bluuebunny/crossref_metadata_2025_split huggingface dataset:
Entropy production and non-Markovian dynamical maps
Authors: Marcantoni S. , Alipour S. , Benatti F. , Floreanini R. , Rezakhani A. T. 
Published: September 2017

AbstractIn the weak-coupling limit approach to open quantum systems, the presence of the bath is eliminated and accounted for by a master equation that introduces dissipative contributions to the system reduced dynamics: within this framework, there are no bath entropy contributions to the entropy balance. We show that, as a consequence, the entropy production fails to be positive for a class of physically legitimate, that is completely positive and trace preserving, non-Markovian dynamical maps. Moreover, in absence of the semigroup property, if the reduced dynamics has a thermal asymptotic state, this need not be stationary. Then even the integrated entropy production becomes negative. These observations imply that, when the conditions leading to reduced dynamics of semigroup type are relaxed, a consistent formulation of the second law of thermodynamics requires that the environment contribution to the entropy balance be explicitly taken into account.
Preferential sensing and response to microenvironment stiffness of human dermal fibroblast cultured on protein micropatterns fabricated by 3D multiphoton biofabrication
Authors: Tong Ming Hui , Huang Nan , Ngan Alfonso Hing Wan , Du Yanan , Chan Barbara Pui 
Published: September 2017

AbstractWhile cells are known to sense and respond to their niche including the matrix and the mechanical microenvironment, whether they preferentially sense and react to the stiffness of their microenvironment regardless of its intrinsic material properties is unknown. In this work, protein micropillar arrays with independently controllable stiffness via alterations in pillar height and elastic modulus via laser power used during photochemical cross-linking, were fabricated using a recently developed multiphoton-based 3D protein micro-patterning technology. Human dermal fibroblasts were cultured on these micropillar arrays and the specific interactions between cells and the protein micropatterns particularly on the formation and maturation of the cell-matrix adhesions, were investigated via immunofluorescence staining of the major molecular markers of the adhesions and the measurement of their cluster size, respectively. Our results showed that the cluster size of focal adhesions increased as the stiffness of the micropillar arrays increased, but it was insensitive to the elastic modulus of the protein micropillars that is one of the intrinsic material properties. This finding provides evidence to the notion that cells preferentially sense and react to the stiffness, but not the elastic modulus of their microenvironment.
Sequence composition predicts immunoglobulin superfamily members that could share the intrinsically disordered properties of antibody CH1 domains
Authors: Hebditch Max , Curtis Robin , Warwicker Jim 
Published: September 2017

AbstractAntibodies are central to the growing sector of protein therapeutics, and increasingly they are being manipulated as fragments and combinations. An improved understanding of the properties of antibody domains in isolation would aid in their engineering. We have conducted an analysis of sequence and domain interactions for IgG antibodies and Fab fragments in the structural database. Of sequence-related properties studied, relative lysine to arginine content was found to be higher in CH1 and CL than in variable domains. As earlier work shows that lysine is favoured over arginine in more soluble proteins, this suggests that individual domains may not be optimised for greater solubility, giving scope for fragment engineering. Across other sequence-based features, CH1 is anomalous. A sequence-based scheme predicts CH1 to be folded, although it is known that CH1 folding is linked to IgG assembly and secretion. Calculations indicate that charge interactions in CH1 domains contribute less to folded state stability than in other Fab domains. Expanding to the immunoglobulin superfamily reveals that a subset of non-antibody domains shares sequence composition properties with CH1, leading us to suggest that some of these may also couple folding, assembly and secretion.
Systemic corticosteroids improve tendon healing when given after the early inflammatory phase
Authors: Blomgran Parmis , Hammerman Malin , Aspenberg Per 
Published: September 2017

