bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contact‐assisted protein structure modeling by global optimization in CASP11
Authors: Joo Keehyoung , Joung InSuk , Cheng Qianyi , Lee Sung Jong , Lee Jooyoung 
Published: December 2015

ABSTRACTWe have applied the conformational space annealing method to the contact‐assisted protein structure modeling in CASP11. For Tp targets, where predicted residue–residue contact information was provided, the contact energy term in the form of the Lorentzian function was implemented together with the physical energy terms used in our template‐free modeling of proteins. Although we observed some structural improvement of Tp models over the models predicted without the Tp information, the improvement was not substantial on average. This is partly due to the inaccuracy of the provided contact information, where only about 18% of it was correct. For Ts targets, where the information of ambiguous NOE (Nuclear Overhauser Effect) restraints was provided, we formulated the modeling in terms of the two‐tier optimization problem, which covers: (1) the assignment of NOE peaks and (2) the three‐dimensional (3D) model generation based on the assigned NOEs. Although solving the problem in a direct manner appears to be intractable at first glance, we demonstrate through CASP11 that remarkably accurate protein 3D modeling is possible by brute force optimization of a relevant energy function. For 19 Ts targets of the average size of 224 residues, generated protein models were of about 3.6 Å
atom accuracy. Even greater structural improvement was observed when additional Tc contact information was provided. For 20 out of the total 24 Tc targets, we were able to generate protein structures which were better than the best model from the rest of the CASP11 groups in terms of GDT‐TS. Proteins 2016; 84(Suppl 1):189–199. © 2015 Wiley Periodicals, Inc.
Investigations in the infra‐red. I: The absorption and reflection spectra of KHF2, KDF2 and RbHF2 in relation to the constitution of the bifluoride ion
Authors: Ketelaar J. A. A. 
Published: December 2015

AbstractAn arrangement is described for the analysis of the infra‐red spectrum using a prism spectrometer and thermo‐electric radiation receivers. Experimental details are given especially of a self‐constructed telluriumconstantan thermo‐element. With this arrangement the absorption and reflection spectra were investigated of crystals of KHF2, KDF2 and of RbHF2 in the quartz and in the rock‐salt region from 1‐17 μ. The spectrum of RbHF2 is similar to that of the isomorphous potassium compound except for a small shift of a few cm−1 toward lower frequencies. Two fundamental frequencies are observed for KHF2 at 1222 cm−1 (8.18 μ) and at 1450 cm−1 (6.90 μ) in absorption, and at 1238 cm−1 (8.08 μ) and at 1490 cm−1 (7.08 μ) in reflection. For KDF2 the corresponding frequencies are 891 cm−1 and 1046 cm−1 in reflection.It is shown, that both frequencies belong to the fundamental asymmetric valence frequency ν3 (the “hydrogen” frequency) of the bifluoride ion. It is further shown, that this doubling of the hydrogen frequency is due to the presence of a double minimum in the potential curve for the hydrogen atom, analogous to the doubling observed in the parallel bands of the NH3‐molecule. The phenomenon of protonic resonance is discussed. The distance between the two levels of the zero pair for KHF2 is estimated to be 25 cm−1, that for the first pair is equal to 185 cm−1. A potential curve is drawn, and the height of the potential hump separating the two minima is estimated as 2570 cm−1 or 7.3 kcal/mol. The analysis of the large number of bands observed shows that all are due to the double “hydrogen” frequency ν3 and higher harmonics in combination with the inactive symmetrical frequency ν1 at 580‐550 cm−1.The stationary state of the HF2−group is a resonance hybride between the two equivalent asymmetric structures. The resonance consists in the migration of the hydrogen ion between the two minima of potential energy, one near each of the two fluorine atoms. However the resonance energy is negligible compared with the total bond energy of the HF2‐group.
Recherches sur L'extinction des Flammes Etude Spéciale du Point de vue de L'effet Antioxygène
Authors: le Bras Jean 
Published: December 2015

