bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions
Authors: Israeli-Ruimy Vered , Bule Pedro , Jindou Sadanari , Dassa Bareket , Moraïs Sarah , Borovok Ilya , Barak Yoav , Slutzki Michal , Hamberg Yuval , Cardoso Vânia , Alves Victor D. , Najmudin Shabir , White Bryan A. , Flint Harry J. , Gilbert Harry J. , Lamed Raphael , Fontes Carlos M. G. A. , Bayer Edward A. 
Published: February 2017

AbstractProtein-protein interactions play a vital role in cellular processes as exemplified by assembly of the intricate multi-enzyme cellulosome complex. Cellulosomes are assembled by selective high-affinity binding of enzyme-borne dockerin modules to repeated cohesin modules of structural proteins termed scaffoldins. Recent sequencing of the fiber-degrading Ruminococcus flavefaciens FD-1 genome revealed a particularly elaborate cellulosome system. In total, 223 dockerin-bearing ORFs potentially involved in cellulosome assembly and a variety of multi-modular scaffoldins were identified, and the dockerins were classified into six major groups. Here, extensive screening employing three complementary medium- to high-throughput platforms was used to characterize the different cohesin-dockerin specificities. The platforms included (i) cellulose-coated microarray assay, (ii) enzyme-linked immunosorbent assay (ELISA) and (iii) in-vivo co-expression and screening in Escherichia coli. The data revealed a collection of unique cohesin-dockerin interactions and support the functional relevance of dockerin classification into groups. In contrast to observations reported previously, a dual-binding mode is involved in cellulosome cell-surface attachment, whereas single-binding interactions operate for cellulosome integration of enzymes. This sui generis cellulosome model enhances our understanding of the mechanisms governing the remarkable ability of R. flavefaciens to degrade carbohydrates in the bovine rumen and provides a basis for constructing efficient nano-machines applied to biological processes.
Ubiquitination mediates Kv1.3 endocytosis as a mechanism for protein kinase C-dependent modulation
Authors: Martínez-Mármol Ramón , Styrczewska Katarzyna , Pérez-Verdaguer Mireia , Vallejo-Gracia Albert , Comes Núria , Sorkin Alexander , Felipe Antonio 
Published: February 2017

AbstractThe voltage-dependent potassium channel Kv1.3 plays essential physiological functions in the immune system. Kv1.3, regulating the membrane potential, facilitates downstream Ca2+-dependent pathways and becomes concentrated in specific membrane microdomains that serve as signaling platforms. Increased and/or delocalized expression of the channel is observed at the onset of several autoimmune diseases. In this work, we show that adenosine (ADO), which is a potent endogenous modulator, stimulates PKC, thereby causing immunosuppression. PKC activation triggers down-regulation of Kv1.3 by inducing a clathrin-mediated endocytic event that targets the channel to lysosomal-degradative compartments. Therefore, the abundance of Kv1.3 at the cell surface decreases, which is clearly compatible with an effective anti-inflammatory response. This mechanism requires ubiquitination of Kv1.3, catalyzed by the E3 ubiquitin-ligase Nedd4-2. Postsynaptic density protein 95 (PSD-95), a member of the MAGUK family, recruits Kv1.3 into lipid-raft microdomains and protects the channel against ubiquitination and endocytosis. Therefore, the Kv1.3/PSD-95 association fine-tunes the anti-inflammatory response in leukocytes. Because Kv1.3 is a promising multi-therapeutic target against human pathologies, our results have physiological relevance. In addition, this work elucidates the ADO-dependent PKC-mediated molecular mechanism that triggers immunomodulation by targeting Kv1.3 in leukocytes.
Dual Immunomagnetic Nanobeads-Based Lateral Flow Test Strip for Simultaneous Quantitative Detection of Carcinoembryonic Antigen and Neuron Specific Enolase
Authors: Lu Wenting , Wang Kan , Xiao Kun , Qin Weijian , Hou Yafei , Xu Hao , Yan Xinyu , Chen Yanrong , Cui Daxiang , He Jinghua 
Published: February 2017

