gebhart/patrepeval huggingface dataset:
Topological and Conformational Analysis of the Initiation and Elongation Complex of T7 RNA Polymerase Suggests a New Twist (2004)

The N-terminal domain of T7 RNA polymerase undergoes large conformational changes in the transition from transcription initiation to elongation. The rigid body displacement of parts of the N-terminal domain (residues 72-152 and 204-258) has been described as a screw motion composed of a rotation by 140 degrees and a translation of >20 A along the rotation axis. Protein-protein interactions between residues 23-42 and the C-terminal domain are present in both the initiation and the elongation complex. Assuming that these interactions are retained during the transition between the two states, we find that topological constraints require a right-handed 220 degrees screw motion of the N-terminal rigid body rather than the proposed 140 degrees left-handed screw motion. In the initiation complex, a loop (residues 153-203) extruding from the N-terminal rigid domain wraps around the N-terminal 30 residues. Assuming the N-terminal rigid domain stays folded during the transition, the N-terminus has to pass through this loop before the rigid domain can undergo the translation leading to the elongation complex. On the basis of these topological constraints, we suggest an alternate sequence of conformational changes leading from transcription initiation to elongation in T7 polymerase.
CHINA'S ECONOMIC REFORM: THE TROIKA (1995)

My perspective of China's economic reform is in the context of a so‐called transitional socialist economy, i.e., a centrally planned economy moving to a market‐based economy. Extensive literature on this covers theories on the big‐bang approach as opposed to the gradualist approach, etc. But the issue is much more subtle than these approaches suggest. It involves what I call the troika , which comprises budgetary reform, enterprise reform, and banking reform.
Rawls on Political Community and Principles of Justice (1990)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Review of PD-1/PD-L1 Inhibitors in Metastatic dMMR/MSI-H Colorectal Cancer (2019)

There are a wide range of therapies for metastatic colorectal cancer (CRC) available, but outcomes remain suboptimal. Learning the role of the immune system in cancer development and progression led to advances in the treatment over the last decade. While the field is rapidly evolving, PD-1, and PD-L1 inhibitors have a leading role amongst immunomodulatory agents. They act against pathways involved in adaptive immune suppression resulting in immune checkpoint blockade. Immunotherapy has been slow to impact the management of this patient population due to disappointing results, mainly when used broadly. Nevertheless, some patients with microsatellite-instability-high (MSI-H) or mismatch repair-deficient (dMMR) CRC appear to be susceptible to checkpoint inhibitors with objective and sustained clinical responses, providing a new therapeutic option for patients with advanced disease. This article provides a comprehensive review of the early and late phase trials with the updated data of PD-1/PD-L1 inhibitors alone or in combination with other therapies (immunotherapy, targeted therapy and chemotherapy). While data is still limited, many ongoing trials are underway, testing the efficacy of these agents in CRC. Current and future challenges of PD-1 and PD-L1 inhibitors are also discussed.
Resolving non-determinism in NFA (2003)

The paper describes the authors experience in simulating nondeterministic finite state automata (NFA) using concurrent programming. The non-determinism is resolved simultaneously by activating a separate thread for all possible transition paths. The approach under discussion may be used to implement specific recognizers in the practice of language processors writing.
Recent Advances in Bio-Based Flame Retardant Additives for Synthetic Polymeric Materials (2019)

It would be difficult to imagine how modern life across the globe would operate in the absence of synthetic polymers. Although these materials (mostly in the form of plastics) have revolutionized our daily lives, there are consequences to their use, one of these being their high levels of flammability. For this reason, research into the development of flame retardant (FR) additives for these materials is of tremendous importance. However, many of the FRs prepared are problematic due to their negative impacts on human health and the environment. Furthermore, their preparations are neither green nor sustainable since they require typical organic synthetic processes that rely on fossil fuels. Because of this, the need to develop more sustainable and non-toxic options is vital. Many research groups have turned their attention to preparing new bio-based FR additives for synthetic polymers. This review explores some of the recent examples made in this field.
Few-mode fibers with improved mode spacing (2015)

