bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate
Authors: Dowierciał Anna , Jarmuła Adam , Wilk Piotr , Rypniewski Wojciech , Kierdaszuk Borys , Rode Wojciech 
Published: June 2013

Abstract
To solve the inhibition mechanism of thymidylate synthase (TS) by N4-hydroxy-dCMP (N4-OH-dCMP), crystallographic studies were undertaken. Structures of three mouse TS (mTS) complexes with the inhibitor were solved, based on crystals formed by the enzyme protein in the presence of either only N4-OH-dCMP [crystal A, belonging to the space group C 1 2 1, with two monomers in asymmetric unit (ASU), measured to 1.75 Å resolution] or both N4-OH-dCMP and N5,10
-methylenetetrahydrofolate (mTHF) (crystals B and C, both belonging to the space group C 2 2 21, each with a single monomer in ASU, measured to resolution of 1.35 Å and 1.17 Å, respectively). Whereas crystal A-based structure revealed the mTS-N4-OH-dCMP binary complex, as expected, crystals B- and C-based structures showed the enzyme to be involved in a ternary complex with N4-OH-dCMP and noncovalently bound dihydrofolate (DHF), instead of expected mTHF, suggesting the inhibition to be a consequence of an abortive enzyme-catalyzed reaction, involving a transfer of the one-carbon group to a hitherto unknown site and oxidation of THF to DHF. Moreover, both C(5) and C(6) inhibitor atoms showed sp3 hybridization, suggesting C(5) reduction, with no apparent indication of C(5) proton release. In accordance with our previous results, in all subunits of these structures the inhibitor molecule was identified as the anti rotamer of imino tautomer, forming, similar to deoxyuridine monophosphate, two hydrogen bonds with a conservative asparagine (mouse Asn220) side chain.
Construction, management, and performance of sparse Markowitz portfolios
Authors: Henriques Julie , Ortega Juan-Pablo 
Published: June 2013

AbstractWe study different implementations of the sparse portfolio construction and rebalancing method introduced by Brodie et al. (Brodie, J., I. Daubechies, C. De Mol, D. Giannone, and I. Loris. 2009. “Sparse and Stable Markowitz Portfolios.”
Global Victimhood: On the Charisma of the Victim in Transitional Justice Processes
Authors: Bonacker Thorsten 
Published: June 2013

AbstractSince the 1990s, transitional justice has become almost synonymous with the concern for the rights of victims. Compared with the Nuremberg Trials – in which victims did not even appear as witnesses – this is a major change and one for which an explanation will be sought here with recourse to neo-institutional research perspective. The core argument put forward in this article is that the change in transitional justice towards a stronger inclusion of victims could be explained as the result of the expansion of a rationalist world culture in which a model of victimhood is created and diffused worldwide, primarily through international organizations and NGOs. This notion of global victimhood developed only after World War II, following the global diffusion of human rights, the change in academic conceptions of traumatic experiences and the advocacy of International NGOs, so that the development of normative pressure on national transitional justice processes placed victims at the centre of processes dealing with the past.
Genetic Selection for Constitutively Trimerized Human HSF1 Mutants Identifies a Role for Coiled-Coil Motifs in DNA Binding
Authors: Neef Daniel W , Jaeger Alex M , Thiele Dennis J 
Published: June 2013

Abstract
Human heat shock transcription factor 1 (HSF1) promotes the expression of stress-responsive genes and is a critical factor for the cellular protective response to proteotoxic and other stresses. In response to stress, HSF1 undergoes a transition from a repressed cytoplasmic monomer to a homotrimer, accumulates in the nucleus, binds DNA, and activates target gene transcription. Although these steps occur as sequential and highly regulated events, our understanding of the full details of the HSF1 activation pathway remains incomplete. Here we describe a genetic screen in humanized yeast that identifies constitutively trimerized HSF1 mutants. Surprisingly, constitutively trimerized HSF1 mutants do not bind to DNA in vivo in the absence of stress and only become DNA binding competent upon stress exposure, suggesting that an additional level of regulation beyond trimerization and nuclear localization may be required for HSF1 DNA binding. Furthermore, we identified a constitutively trimerized and nuclear-localized HSF1 mutant, HSF1 L189P, located in LZ3 of the HSF1 trimerization domain, which in response to proteotoxic stress is strongly compromised for DNA binding at the Hsp70 and Hsp25 promoters but readily binds to the interleukin-6 promoter, suggesting that HSF1 DNA binding is in part regulated in a locus-dependent manner, perhaps via promoter-specific differences in chromatin architecture. Furthermore, these results implicate the LZ3 region of the HSF1 trimerization domain in a function beyond its canonical role in HSF1 trimerization.
Hydrogen-plasma etching of thin amorphous silicon layers for heterojunction interdigitated back-contact solar cells
Authors: Granata Stefano. N. , Bearda Twan , Gordon Ivan , Poortmans Jef , Mertens Robert 
Published: June 2013