AbstractA novel immunomagnetic nanobeads -based lateral flow test strip was developed for the simultaneous quantitative detection of neuron specific enolase (NSE) and carcinoembryonic antigen (CEA), which are sensitive and specific in the clinical diagnosis of small cell lung cancer. Using this nanoscale method, high saturation magnetization, carboxyl-modified magnetic nanobeads were successfully synthesized. To obtain the immunomagnetic probes, a covalent bioconjugation of the magnetic nanobeads with the antibody of NSE and CEA was carried out. The detection area contained test line 1 and test line 2 which captured the immune complexes sensitively and formed sandwich complexes. In this assay, cross-reactivity results were negative and both NSE and CEA were detected simultaneously with no obvious influence on each other. The magnetic signal intensity of the nitrocellulose membrane was measured by a magnetic assay reader. For quantitative analysis, the calculated limit of detection was 0.094 ng/mL for NSE and 0.045 ng/mL for CEA. One hundred thirty clinical samples were used to validate the test strip which exhibited high sensitivity and specificity. This dual lateral flow test strip not only provided an easy, rapid, simultaneous quantitative detection strategy for NSE and CEA, but may also be valuable in automated and portable diagnostic applications.
Superresolution imaging of nanoscale chromosome contacts
Authors: Wang Yejun , Ratna Prasuna , Shivashankar G. V. 
Published: February 2017

AbstractCo-expression of a specific group of genes requires physical associations among these genes, which form functional chromosomal contacts. While DNA fluorescence in situ hybridization (FISH) pinpoints the localization of genes within the 3D nuclear architecture, direct evidence of physical chromosomal contacts is still lacking. Here, we report a method for the direct visualization of transcription-dependent chromosomal contacts formed in two distinct mechanical states of cells. We prepared open chromatin spreads from isolated nuclei, ensuring 2D rendering of chromosome organization. Superresolution imaging of these chromatin spreads resolved the nanoscale organization of genome contacts. We optimized our imaging method using chromatin spreads from serum+/− cells. We then showed direct visualization of functional gene clusters targeted by YAP (Yes-associated protein) and SRF (Serum response factor) transcription factors. In addition, we showed the association of NF-κB bound gene clusters induced by TNF-α addition. Furthermore, EpiTect ChIP qPCR results showed that these nanoscale clusters were enriched with corresponding transcription factors. Taken together, our method provides a robust platform to directly visualize and study specific genome-wide chromosomal contacts.
Visualizing dynamics of angiogenic sprouting from a three-dimensional microvasculature model using stage-top optical coherence tomography
Authors: Takahashi Haruko , Kato Keisuke , Ueyama Kenji , Kobayashi Masayoshi , Baik Gunwoong , Yukawa Yasuhiro , Suehiro Jun-ichi , Matsunaga Yukiko T. 
Published: February 2017

AbstractThree-dimensional (3D) in vitro microvasculature in a polydimethylsiloxane-based microdevice was developed as a physiologically relevant model of angiogenesis. The angiogenic process is monitored using stage-top optical coherence tomography (OCT). OCT allows non-invasive monitoring of the 3D structures of the prepared host microvasculature and sprouted neovasculature without fluorescence staining. OCT monitoring takes only a few minutes to scan through the several-millimetre scale range, which provides the advantage of rapid observation of living samples. The obtained OCT cross-sectional images capture 3D features of the angiogenic sprouting process and provide information on the dynamics of luminal formation. The stage-top system used in this study enables the observer to visualize the in vitro dynamics of 3D cultured cells simply and conveniently, offering an alternative monitoring method for studies on angiogenesis and providing quantitative information about vascular morphological changes.
Dielectric properties of almond kernels associated with radio frequency and microwave pasteurization
Authors: Li Rui , Zhang Shuang , Kou Xiaoxi , Ling Bo , Wang Shaojin 
Published: February 2017