A simple and intuitive optimization approach is described for the design of composite rotationally asymmetric refractive index fiber profiles with substantially improved mode spacing.
Conducting a winning literature search (2010)

So what is a "winning literature search"? Simply put, it is one that provides you with the information you need to find the types of articles that will help you with clinical practice or research. Literature searching is a combination of an art and a science. Understanding the basic anatomy and physiology of searching can get you started on finding the information you need.
A Client-Transparent Approach to Defend Against Denial of Service Attacks (2006)

Denial of service (DoS) attacks attempt to consume a server's resources (network bandwidth, computing power, main memory, disk bandwidth etc.) to near exhaustion so that there are no resources left to handle requests from legitimate clients. An effective solution to defend against DoS attacks is to filter DoS attack requests at the earliest point (say, the Web site's firewall), before they consume much of the server's resources. Most defenses against DoS attacks attempt to filter requests from inauthentic clients before they consume much of the server's resources. Client authentication using techniques like IPSec or SSL may often require changes to the client-side software and may additionally require superuser privileges at the client for deployment. Further, using digital signatures (as in SSL) makes verification very expensive, thereby making the verification process itself a viable DoS target for the adversary. In this paper, we propose a light-weight client transparent technique to defend against DoS attacks with two unique features: (i) Our technique can be implemented entirely using JavaScript support provided by a standard client-side browser like Mozilla FireFox or Microsoft Internet Explorer. Client transparency follows from the fact that: (i) no changes to client-side software are required, (ii) no client-side superuser privileges are required, and (iii) clients (human beings or automated clients) can browse a DoS protected Web site in the same manner that they browse other Web sites, (ii) Although we operate using the client-side browser (HTTP layer), our technique enables fast IP level packet filtering at the server's firewall and requires no changes to the application(s) hosted by the Web server. In this paper we present a detailed design of our technique along with a detailed security analysis. We also describe a concrete implementation of our proposal on the Linux kernel and present an evaluation using two applications: bandwidth intensive Apache HTTPD and database intensive TPCW. Our experiments show that our approach incurs a low performance overhead and is resilient to DoS attacks
Applications of random sampling in computational geometry, II (1988)

Random sampling is used for several new geometric algorithms. The algorithms are “Las Vegas,” and their expected bounds are with respect to the random behavior of the algorithms. One algorithm reports all the intersecting pairs of a set of line segments in the plane, and requires Ο(A + n log n) expected time, where A is the size of the answer, the number of intersecting pairs reported. The algorithm requires Ο(n) space in the worst case. Another algorithm computes the convex hull of a point set in E3 in Ο(n log A) expected time, where n is the number of points and A is the number of points on the surface of the hull. A simple Las Vegas algorithm triangulates simple polygons in Ο(n log log n) expected time. Algorithms for half-space range reporting are also given. In addition, this paper gives asymptotically tight bounds for a combinatorial quantity of interest in discrete and computational geometry, related to halfspace partitions of point sets.
Interface-mediated ultrafast carrier conduction in oxide thin films and superlattices for energy (2009)

Some recent observations on carrier (electronic and ionic) transport in thin film and nanostructured metal oxides and superlattices, where interfaces play a dominant role in overall conductivity response, are reviewed. Conduction in nominally pure oxides is compared to heavily aliovalently doped oxides (that correspond to changes in the Debye length over few orders of magnitude). The role of dopant segregation and their spatial variation in affecting transport is pointed out. The ability to utilize interfaces in enabling ultrafast-ion conduction as well as the creation of novel interfacial materials and implications in energy technologies as well as some scientific questions that may warrant further attention are highlighted.
Bivariate holomorphic embedding applied to the power flow problem (2016)