AbstractEn utilisant un appareil basé sur le principe du courant gazeux, on a étudié l'extinction de flammes de combustibles divers à l'aide de trois sortes d'extincteurs: l'azote, le bromure d'éthyle et le térachlorure de carbone. Les combustibles sur lesquels ont porté les essais ont été: l'hydrogène, le méthane, l'oxyde de carbone, le gaz d'éclairage, le benzène, le toluène, le xylène, les alcools méthylique, éthylique, propylique et butylique, enfin le sulfure de carbone. Dans des expériences spéciales, on a cherché à élucider les mécanismes extincteurs; on a pu montrer ainsi que le bromure d'éthyle agit comme étouffeur, c'est‐à‐dire d'une façon tout à fait analogue à celle d'une vapeur combustible. Mais le tétrachlorure de carbone se comporte de manières très différentes selon la nature de la flamme sur laquelle il agit et son effet antioxygène est toujours plus ou moins masqué.En outre, l'appareillage permet de déterminer aisément les limites supérieure et inférieure d'inflammabilité des combustibles; certains des chiffres indiqués constituent des résultats nouveaux.On a constaté enfin qu'il était possible d'appliquer une loi, analogue à celle de Le Châtelier, pour calculer les taux extincteurs envers des mélanges de combustibles.
Neighbouring group participation in the photolysis of aryl esters of unsaturated 1,4‐dicarboxylic acids
Authors: Alvaro M. , Garcia H. , Primo J. , Miranda M. A. 
Published: December 2015

AbstractPhotolysis of the aryl maleates la,b produces homolysis of the carbonyl‐aryloxy bond, followed by internal addition of the acyl radical to the neighbouring carbonyl group, giving the unexpected products 3 or 4; by contrast the aryl fumarates 2a,b follow the “normal” photo‐Fries pathway.
Synthesis of racemic myo‐inositol 1,3,4‐trisphosphate via a phosphite‐triester approach
Authors: Dreef C. E. , van der Marel G. A. , van Boom J. H. 
Published: December 2015

AbstractPhosphitylation of (±)‐2,4,5‐tri‐0‐benzyl‐myo‐Inositol with bis(2‐cyanoethyl) chlorophosphine gave, after oxidation followed by basic hydrolysis and subsequently hydrogenolysis, (±)‐myo‐Inositol 1,3,4‐trisphosphate.
Role of Acid Sphingomyelinase in Shifting the Balance Between Proinflammatory and Reparative Bone Marrow Cells in Diabetic Retinopathy
Authors: Chakravarthy Harshini , Navitskaya Svetlana , O'Reilly Sandra , Gallimore Jacob , Mize Hannah , Beli Eleni , Wang Qi , Kady Nermin , Huang Chao , Blanchard Gary J. , Grant Maria B. , Busik Julia V. 
Published: December 2015

Abstract
The metabolic insults associated with diabetes lead to low-grade chronic inflammation, retinal endothelial cell damage, and inadequate vascular repair. This is partly due to the increased activation of bone marrow (BM)-derived proinflammatory monocytes infiltrating the retina, and the compromised function of BM-derived reparative circulating angiogenic cells (CACs), which home to sites of endothelial injury and foster vascular repair. We now propose that a metabolic link leading to activated monocytes and dysfunctional CACs in diabetes involves upregulation of a central enzyme of sphingolipid signaling, acid sphingomyelinase (ASM). Selective inhibition of ASM in the BM prevented diabetes-induced activation of BM-derived microglia-like cells and normalized proinflammatory cytokine levels in the retina. ASM upregulation in diabetic CACs caused accumulation of ceramide on their cell membrane, thereby reducing membrane fluidity and impairing CAC migration. Replacing sphingomyelin with ceramide in synthetic membrane vesicles caused a similar decrease in membrane fluidity. Inhibition of ASM in diabetic CACs improved membrane fluidity and homing of these cells to damaged retinal vessels. Collectively, these findings indicate that selective modulation of sphingolipid metabolism in BM-derived cell populations in diabetes normalizes the reparative/proinflammatory cell balance and can be explored as a novel therapeutic strategy for treating diabetic retinopathy.
Concise Review: Balancing Stem Cell Self-Renewal and Differentiation with PLZF
Authors: Liu Tong Ming , Lee Eng Hin , Lim Bing , Shyh-Chang Ng 
Published: December 2015