AbstractTo develop advanced pasteurization treatments based on radio frequency (RF) or microwave (MW) energy, dielectric properties of almond kernels were measured by using an open-ended coaxial-line probe and impedance analyzer at frequencies between 10 and 3000 MHz, moisture contents between 4.2% to 19.6% w.b. and temperatures between 20 and 90 °C. The results showed that both dielectric constant and loss factor of the almond kernels decreased sharply with increasing frequency over the RF range (10–300 MHz), but gradually over the measured MW range (300–3000 MHz). Both dielectric constant and loss factor of almond kernels increased with increasing temperature and moisture content, and largely enhanced at higher temperature and moisture levels. Quadratic polynomial equations were developed to best fit the relationship between dielectric constant or loss factor at 27, 40, 915 or 2450 MHz and sample temperature/moisture content with R2 greater than 0.967. Penetration depth of electromagnetic wave into samples decreased with increasing frequency (27–2450 MHz), moisture content (4.2–19.6% w.b.) and temperature (20–90 °C). The temperature profiles of RF heated almond kernels under three moisture levels were made using experiment and computer simulation based on measured dielectric properties. Based on the result of this study, RF treatment has potential to be practically used for pasteurization of almond kernels with acceptable heating uniformity.
A new approach to quantification of mAb aggregates using peptide affinity probes
Authors: Cheung Crystal S. F. , Anderson Kyle W. , Patel Pooja M. , Cade Keale L. , Phinney Karen W. , Turko Illarion V. 
Published: February 2017

AbstractUsing mAbs as therapeutic molecules is complicated by the propensity of mAbs to aggregate at elevated concentrations, which can lead to a variety of adverse events in treatment. Here, we describe a proof-of-concept for new methodology to detect and quantify mAb aggregation. Assay development included using an aggregated mAb as bait for screening of phage display peptide library and identifying those peptides with random sequence which can recognize mAb aggregates. Once identified, the selected peptides can be used for developing quantitative methods to assess mAb aggregation. Results indicate that a peptide binding method coupled with mass spectrometric detection of bound peptide can quantify mAb aggregation and potentially be useful for monitoring aggregation propensity of therapeutic protein candidates.
Reduced Necrosis and Content of Apoptotic M1 Macrophages in Advanced Atherosclerotic Plaques of Mice With Macrophage-Specific Loss of Trpc3
Authors: Solanki Sumeet , Dube Prabhatchandra R. , Birnbaumer Lutz , Vazquez Guillermo 
Published: February 2017

AbstractIn previous work we reported that ApoeKO mice transplanted with bone marrow cells deficient in the Transient Receptor Potential Canonical 3 (TRPC3) channel have reduced necrosis and number of apoptotic macrophages in advanced atherosclerotic plaques. Also, in vitro studies with polarized macrophages derived from mice with macrophage-specific loss of TRPC3 showed that M1, but not M2 macrophages, deficient in Trpc3 are less susceptible to ER stress-induced apoptosis than Trpc3 expressing cells. The questions remained (a) whether the plaque phenotype in transplanted mice resulted from a genuine effect of Trpc3 on macrophages, and (b) whether the reduced necrosis and macrophage apoptosis in plaques of these mice was a manifestation of the selective effect of TRPC3 on apoptosis of M1 macrophages previously observed in vitro. Here, we addressed these questions using Ldlr knockout (Ldlr−/−) mice with macrophage-specific loss of Trpc3 (MacTrpc3−/−/Ldlr−/− → Ldlr−/−). Compared to controls, we observed decreased plaque necrosis and number of apoptotic macrophages in MacTrpc3−/−/Ldlr−/− → Ldlr−/− mice. Immunohistochemical analysis revealed a reduction in apoptotic M1, but not apoptotic M2 macrophages. These findings confirm an effect of TRPC3 on plaque necrosis and support the notion that this is likely a reflection of the reduced susceptibility of Trpc3-deficient M1 macrophages to apoptosis.
Awake Craniotomy for Left Insular Low-Grade Glioma Removal on a Patient with Learning Disabilities
Authors: Vranic Andrej , Koritnik Blaz , Markovic-Bozic Jasmina 
Published: February 2017

Introduction Low-grade gliomas (LGG) are slow-growing primary brain tumors in adults, with high tropism for eloquent areas. Standard approach in treatment of LGG is awake craniotomy with intraoperative cortical mapping — a method which is usually used on adult and fully cooperative patients.
Case Report We present the case of a patient with learning disabilities (PLD) who was operated for left insular LGG awake craniotomy, and intraoperative cortical mapping were performed and the tumor was gross totally removed.
Conclusion Awake surgery for left insular LGG removal is challenging; however, it can be performed safely and successfully on PLD.
Concomitant Sternal Fracture in Flail Chest: An Analysis of 21,741 Polytrauma Patients from the TraumaRegister DGU®
Authors: Krinner Sebastian , Langenbach Andreas , Oppel Pascal , Lefering Rolf , Taylor Dominic , Hennig Friedrich , Mauerer Andreas , Schulz-Drost Stefan ,   the TraumaRegister DGU
Published: February 2017