AbstractInflammation initiates tendon healing and then normally resolves more or less completely. Unresolved inflammation might disturb the remodeling process. We hypothesized that suppression of inflammation during the early remodeling phase by systemic dexamethasone treatment can improve healing. 36 rats underwent Achilles tendon transection and were randomized to dexamethasone or saline on days 0–4 after surgery (early inflammatory phase), and euthanasia day 7. Another 54 rats received injections days 5–9 (early remodeling phase) and were euthanized day 12 for mechanical, histological and flow cytometric evaluation. Dexamethasone treatment days 0–4 reduced the cross-sectional area, peak force and stiffness by day 7 to less than half (p < 0.001 for all), while material properties (peak stress and elastic modulus) were not significantly affected. In contrast, dexamethasone treatment days 5–9 increased peak force by 39% (p = 0.002) and stiffness by 58% (p < 0.001). The cross-sectional area was reduced by 42% (p < 0.001). Peak stress and elastic modulus were more than doubled (p < 0.001 for both). Semi-quantitative histology at day 12 showed that late dexamethasone treatment improved collagen alignment, and flow cytometry revealed reduced numbers of CD8a+ cytotoxic T cells in the tendon callus. These results suggest that downregulation of lingering inflammation during the early remodeling phase can improve healing.
Association between exposure to air pollution during pregnancy and false positives in fetal heart rate monitoring
Authors: Morokuma Seiichi , Michikawa Takehiro , Yamazaki Shin , Nitta Hiroshi , Kato Kiyoko 
Published: September 2017

AbstractFetal heart rate (FHR) monitoring is essential for fetal management during pregnancy and delivery but results in many false-positive diagnoses. Air pollution affects the uterine environment; thus, air pollution may change FHR reactivity. This study assessed the association between exposure to air pollution during pregnancy and FHR monitoring abnormalities using 2005–2010 data from the Japan Perinatal Registry Network database. Participants were 23,782 singleton pregnant women with FHR monitoring, without acidemia or fetal asphyxia. We assessed exposure to air pollutants, including particulate matter (PM), ozone, nitrogen dioxide (NO2), and sulfur dioxide (SO2). In a multi-trimester model, first-trimester PM exposure was associated with false positives in FHR monitoring (odds ratio [OR] per interquartile range (10.7 μg/m3) increase = 1.20; 95% CI: 1.05–1.37), but not second-trimester exposure (OR = 1.05; 95% CI: 0.91–1.21) and third-trimester exposure (OR = 1.06; 95% CI: 0.96-1.17). The association with first-trimester PM exposure persisted after adjustment for exposure to ozone, NO2, and SO2; however, ozone, NO2, and SO2 exposure was not associated with false positives in FHR monitoring. First-trimester PM exposure may alter fetal cardiac response and lead to false positives in FHR monitoring.
Enhanced HIF2α expression during human trophoblast differentiation into syncytiotrophoblast suppresses transcription of placental growth factor
Authors: Fujii Tatsuya , Nagamatsu Takeshi , Morita Kazuki , Schust Danny J. , Iriyama Takayuki , Komatsu Atsushi , Osuga Yutaka , Fujii Tomoyuki 
Published: September 2017

AbstractPlacental growth factor (PlGF), abundantly produced from trophoblasts is involved in placental angiogenesis. The regulatory mechanism of its expression is poorly understood. Hypoxia inducible factors (HIFs) are centrally involved in the modulation of cellular function in response to low oxygen conditions. This study aimed to clarify HIF1α and HIF2α expression patterns during cytotrophoblast differentiation into syncytiotrophoblast and the impact of any changes on PlGF expression. HIF proteins were induced remarkably under low oxygen condition (2%). HIF1α expression decreased and HIF2α expression increased when syncytialization of cultured cytotrophoblasts is progressed. Those expression changes of HIF proteins in the process of in-vitro syncytialization was congruent with the immunohistochemical findings in preeclamptic placenta as well as uncomplicated placenta. Low oxygen condition was also associated with reduced PlGF production in syncytializing primary cells and BeWo choriocarcinoma cells. Small interfering RNA-mediated HIF2α knockdown in BeWo cells abrogated hypoxia-associated decreases in PlGF secretion; HIF1α silencing had no significant effect on PlGF secretion. In summary, HIF2α, rather than HIF1α, is most affected by reduced oxygen level during syncytialization and increases in HIF2α trigger a reduction of PlGF production. Our findings suggest new and important connections between HIF proteins and PlGF pathways in the regulation of placental angiogenesis.
Global network random walk for predicting potential human lncRNA-disease associations
Authors: Gu Changlong , Liao Bo , Li Xiaoying , Cai Lijun , Li Zejun , Li Keqin , Yang Jialiang 
Published: September 2017