Abstract
In recent years, the highly conserved promyelocytic leukemia zinc finger (PLZF, also known as ZBTB16, ZNF145) has attracted attention as a multifunctional transcription factor involved in major biological processes during development. As a transcription factor, PLZF shows tight regulation in its cell-type-specific and stage-specific expression patterns. Emerging evidence shows that PLZF regulates the balance of self-renewal and differentiation in stem cells. However, the gene regulatory network of PLZF is only beginning to be understood. In this review, we discuss the diverse functions of PLZF, in particular its role in self-renewal versus differentiation of stem cells. We also discuss the current state of knowledge on the gene regulatory network of PLZF, in conjunction with its upstream factors, post-translational modifications and binding cofactors for multiprotein complexes. This review aims to provide the reader with an in-depth understanding of the molecular mechanisms underlying PLZF and the potential applications in tissue regeneration.
Trends in dementia incidence: Evolution over a 10‐year period in France
Authors: Grasset Leslie , Brayne Carol , Joly Pierre , Jacqmin‐Gadda Hélène , Peres Karine , Foubert‐Samier Alexandra , Dartigues Jean‐François , Helmer Catherine 
Published: December 2015

AbstractIntroductionFew recent studies have suggested declining trends in dementia frequency. French cohorts with long follow‐up allowed us to explore incidence evolution trends.MethodsTwo different populations of subjects aged ≥65 years included in 1988–1989 (n = 1469) and 1999–2000 (n = 2104) were followed up over 10 years, with systematic assessment for cognition and dementia. Multistates illness‐death models were used to compare dementia incidence using both clinical and algorithmic diagnoses.ResultsUsing the algorithmic diagnosis, incidence declined significantly overall and for women (age‐adjusted hazard ratio [HR] = 0.62; confidence interval (CI) = 0.48–0.80 for women between the two populations). Differences in education, vascular factors, and depression accounted only to some extent for this reduction (women full‐adjusted HR = 0.73; CI = 0.57–0.95). No significant decreasing trends were found for men or when using the clinical diagnosis for either sex.DiscussionOur study provides further support for a decrease in dementia incidence in women using algorithmic diagnosis. Changes in diagnostic boundaries mask this reduction.
The Mesozoic successions of western Sierra de Zacatecas, Central Mexico: provenance and tectonic implications
Authors: ORTEGA-FLORES BERLAINE , SOLARI LUIGI A. , ESCALONA-ALCÁZAR FELIPE DE JESÚS 
Published: December 2015

AbstractCentral Mexico was subject to active tectonics related to subduction processes while it occupied a position in western equatorial Pangea during early Mesozoic time. The subduction of the palaeo-Pacific plate along the western North American and South American active continental margins produced volcanic arc successions which were subsequently rifted and re-incorporated to the continental margin. In this context, the fringing arcs are important in unravelling the continental accretionary record. Using petrographic analysis, detrital zircon geochronology and structural geology, this paper demonstrates that the Guerrero Arc (Guerrero Terrane) formed on top of a felsic volcaniclastic unit (Middle Jurassic La Pimienta Formation) and siliciclastic strata (Upper Triassic Zacatecas Formation and Arteaga Complex) of continental Mexican provenance, deposited across the continental margin and oceanic substrate. This assemblage was rifted away from continental Mexico to form an intervening oceanic assemblage (Upper Jurassic – Lower Cretaceous Las Pilas Volcanosedimentary Complex of the Arperos Basin), then accreted back more or less at the same place, all above the same east-dipping subduction zone. The accretion of the Guerrero Arc to the Mexican continental mainland (Sierra Madre Terrane) caused the deposition of a siliciclastic unit (La Escondida Phyllite), which recycled detritus from the volcaniclastic and siliciclastic underlying strata.
Alterations of mucosa of the larynx and hypopharynx in patients with mucopolysaccharidoses
Authors: Keilmann A , Bendel F , Nospes S , Lampe C , Läßig A K 
Published: December 2015

AbstractObjective:This study aimed to: assess the mucosal alterations of the larynx and hypopharynx typical for mucopolysaccharidoses, in a standardised manner; compare the severity in different subtypes of mucopolysaccharidoses; and monitor the effect of an enzyme replacement therapy.Methods:A classification for mucosal alterations of the larynx and hypopharynx was developed and utilised in 55 patients with mucopolysaccharidoses. Fifteen patients who started treatment with enzyme replacement therapy were followed longitudinally.Results:The most severe alterations were seen in the posterior region of the larynx and the arytenoids, and in the region of the false vocal folds. The alterations were most severe in patients with mucopolysaccharidosis II. No clear trend was observed in the patients who received enzyme replacement therapy.Conclusion:Quantification of mucosal alterations of the hypopharynx and larynx in mucopolysaccharidoses patients can provide information about the disease's natural process and about the efficacy of enzyme replacement therapy.
The Declining Role of Latin America in Global Agricultural Trade, 1963–2000
Authors: SERRANO RAÚL , PINILLA VICENTE 
Published: December 2015