Background Isolated sternal fractures (SFs) rarely show complications, but their influence in a thorax trauma of the seriously injured still remains unclear.
Methods A retrospective analysis of the TraumaRegister DGU® was performed involving the years 2009 to 2013 (Injury Severity Score [ISS] ≥ 16, primary admission to a trauma center). Cohort formation: Unilateral and bilateral flail chest (FC) injuries with and without a concomitant SF, respectively.
Results In total, 21,741 patients (25% female) met the inclusion criteria, with 3,492 (16.1%) showing SF. Unilateral FC patients were on average 53.6 ± 18.4 years old, and bilateral FC patients were on average 55.2 ± 17.7 years old. The ISS in unilateral FC and bilateral FC amounted to 31.2 ± 13.0 and 43.4 ± 13.1 points, respectively. FC with an SF occurred more frequently as an injury to car occupants and less frequently as an injury to motorcyclists or in injuries due to falls.
Conclusion Patients with an SF additional to an FC had longer hospital and intensive care unit stays and were longer artificially respirated than those patients without an SF. SF indicates possible cardiac and thoracic spine injuries.
Law, finance, and the international mobility of corporate governance
Authors: Cumming Douglas , Filatotchev Igor , Knill April , Reeb David Mitchell , Senbet Lemma 
Published: February 2017

AbstractWe introduce the topic of this Special Issue on the “Role of Financial and Legal Institutions in International Governance”, with a particular emphasis on a notion of “international mobility of corporate governance”. Our discussion places the Special Issue at the intersection of law, finance, and international business, with a focus on the contexts of foreign investors and directors. Country-level legal and regulatory institutions facilitate foreign ownership, foreign directors, raising external financial capital, and international M&A activity. The interplay between the impact of foreign ownership and foreign directors on firm governance and performance depends on international differences in formal/regulatory institutions. In addition to legal conditions, informal institutions such as political connections also shape the economic value of foreign ownership and foreign directors. We highlight key papers in the literature, provide an overview of the new papers in this Special Issue, and offer suggestions for future research.
Stylistic fronting and related constructions in the Insular Scandinavian Languages
Authors: Angantýsson Ásgrímur 
Published: February 2017

Abstract
This chapter reports on the similarities and differences between Stylistic Fronting (SF) and related constructions in Icelandic and Faroese. Contrary to the claim that “any category can become an expletive” (Holmberg 2000), it is argued that stylistically fronted elements and overt expletives are not equivalent. In both languages, expletive insertion is preferred over SF in complement clauses, but in Faroese, unlike in Icelandic, expletive insertion is preferred over SF in adverbial clauses and relative clauses as well. The overall data presented and discussed here suggest that the possibility of SF is partly conditioned by the clause type and the nature of the element fronted by SF and partly by lexical/idiomatic factors.
Science transformed? A comparative analysis of ‘societal relevance’ rhetoric and practices in 14 Canadian Networks of Centres of Excellence
Authors: Coutinho Aline , Young Nathan 
Published: February 2017

Abstract
One of the most hotly debated ideas in science studies is the claim that contemporary science is in the midst of a transformation. While ‘transformationalist’ arguments and concepts vary, their core principle is that the norms, values and practices that have enforced the separation of science from society are being challenged by new expectations that scientists pursue closer connections with industry, government and/or civil society, and address research questions of immediate value to non-academic partners. While many major funding agencies have embraced this idea and now pressure scientists to enhance the ‘societal relevance’ of their work, the impact of these changes on scientific practices is still unclear. This paper reports findings from a comparative meso-level analysis of 14 large Canadian research networks funded by an agency with an explicit transformationalist mandate – the Networks of Centres of Excellence (NCE) programme. Documents and web communications from these 14 NCEs, as well as from the central programme administration office, are analysed and compared to key transformationalist concepts, such as Mode 2 science, post-normal science, the triple helix model, academic capitalism and strategic science. We find that transformationalist ideas have a strong rhetorical presence across the 14 NCE projects and the central office, but that a great deal of inconsistency and confusion exists at the level of implementation and assessment of outcomes. Easily quantifiable outputs, such as the commercialization of research findings, are favoured over softer qualitative outcomes, such as public engagement and knowledge sharing. We conclude by arguing that the NCE programme is having an observable impact on the rhetoric of science, but any resulting transformations in practice are incremental rather than radical.
Ferritin 2 domain-containing protein found in lacquer tree (Toxicodendron vernicifluum) sap has negative effects on laccase and peroxidase reactions
Authors: Kitajima Sakihito , Imamura Taiki , Iibushi Junpei , Ikenaga Makoto , Tachibana Yoichi , Andoh Nobuyuki , Oyabu Hiroshi , Hirooka Kiyoo , Shiina Takashi , Ishizaki Yoko 
Published: February 2017

