 14.2 years. The mean age at implantation for the CI group was 2.1 years (SD 0.9). The use of IRs, DIRs, acknowledgments, and comments was compared between the two groups. The use and magnitude of fundamental frequency (F0) rises on IRs and DIRs was also compared.

Results:
The CI users differed from the NH speakers in how they resolved communication breakdown. The CI users showed a preference for repeating DIRs, rather than seeking information as did the NH speakers. A nonparametric Mann–Whitney U test indicated that the CI users issued more DIRs (U = 8, p = 0.01), produced fewer IRs (U = 13, p = 0.05) and fewer acknowledgments (U = 5, p = 0.003) than their NH counterparts. The CI users also differed in how they used F0 rises as a prosodic cue to signal IRs and DIRs. The CI users produced larger F0 rises on DIRs than on IRs, a pattern opposite to that displayed by the NH speakers. An independent samples t-test revealed that the CI users produced smaller rises on IRs compared with those produced by the NH speakers [t(12) = −2.762, p = 0.02].

Conclusions:
The CI users differed from the NH speakers in how they resolved communication breakdown. The CI users showed a preference for repeating DIRs, rather than seeking information to understand their interlocutor’s point of view. Their use of prosody to signal discourse function also differed from their NH peers. These differences may indicate a lack of understanding of how prosody is used to signal discourse modality by the CI users. This study highlights the need for further research focused on the interaction of prosody, discourse, and language comprehension.