AbstractIn the second half of the twentieth century, Latin American countries lost a substantial part of their importance in worldwide exports of agricultural and food products. Given this context, the objective of this article is to analyse the determinants of the evolution of agricultural exports from Latin America, paying special attention to the influence of regional processes of economic integration on exports and to their degree of participation in intra-industrial trade. We propose a gravity model with a data panel of total exports and product groups for six Latin American countries towards 39 destinations between 1963 and 2000.
The impending demise of the item in visual search
Authors: Hulleman Johan , Olivers Christian N. L. 
Published: December 2015

AbstractThe way the cognitive system scans the visual environment for relevant information – visual search in short – has been a long-standing central topic in vision science. From its inception as a research topic, and despite a number of promising alternative perspectives, the study of visual search has been governed by the assumption that a search proceeds on the basis of individual items (whether processed in parallel or not). This has led to the additional assumptions that shallow search slopes (at most a few tens of milliseconds per item for target-present trials) are most informative about the underlying process, and that eye movements are an epiphenomenon that can be safely ignored. We argue that the evidence now overwhelmingly favours an approach that takes fixations, not individual items, as its central unit. Within fixations, items are processed in parallel, and the functional field of view determines how many fixations are needed. In this type of theoretical framework, there is a direct connection between target discrimination difficulty, fixations, and reaction time (RT) measures. It therefore promises a more fundamental understanding of visual search by offering a unified account of both eye movement and manual response behaviour across the entire range of observed search efficiency, and provides new directions for research. A high-level conceptual simulation with just one free and four fixed parameters shows the viability of this approach.
War by other means: Mobile gaming and the 2014 Israel-Gaza Conflict
Authors: Schulzke Marcus 
Published: December 2015

AbstractThe 2014 Israel-Gaza Conflict inspired the creation of over a dozen games for mobile phones and tablets. These games, which allowed players to Bomb Gaza City, operate the Iron Dome missile defence system, and direct rockets into Israeli settlements, marked an important shift in the mediatisation of war in three ways. First, whereas propaganda is frequently described as a top-down process by which elites influence mass audiences, the mobile war games about Gaza were created by non-elite indie game developers, thereby illustrating these games’ capacities for allowing new actors to participate in ideological contestation. Second, the games were not simply reflections on the conflict, but part of it. They were released while the fighting was in progress and helped to constitute the ideological battleground. Finally, the games reproduced established propaganda techniques in distinctive ways that were shaped by the mobile gaming medium.
‘Creeping’ Advisory Jurisdiction of International Courts and Tribunals? The case of the International Tribunal for the Law of the Sea
Authors: RUYS TOM , SOETE ANEMOON 
Published: December 2015

AbstractOn 2 April 2015, the full International Tribunal for the Law of the Sea (ITLOS) rendered its first advisory opinion in reply to a request of the Sub-Regional Fisheries Commission regarding illegal, unreported and unregulated fishing. Unlike any other court or tribunal with advisory competence, including the Seabed Disputes Chamber, ITLOS’ advisory jurisdiction is not explicitly enshrined in its constituent instrument, but was rather asserted in the Tribunal’s, homemade, rules of procedure. In spite of strong objections from various states, ITLOS affirmed a broad advisory jurisdictionratione materiaeandpersonae, and found that there were no compelling reasons to exercise its discretionary power to dismiss the request. The request and the Tribunal's handling thereof raise interesting questions regarding the opportunities and risks inherent to, and the outer limits of, the advisory jurisdiction of international courts and tribunals. This contribution takes a look at the advisory jurisdiction of the full Tribunal, having regard to the experiences of other international courts and tribunals.
Disjunctive answer set solvers via templates
Authors: BROCHENIN REMI , MARATEA MARCO , LIERLER YULIYA 
Published: December 2015