AbstractThere is more and more evidence that the mutation and dysregulation of long non-coding RNA (lncRNA) are associated with numerous diseases, including cancers. However, experimental methods to identify associations between lncRNAs and diseases are expensive and time-consuming. Effective computational approaches to identify disease-related lncRNAs are in high demand; and would benefit the detection of lncRNA biomarkers for disease diagnosis, treatment, and prevention. In light of some limitations of existing computational methods, we developed a global network random walk model for predicting lncRNA-disease associations (GrwLDA) to reveal the potential associations between lncRNAs and diseases. GrwLDA is a universal network-based method and does not require negative samples. This method can be applied to a disease with no known associated lncRNA (isolated disease) and to lncRNA with no known associated disease (novel lncRNA). The leave-one-out cross validation (LOOCV) method was implemented to evaluate the predicted performance of GrwLDA. As a result, GrwLDA obtained reliable AUCs of 0.9449, 0.8562, and 0.8374 for overall, novel lncRNA and isolated disease prediction, respectively, significantly outperforming previous methods. Case studies of colon, gastric, and kidney cancers were also implemented, and the top 5 disease-lncRNA associations were reported for each disease. Interestingly, 13 (out of the 15) associations were confirmed by literature mining.
Identification of 7-(4′-Cyanophenyl)indoline-1-benzenesulfonamide as a mitotic inhibitor to induce apoptotic cell death and inhibit autophagy in human colorectal cancer cells
Authors: Wu Tung-Yun , Cho Ting-Yu , Lu Chung-Kuang , Liou Jing-Ping , Chen Mei-Chuan 
Published: September 2017

AbstractTargeting cellular mitosis in tumor cells is an attractive cancer treatment strategy. Here, we report that B220, a synthetic benzenesulfonamide compound, could represent a new mitotic inhibitor for the treatment of colorectal cancer. We examined the action mechanism of B220 in the colorectal carcinoma HCT116 cell line, and found that treatment of cells with B220 caused cells to accumulate in G2/M phase, with a concomitant induction of the mitotic phase markers, MPM2 and cyclin B1. After 48 h of B220 treatment, cells underwent apoptotic cell death via caspase-3 activation and poly(ADP ribose) polymerase (PARP) cleavage. In addition, B220 inhibits autophagy by blocking conversion of microtubule-associated protein 1 light chain 3 (LC3-I) to LC3-II and inhibiting autophagic flux. Notably, blockade of autophagy by pharmacological inhibition or using an Atg5-targeting shRNA reduced B220-induced cytotoxicity. Conversely, the autophagy inducer NVP-BEZ235 shows a synergistic interaction with B220 in HCT116 cells, indicating autophagy was required for the observed cell death. In summary, these results indicate B220 combined with the induction of autophagy using the dual PI3K/mTOR inhibitor, NVP-BEZ235, might be an attractive strategy for cancer therapy, and provides a framework for further development of B220 as a new therapeutic agent for colon cancer treatment.
Multi‐objective generation dispatch considering the trade‐off between economy and security
Authors: Qiu Jing , Zhao Junhua , Wang Dongxiao 
Published: September 2017

This study presents a multi‐objective generation dispatch model based on security‐constrained optimal power flow, in order to handle the contradictory economic and security objectives. In addition to the deterministic N −1 security criterion, a risk index is proposed to quantify the system security degree on a probabilistic basis. The risk index is defined as the summation of the products of the contingency probability and the associated severity function. Moreover, the cost of interruptible load is added into the generation cost, formulating the economic objective. In the meantime, wind power outputs and load variations are considered as uncertainties in the dispatch process. Furthermore, a multi‐objective evolutionary algorithm is employed and developed to provide a set of trade‐off solutions. The proposed approach is verified by the 4‐bus and IEEE 24‐bus systems. Numerical results show that the proposed approach can effectively investigate the impacts of demand response on system economy and security. The obtained Pareto optimal solutions are less likely to incur insecurity risk and are robust to the studied stochastic variations.
TANAMI: Tracking Active Galactic Nuclei with Austral Milliarcsecond Interferometry
Authors: Müller C. , Kadler M. , Ojha R. , Schulz R. , Trüstedt J. , Edwards P. G. , Ros E. , Carpenter B. , Angioni R. , Blanchard J. , Böck M. , Burd P. R. , Dörr M. , Dutka M. S. , Eberl T. , Gulyaev S. , Hase H. , Horiuchi S. , Katz U. , Krauß F. , Lovell J. E. J. , Natusch T. , Nesci R. , Phillips C. , Plötz C. , Pursimo T. , Quick J. F. H. , Stevens J. , Thompson D. J. , Tingay S. J. , Tzioumis A. K. , Weston S. , Wilms J. , Zensus J. A. 
Published: September 2017