ABSTRACTIn this study, A H2-plasma is studied as a dry method to etch thin layers of amorphous silicon aSi:H(i) deposited on a crystalline wafer. It is found that H2-plasma etches aSi:H(i) selectively toward silicon nitrides hard masks with an etch rate below 3nm/min. Depending on power density and temperature of the substrate during the H2-plasma, the energy bandgap, the hydrides distribution and the void concentration of the aSi:H(i) layers are modified and the amorphous-to-crystalline transition is approached. At high temperature (>250C) and low plasma power (<20mW/cm2), the dihydride (SiH2) content increases and the bandgap widens. The etch rates stays below 0.5 nm/min. At low temperature (<150°C) and high power (>70mW/cm2), the void concentration increases significantly and etch rates up to 3nm/min are recorded.These findings are supported by a theoretical model that indicates formation of Si-H-Si precursors in the layer during exposure to H2-plasma. According to the experimental conditions, these precursors either diffuses and forms Si-Si strong bonds or are removed from the film, causing layer etching.
Use of Micro-CT Scanning Visualisations To Improve Interpretation of Formation Damage Laboratory Tests Including a Case Study From the South Morecambe Field
Authors: Green Justin , Cameron Ruaridh , Patey Ian , Nagassar Vishal , Quine Mark 
Published: June 2013

Abstract
Formation damage testing is commonly used to gather information and aid in risk-reduction when making operational decisions. The nature of laboratory testing means that it is a higher risk to rely on permeability and pressure measurements alone, so various techniques (including scanning electron microscopy and thin section) are used to gather additional information and aid interpretation. The current techniques provide excellent high-resolution data but are limited in terms of capturing the change throughout an entire core sample.
The paper presents a new approach which utilises micro-CT scanning to produce high-resolution data of entire core samples. The images of core produced are superior to those from the commonly-used medical scanners, and give insight into core properties as well as areas such as drilling mud constituents infiltration, mud-cake structure and thickness, and alterations in the pore network. Through a technique that we have called "difference mapping", data sets captured before and after laboratory testing are compared to reveal the distribution of changes within samples. Difference maps can be used to provide additional interpretation of tests results as well as combining with current techniques to target their sampling locations. The combination of laboratory data with tools that allow visualisation of both the distribution and nature of damaging mechanisms makes laboratory data more valuable and therefore decreases risk in operational decision-making.
The technique is illustrated by a case study from Centrica's South Morecambe gas field. Here a series of experiments were carried out to aid in the selection of drilling mud for a cased & perforated well. Whilst permeability was relevant, it was most important to have a fluid that did not contribute deep damaging mechanisms or produce high fluid losses. Laboratory test data showed very significant reductions in permeability, which would normally be a concern if there was not an understanding of the nature of damage. Micro-CT scanning, in combination with geological analysis, showed that the damaging mechanisms were concentrated within the drilling mud-cake, attachment of the drilling mud-cake to the core sample, and drilling mud constituents within the first few pores of the core sample. Only scattered change, caused by some drilling mud filtrate retention and clay fines mobilisation, was seen deeper in the majority of samples; in a cased & perforated scenario the vast majority of damage would therefore be expected to be bypassed. This illustrated the value of the combination of micro-CT scanning and geological techniques to allow greater insight and more meaningful conclusions.
Using Fiber-Optic-Enabled Coiled Tubing to Quantify Fluid Placement and Optimize Stimulation Effectiveness During Matrix Stimulation Treatments in Carbonate Reservoirs
Authors: Ramondenc Pierre , Baez Fernando 
Published: June 2013