Abstract
Lacquer tree sap, a raw material of traditional paints in East Asia, is hardened through laccase-catalyzed oxidation and the following polymerization of phenolic compound urushiol. In the sap’s water-insoluble fraction, we found two plantacyanins and a ferritin 2 domain-containing protein (TvFe2D, a homolog of Arabidopsis AT1G47980 and AT3G62730). The recombinant TvFe2D protein suppressed the accumulation of laccase-catalyzed oxidation products of a model substrate syringaldazine without decreasing oxygen consumption, the second substrate of laccase. The suppression was also observed when another substrate guaiacol or another oxidizing enzyme peroxidase was used. The functional domain of the suppression was the C-terminal half, downstream of the ferritin 2 domain. The results suggest that this protein may be involved in regulating the sap polymerization/hardening. We also discuss the possibility that homologous proteins of TvFe2D in other plants might be involved in the laccase- or peroxidase-mediated polymerization of phenolic compounds, such as lignin and flavonoids.
DiagnoProt: a tool for discovery of new molecules by mass spectrometry
Authors: Silva André R.F , Lima Diogo B , Leyva Alejandro , Duran Rosario , Batthyany Carlos , Aquino Priscila F , Leal Juliana C , Rodriguez Jimmy E , Domont Gilberto B , Santos Marlon D.M , Chamot-Rooke Julia , Barbosa Valmir C , Carvalho Paulo C 
Published: February 2017

Abstract

Motivation
Around 75% of all mass spectra remain unidentified by widely adopted proteomic strategies. We present DiagnoProt, an integrated computational environment that can efficiently cluster millions of spectra and use machine learning to shortlist high-quality unidentified mass spectra that are discriminative of different biological conditions.

Results
We exemplify the use of DiagnoProt by shortlisting 4366 high-quality unidentified tandem mass spectra that are discriminative of different types of the Aspergillus fungus.

Availability and Implementation
DiagnoProt, a demonstration video and a user tutorial are available at http://patternlabforproteomics.org/diagnoprot.

Supplementary information
Supplementary data are available at Bioinformatics online.
Standard Setting for Clinical Performance of Basic Perioperative Transesophageal Echocardiography
Authors: Bick Julian S. , Wanderer Jonathan P. , Myler Conrad S. , Shaw Andrew D. , McEvoy Matthew D. 
Published: February 2017

Abstract

Background
Credible methods for assessing competency in basic perioperative transesophageal echocardiography examinations have not been reported. The authors’ objective was to demonstrate the collection of real-world basic perioperative transesophageal examination performance data and establish passing scores for each component of the basic perioperative transesophageal examination, as well as a global passing score for clinical performance of the basic perioperative transesophageal examination using the Angoff method.

Methods
National Board of Echocardiography (Raleigh, North Carolina) advanced perioperative transesophageal echocardiography–certified anesthesiologists (n = 7) served as subject matter experts for two Angoff standard-setting sessions. The first session was held before data analysis, and the second session for calibration of passing scores was held 9 months later. The performance of 12 anesthesiology residents was assessed via the new passing score grading system.

Results
The first standard-setting procedure resulted in a global passing score of 63 ± 13% on a basic perioperative transesophageal examination. The global passing score from the second standard-setting session was 73 ± 9%. Three hundred seventy-one basic perioperative transesophageal examinations from 12 anesthesiology residents were included in the analysis and used to guide the second standard-setting session. All residents scored higher than the global passing score from both standard-setting sessions.

Conclusions
To the authors’ knowledge, this is the first demonstration that the collection of real-world anesthesia resident basic perioperative transesophageal examination clinical performance data is possible and that automated grading for competency assessment is feasible. The authors’ findings demonstrate at least minimal basic perioperative transesophageal examination clinical competency of the 12 residents.