Context. TANAMI is a multiwavelength program monitoring active galactic nuclei (AGN) south of − 30° declination including high-resolution very long baseline interferometry (VLBI) imaging, radio, optical/UV, X-ray, and γ-ray studies. We have previously published first-epoch8.4 GHz VLBI images of the parsec-scale structure of the initial sample. In this paper, we present images of 39 additional sources. The full sample comprises most of the radio- and γ-ray brightest AGN in the southern quarter of the sky, overlapping with the region from which high-energy (> 100 TeV) neutrino events have been found.
Aims. We characterize the parsec-scale radio properties of the jets and compare them with the quasi-simultaneous Fermi/LAT γ-ray data. Furthermore, we study the jet properties of sources which are in positional coincidence with high-energy neutrino events compared to the full sample. We test the positional agreement of high-energy neutrino events with various AGN samples.
Methods. TANAMI VLBI observations at 8.4 GHz are made with southern hemisphere radio telescopes located in Australia, Antarctica, Chile, New Zealand, and South Africa.
Results. Our observations yield the first images of many jets below − 30° declination at milliarcsecond resolution. We find that γ-ray loud TANAMI sources tend to be more compact on parsec-scales and have higher core brightness temperatures than γ-ray faint jets, indicating higher Doppler factors. No significant structural difference is found between sources in positional coincidence with high-energy neutrino events and other TANAMI jets. The 22 γ-ray brightest AGN in the TANAMI sky show only a weak positional agreement with high-energy neutrinos demonstrating that the > 100 TeV IceCube signal is not simply dominated by a small number of the γ-ray brightest blazars. Instead, a larger number of sources have to contribute to the signal with each individual source having only a small Poisson probability for producing an event in multi-year integrations of current neutrino detectors.
A Multipronged Intervention for Treatment of Psychotic Symptoms from Post-football Traumatic Brain Injury in an Adolescent Male: A Case Report
Authors: Ashish Dev , Stickel Ariana , Kaszniak Alfred , Shisslak Catherine 
Published: September 2017

Abstract
Introduction Traumatic brain injury (TBI) is common in adolescents. TBI can result in impaired cognitive functioning and mood disturbance. In some cases, TBI results in psychotic symptoms. There is little documentation for treatment of psychotic symptoms resulting from TBI.
Case presentation The present case study reviews an adolescent male who was seen in an outpatient behavioral health clinic, following a football-related TBI. The TBI resulted in postconcussive syndrome including psychotic symptoms (i.e., visual and auditory hallucinations) and increased anxiety.
Management and Outcome The adolescent underwent 12 individual sessions of Acceptance and Commitment Therapy (ACT) and 7 sessions of family therapy for his anxiety and psychotic symptoms. He also underwent Vestibulo-Ocular Therapy. At the end of treatment, the patient's anxiety symptoms and those related to post-concussive syndrome were in remission with no hallucinations experienced for >6 months.
Discussion The results provide encouragement for systematic randomized controlled trials of individual and family behavioral interventions as part of an integrated treatment approach for mild TBI.
Venous and Arterial Thromboses: Two Sides of the Same Coin?
Authors: Lippi Giuseppe , Favaloro Emmanuel 
Published: September 2017