Abstract
When performing matrix stimulation treatments, coiled tubing (CT) is a preferred placement technique due to the ability to spot fluid in front of the target zone(s). This method becomes a key solution when formation heterogeneities require a very selective fluid placement strategy.
In today's industry, the most common approach is to design a treatment with volumes of stimulation and diverter fluids that are determined largely based on local practices. Often, it amounts to targeting a uniform stimulation, thus requiring a predefined amount of treatment fluid per length of total pay zone. That approach, although widely used and accepted, may not necessarily yield an optimum stimulation.
We present an alternative technique that relies on the accurate quantification of fluid placement along the formation in order to define the respective volumes of stimulation and diverter fluids to be pumped. This method relies on the analysis of the distributed temperature sensing (DTS) data recorded by a fiber-optic line enclosed inside the CT and data processing through a fast interpretation algorithm to yield a zonal coverage profile. During a job, DTS data corresponding to the preflush can be used to estimate the initial placement distribution across the pay zone. This allows stimulation engineers to determine the best strategy for the subsequent well stimulation treatment, including fluid volumes and placement sequence. After every major pumping stage, a new DTS analysis assesses how the formation reacted to the treatment, improving placement strategy.
This method has been used in multiple matrix stimulation treatments of injector and producer wells. The described innovative approach allows engineers to make more informed decisions between stages, optimizing fluid resources, fluid placement and, ultimately, stimulation effectiveness. It also leads to noteworthy advantages when designing new acidizing treatments, as companies can build on previous experience from similar wells and fields.
Permeametry Pitfalls and Opportunities
Authors: Wehunt C. D. , Nasr-El-Din H. A. 
Published: June 2013

Abstract
Permeameters have been used for more than 80 years in the oil and gas industry, either to measure porous media permeability ("K" studies) or to interpret permeability alterations by various unintended or deliberate processes ("AK" studies). It is the latter experiment class—the AK studies—which are this paper's focus.
Darcy's law is an empirical observation that permeability is proportional to the fluid velocity and the applied pressure gradient, and inversely proportional to the fluid viscosity. In experimental utopia, the simplest variable to measure is the only one that must be recorded during an experiment; however, in practice, interpretation errors frequently arise from ignoring factors that are more difficult to measure or predict, such as viscosity changes within cores during a test. Using data from previously published studies, this paper examines some interpretation pitfalls from past experiments and shows how some of these can be avoided. In addition to ignoring changes in factors that are not actually constant, another pitfall is not fully utilizing the available information. This paper identifies permeametry interpretation improvement opportunities for past or future studies using commonly available data, especially for those tests involving, parallel-flow, dual- or multi-cell tests, or carbonate matrix acidizing optimization studies.
Numerical Simulation of Improved Heavy Oil Recovery by Low-Salinity Water Injection and Polymer Flooding
Authors: Alzayer Hassan , Sohrabi Mehran 
Published: June 2013

Abstract
As heavy oil resources are making an ever-increasing contribution to the energy supply of the world, maximizing recovery from these wreservoirs has attracted significant attention in recent years. Leveraging low salinity waterflooding and polymer flooding to improve heavy oil recovery will be the focus of this paper. While low salinity waterflooding performance in light (conventional) oil reservoirs has been investigated extensively, it has not been applied in heavy oil systems.
Published literature recorded higher oil recovery by injection of low salinity water. One major component among several mechanisms of this increase in oil recovery is due to the lower residual oil saturation (Sorw) by wettability alteration. Therefore, published data was used to produce a correlation between Sorw (high salinity water) and Sorw (low salinity water). A sector model with 36,000 grid cells was used to evaluate the performance of several injection scenarios involving low salinity water and polymer under the conditions of a heavy oil reservoir at the depth of 3,000 ft with oil viscosity of 80 centipoise (20° API). The thickness of the reservoir is less than 100 ft.
The simulated results showed that low salinity waterflooding could increase the estimated ultimate recovery by approximately 5% of original oil in place (OOIP) while the polymer flood provided a similar increase with better efficiency. Subsequent simulations that combine both low salinity waterflooding and polymer resulted in an additional oil recovery of 7.5% to 10% of OOIP.
The results of this study show significant potential for enhancing heavy oil recovery by low salinity waterflooding augmented by polymer injection and multilateral horizontal wells. The commercial viability of such methods to improve heavy oil recovery would make a significant step towards increasing the recovery factor from heavy oil and viscous oil reservoirs. Subsequently, the results would need to be validated by laboratory experiments to establish clear correlation between relative permeability end points with both viscosity and water salinity on heavy oil systems.
Favorable Effects of Insulin Sensitizers Pertinent to Peripheral Arterial Disease in Type 2 Diabetes
Authors: Althouse Andrew D. , Abbott J. Dawn , Sutton-Tyrrell Kim , Forker Alan D. , Lombardero Manuel S. , Buitrón L. Virginia , Pena-Sing Ivan , Tardif Jean-Claude , Brooks Maria Mori ,   for the BARI 2D Study Group
Published: June 2013