AbstractAnswer set programming is a declarative programming paradigm oriented towards difficult combinatorial search problems. A fundamental task in answer set programming is to compute stable models, i.e., solutions of logic programs. Answer set solvers are the programs that perform this task. The problem of deciding whether a disjunctive program has a stable model is ΣP2-complete. The high complexity of reasoning within disjunctive logic programming is responsible for few solvers capable of dealing with such programs, namely dlv, gnt, cmodels, clasp and wasp. In this paper, we show that transition systems introduced by Nieuwenhuis, Oliveras, and Tinelli to model and analyze satisfiability solvers can be adapted for disjunctive answer set solvers. Transition systems give a unifying perspective and bring clarity in the description and comparison of solvers. They can be effectively used for analyzing, comparing and proving correctness of search algorithms as well as inspiring new ideas in the design of disjunctive answer set solvers. In this light, we introduce a general template, which accounts for major techniques implemented in disjunctive solvers. We then illustrate how this general template captures solvers dlv, gnt, and cmodels. We also show how this framework provides a convenient tool for designing new solving algorithms by means of combinations of techniques employed in different solvers.
How did partners experience cancer patients' participation in a phase I study? An observational study after a patient's death
Authors: Langenberg Simone M.C.H. , Peters Marlies E.W.J. , van der Graaf Winette T.A. , Wymenga Anke N. Machteld , Prins Judith B. , van Herpen Carla M.L. 
Published: December 2015

AbstractObjective:It can be assumed that patients' participation in a phase I study will have an important impact on their partners' life. However, evaluation of partners' experiences while patients are undergoing experimental treatment and of their well-being after the patient's death is lacking. We aimed to explore partners' experience of patients' participation in phase I studies and to investigate their well-being after a patient's death.Method:This was an observational study conducted after the patient's death. Partners of deceased patients who had participated in a phase I study completed a questionnaire designed by us for experience evaluation and the Beck Depression Inventory for Primary Care, the Hospital Anxiety and Depression Scale, the Inventory of Traumatic Grief, and the RAND-36 Health Survey.Results:The median age of the 58 participating partners was 58 years (range: 51–65), and 67% was female. Partners reported negative effects on patients' quality of life, but only 5% of partners regretted patients' participation. Approximately two years after the patients' death, 19% of partners scored for depression, 36% for psychological distress, and 46% for complicated grief, and partners generally scored significantly lower on social and mental functioning compared to normative comparators.Significance of Results:Although partners reported negative consequences on patients' quality of life, most did not regret patients' participation in the phase I studies. Prevalence of depression, psychological distress, and complicated grief seemed important problems after a patient's death, and these must be considered when shaping further support for partners of patients participating in phase I trials.
Nucleoprotein of influenza A virus negatively impacts antiapoptotic protein API5 to enhance E2F1-dependent apoptosis and virus replication
Authors: Mayank A K , Sharma S , Nailwal H , Lal S K 
Published: December 2015

AbstractApoptosis of host cells profoundly influences virus propagation and dissemination, events that are integral to influenza A virus (IAV) pathogenesis. The trigger for activation of apoptosis is regulated by an intricate interplay between cellular and viral proteins, with a strong bearing on IAV replication. Though the knowledge of viral proteins and mechanisms employed by IAV to induce apoptosis has advanced considerably of late, we know relatively little about the repertoire of host factors targeted by viral proteins. Thus, identification of cellular proteins that are hijacked by the virus will help us not only to understand the molecular underpinnings of IAV-induced apoptosis, but also to design future antiviral therapies. Here we show that the nucleoprotein (NP) of IAV directly interacts with and suppresses the expression of API5, a host antiapoptotic protein that antagonizes E2F1-dependent apoptosis. siRNA-mediated depletion of API5, in NP-overexpressed as well as IAV-infected cells, leads to upregulation of apoptotic protease activating factor 1 (APAF1), a downstream modulator of E2F1-mediated apoptosis, and cleavage of caspases 9 and 3, although a reciprocal pattern of these events was observed on ectopic overexpression of API5. In concordance with these observations, annexin V and 7AAD staining assays exhibit downregulation of early and late apoptosis in IAV-infected or NP-transfected cells on overexpression of API5. Most significantly, while overexpression of API5 decreases viral titers, cellular NP protein as well as mRNA levels in IAV-infected A549 cells, silencing of API5 expression causes a steep rise in the same parameters. From the data reported in this manuscript, we propose a proapoptotic role for NP in IAV pathogenesis, whereby it suppresses expression of antiapoptotic factor API5, thus potentiating the E2F1-dependent apoptotic pathway and ensuring viral replication.