AbstractArterial and venous thromboses are sustained by development of intraluminal thrombi, respectively, within the venous and arterial systems. The composition and structure of arterial and venous thrombi have been historically considered as being very different. Arterial thrombi (conventionally defined as “white”) have been traditionally proposed to be composed mainly of fibrin and platelet aggregates, whilst venous thrombi (conventionally defined as “red”) have been proposed as mostly being enriched in fibrin and erythrocytes. This archaic dichotomy seems ever more questionable, since it barely reflects the pathophysiology of thrombus formation in vivo. Both types of thrombi are actually composed of a complex fibrin network but, importantly, also contain essentially the same blood-borne cells (i.e., red blood cells, leukocytes, and platelets), and it is only the relative content of these individual elements that differ between venous and arterial clots or, otherwise, between thrombi generated under different conditions of blood flow and shear stress. Convincing evidence now suggests that either white or red intracoronary thrombi may be present in patients with myocardial infarction and, even more importantly, red thrombi may be more prone to distal embolization during percutaneous coronary intervention than those with lower content of erythrocytes. Conversely, it is now accepted that components traditionally considered to be involved “only” in arterial thrombosis are also represented in venous thrombosis. Thus, platelets comprise important components of venous clots, although they may be present in lower amounts here than in arterial thrombi, and von Willebrand factor is also represented in both arterial and venous thrombi. Of importance, such evidence thus supports the concept that adjunctive treatment normally associated to prevention of arterial thrombosis (e.g., aspirin) may have a role also in prevention and treatment of venous thrombosis.
Inhibition of EBV-mediated membrane fusion by anti-gHgL antibodies
Authors: Sathiyamoorthy Karthik , Jiang Jiansen , Möhl Britta S. , Chen Jia , Zhou Z. Hong , Longnecker Richard , Jardetzky Theodore S. 
Published: September 2017

Significance
Herpesviruses infect a large percentage of the human population and are responsible for a significant human health disease burden. EBV, like other herpesviruses, expresses a set of glycoproteins—gH, gL, and gB—responsible for virus entry into cells, which are targets of protective antibody responses and potential candidates for vaccine development. Here we study the interactions and mechanisms of two anti-EBV antibodies that recognize the gHgL complex, providing a foundation for understanding herpesvirus neutralization.
Graphs in kinematics—a need for adherence to principles of algebraic functions
Authors: Sokolowski Andrzej 
Published: September 2017

Abstract
Graphs in physics are central to the analysis of phenomena and to learning about a system’s behavior. The ways students handle graphs are frequently researched. Students’ misconceptions are highlighted, and methods of improvement suggested. While kinematics graphs are to represent a real motion, they are also algebraic entities that must satisfy conditions for being algebraic functions. To be algebraic functions, they must pass certain tests before they can be used to infer more about motion. A preliminary survey of some physics resources has revealed that little attention is paid to verifying if the position, velocity and acceleration versus time graphs, that are to depict real motion, satisfy the most critical condition for being an algebraic function; the vertical line test. The lack of attention to this adherence shows as vertical segments in piecewise graphs. Such graphs generate unrealistic interpretations and may confuse students. A group of 25 college physics students was provided with such a graph and asked to analyse its adherence to reality. The majority of the students (N  =  16, 64%) questioned the graph’s validity. It is inferred that such graphs might not only jeopardize the function principles studied in mathematics but also undermine the purpose of studying these principles. The aim of this study was to bring this idea forth and suggest a better alignment of physics and mathematics methods.
A collaborative filtering-based approach to biomedical knowledge discovery
Authors: Lever Jake , Gakkhar Sitanshu , Gottlieb Michael , Rashnavadi Tahereh , Lin Santina , Siu Celia , Smith Maia , Jones Martin R , Krzywinski Martin , Jones Steven J M 
Published: September 2017

Abstract

Motivation
The increase in publication rates makes it challenging for an individual researcher to stay abreast of all relevant research in order to find novel research hypotheses. Literature-based discovery methods make use of knowledge graphs built using text mining and can infer future associations between biomedical concepts that will likely occur in new publications. These predictions are a valuable resource for researchers to explore a research topic. Current methods for prediction are based on the local structure of the knowledge graph. A method that uses global knowledge from across the knowledge graph needs to be developed in order to make knowledge discovery a frequently used tool by researchers.

Results
We propose an approach based on the singular value decomposition (SVD) that is able to combine data from across the knowledge graph through a reduced representation. Using cooccurrence data extracted from published literature, we show that SVD performs better than the leading methods for scoring discoveries. We also show the diminishing predictive power of knowledge discovery as we compare our predictions with real associations that appear further into the future. Finally, we examine the strengths and weaknesses of the SVD approach against another well-performing system using several predicted associations.

Availability and implementation
All code and results files for this analysis can be accessed at https://github.com/jakelever/knowledgediscovery.

Supplementary information
Supplementary data are available at Bioinformatics online.