OBJECTIVE
The aim of this manuscript was to report the risk of incident peripheral arterial disease (PAD) in a large randomized clinical trial that enrolled participants with stable coronary artery disease and type 2 diabetes and compare the risk between assigned treatment arms.

RESEARCH DESIGN AND METHODS
The Bypass Angioplasty Revascularization Investigation 2 Diabetes (BARI 2D) trial randomly assigned participants to insulin sensitization (IS) therapy versus insulin-providing (IP) therapy for glycemic control. Results showed similar 5-year mortality in the two glycemic treatment arms. In secondary analyses reported here, we examine the effects of treatment assignment on the incidence of PAD. A total of 1,479 BARI 2D participants with normal ankle-brachial index (ABI) (0.91–1.30) were eligible for analysis. The following PAD-related outcomes are evaluated in this article: new low ABI ≤0.9, a lower-extremity revascularization, lower-extremity amputation, and a composite of the three outcomes.

RESULTS
During an average 4.6 years of follow-up, 303 participants experienced one or more of the outcomes listed above. Incidence of the composite outcome was significantly lower among participants assigned to IS therapy than those assigned to IP therapy (16.9 vs. 24.1%; P &lt; 0.001). The difference was significant in time-to-event analysis (hazard ratio 0.66 [95% CI 0.51–0.83], P &lt; 0.001) and remained significant after adjustment for in-trial HbA1c (0.76 [0.59–0.96], P = 0.02).

CONCLUSIONS
In participants with type 2 diabetes who are free from PAD, a glycemic control strategy of insulin sensitization may be the preferred therapeutic strategy to reduce the incidence of PAD and subsequent outcomes.
Spectral Calculus and Lipschitz Extension for
Barycentric Metric Spaces
Authors: Mendel Manor , Naor Assaf 
Published: June 2013

Abstract
The metric Markov cotype of barycentric metric spaces is computed, yielding the first class of metric spaces that are not Banach spaces for which this bi-Lipschitz invariant is understood. It is shown that this leads to new nonlinear spectral calculus inequalities, as well as a unified framework for Lipschitz extension, including new Lipschitz extension results for CAT (0) targets. An example that elucidates the relation between metric Markov cotype and Rademacher cotype is analyzed, showing that a classical Lipschitz extension theorem of Johnson, Lindenstrauss and Benyamini is asymptotically sharp.
Geometric Convergence of Iterative Methods for a Problem with M-matrices and Diagonal Multivalued Operators
Authors: Lapin Alexander 
Published: June 2013

Abstract A finite-dimensional problem with several M-matrices and diagonal
maximal monotone operators is studied. This problem includes variational inequalities
with M-matrices as a partial case and appears, in particular, as a mesh approximation
for a free boundary problem with several constraints and nonlinear relations.
The existence of an unique solution for the problem is studied, as well as the convergence
and geometric rate of the convergence for a class of the iterative methods, the
Schwarz alternating-type methods among them.
The application of the general results to a mesh scheme for a dam problem is considered.
Parallel iterative methods are constructed on the basis of the domain decomposition,
geometric convergence of these methods is justified.
Functional-Discrete Method with a High Order of Accuracy for the Eigenvalue Transmission Problem
Authors: Makarov V.L. , Rossokhata N.O. , Bandurskii B.I. 
Published: June 2013

AbstractWe develop a functional-discrete method with a high order of accuracy
to find a numerical solution of an eigenvalue transmission problem. It allows to
approximate the trial eigenvalue with any desired accuracy. This approach has no
restriction on the number of eigenvalues, an approximation to which can be found.
The convergence rate is proved as in the case of the geometric series. It is shown that
depending on the data of the original problem, two kinds of eigenvalue sequences may
exist. For the first one, the convergence rate increases as the ordinal number of the trial
eigenvalue increases. For the second one, the convergence rate is the same for all eigenvalues
and does not depend on the ordinal number of the trial eigenvalue. Based on the
asymptotic behavior of the eigenvalues of the basic problem and the functional-discrete
method, a qualitative result on the arrangement of eigenvalues of the original problem
is established. A number of numerical examples are given to support the theory.
New evidence on the origin of non-spinose pitted–cancellate species of the early Danian planktonic foraminifera
Authors: Arenillas Ignacio , Arz Jose Antonio 
Published: June 2013

Abstract
Intermediate forms identified in some of the most continuous lower Danian sections allow a better understanding of the origin and evolution of pitted (Globanomalina) and cancellate (Praemurica) planktonic foraminifera. Both Globanomalina and Praemurica are part of a major Paleocene lineage, namely the “non-spinose lineage”, which started to diverge in the early Danian. Transitional specimens strongly suggest the evolution from Parvularugoglobigerina to Globanomalina, and then to Praemurica. These evolutionary turnovers were quite rapid (probably lasting less than 10 kyr), and seem to have begun in the time equivalent of the lower part of the E. simplicissima Subzone, namely the middle part of the standard Zone Pa. The initial evolutionary trends within this non-spinose lineage were the increase of test size and lip thickness, and the evolution from tiny pore-murals to large pore-pits, and from smooth to pitted and finally cancellate walls. Biostratigraphic data suggest that evolution of the wall texture preceded the morphological evolution within each genus. The oldest species of both Globanomalina and Praemurica, namely G. archeocompressa and Pr. taurica, initially retained the external morphology of the ancestral Parvularugoglobigerina eugubina. Since their divergence, Globanomalina and Praemurica followed a separate evolutionary path, evolving into morphologically different species.
Stelis Minima Schenck, 1859 (Hymenoptera: Apoidea: Megachilidae) - A Species of Wild Bee New to Polish Fauna
Authors: Celary Waldemar , Wiśniowski Bogdan 
Published: June 2013

Summary
The paper presents information on Stelis minima Schenck, 1859, a species of cleptoparasitic bee new to Polish fauna representing the family Megachilidae. Stelis minima. probably inhabits most of Europe except for the southern and northern parts of the continent. The species was also found in the southern part of Finland, where it reaches its northern range limit (ca. 62°N). During the years 2002- 2006 four specimens of S. minima were collected in the Kraków-Częstochowa Upland (1 male) and Roztocze region (2 females and 1 male). All specimens were observed close to nests of probable host species of solitary bees - Chelostoma campanularum (Kirby, 1802) and Heriades truncorum (Linnaeus, 1758). The female of Stelis minima can be distinguished from other Central European species by the following characteristics: rounded head, clypeus about 1.5 times wider than its length, legs black, hind basitarsus almost parallel sided (not broadened on the distal part), distances between punctures on mesopleurae ca. as big as their diameter, posterior margins of metasomal tergites (T) black and without lateral bands of hair, T1 or T1-2 with small, lateral, yellowish white maculae; the maculae are sometimes absent. The male Stelis minima can be separated from other Central European species by the following characteristics: clypeus short (not covering mandibles), legs black, distances between punctures on mesopleurae and tergites T4-5 ca. as big as their diameter, posterior margins of metasomal tergites black and without lateral bands of hair, T1-2 or T1-3 with small, lateral yellowish white maculae, posterior margin of seventh tergite with short mid-process, posterior margin of third sternite with triangular emargination in the middle, posterior margin of fourth sternite with a tooth-like, mid-process.