Iterative methods for solving the power flow problem, including the Newton Raphson method and fast decoupled methods require good starting points, otherwise they may not converge or may converge to the wrong (low voltage) solution. The holomorphic embedding method (HEM) is a recursive, not iterative, method which uses the no-load condition as its starting points and is theoretically guaranteed to converge to the operable, high-voltage (HV) solution if one exists. The HEM method uses Padé approximant as a means of analytic continuation and is capable of finding the HV solution up to the saddle node bifurcation point (SNBP). The univariate HEM has been proven to be an efficient tool in experiments. However, a key drawback of the univariate HEM is that it lacks flexibility: the method can calculate the solutions only when the load/generation profile is scaled as a whole. A straightforward improvement is to use a multi-variate HEM combined with multi-variate Padé approximants. This paper presents a bivariate HEM formulation, which uses a corresponding bivariate Padé (Chisholm) approximant. Simulations on a three-bus and a modified IEEE 14-bus system show that the method can yield accurate voltage solutions and accurate values of the SNBPs.
Automatic Realistic 3D Garment Generation Based on Two Images (2016)

Realistic garment model generation has a great practical significance, especially in 3D virtual try-on. However, the creation of realistic models for most 3D virtual try-on systems is labor intensive and requires strong domain knowledge. Thus, we propose a method to automatically generate realistic 3D garment model based on a front and a back images of a garment product. We classify the garment type based on the distribution characteristics of several feature points selected from silhouette points set. Besides, we propose a method to classify the component design attributes by using a classifier trained by SVM algorithm based on HOG features. Our system can create texture map as well. All of these processes can be handled automatically, which helps novice users to generate realistic 3D garments without any other manipulation after input two images. The experiments demonstrate the effectiveness and efficiency of our method on generating realistic garment models.
Ultra-low-loss tunable piezoelectric-actuated metasurfaces achieving 360° or 180° dynamic phase shift at millimeter-waves (2020)

Phase shifting metasurfaces typically consist of an ordered metallic geometry that is patterned onto a dielectric substrate and incorporate active devices or materials that enable dynamic tuning. Existing methods at mm-wave and submillimeter bands typically suffer from high losses, which are predominantly produced by the inherent limitations of the tuning elements or materials. This report presents a new, ultra-low-loss and phase-tunable, reflection type metasurface design, which outperforms previously reported technologies in terms of phase shifting and loss. The proposed technique utilizes a variable air cavity, formed between a periodic array and a ground plane, which is controlled by means of a piezoelectric actuator. Two metasurface designs are presented and experimentally tested. Firstly, a square patch element metasurface that is capable of achieving a continuous 180° phase shift across a wide bandwidth, between 35 and 65 GHz. Also presented is a double-cross element metasurface that provides full 360° phase control between 57 and 62 GHz. The variable air cavity is controlled by means of a piezoelectric actuator that supports and varies the height of a ground plane, providing highly accurate, millisecond, displacement. Unlike conventional tuning methods, the tuning mechanism, in this case the moving ground plane, introduces no additional sources of loss and enables an average loss performance of 1 dB. Full-wave simulations are presented and experimentally validated with measurements of both metasurface prototypes. The proposed approach is scalable from microwave up to THz frequencies, due to the electro-mechanical and low loss nature of the tuning.
Maximum energy transfer in near-field thermal radiation at nanometer distances (2009)

Radiative energy transfer at nanoscale distances can exceed that of blackbody radiation by several orders of magnitude due to photon tunneling and the excitation of surface polaritons. While significant progress has been made recently in understanding near-field thermal radiation, an outstanding question remains as whether there exists an upper limit of near-field radiation for arbitrarily selected material properties at finite separation distances. We investigate the maximum achievable radiative heat flux between two parallel plates separated by a vacuum gap from 0.1 to 100 nm. By assuming a frequency-independent dielectric function and introducing a cutoff parallel wavevector component, we find that the ideal dielectric function for the two media that will maximize the near-field radiative transfer is −1+iδ, where δ is the imaginary part. For vacuum gaps greater than 1 nm, the near-field heat transfer peaks when δ⪡1, while at subnanometer gaps, the peak in the energy transfer shifts toward larger values of δ. The determination of the maximum radiative flux at nanometer distances will benefit emerging applications of near-field radiation for energy harvesting and nanothermal manufacturing.
Considerations about sample-size sensitivity of a family of edited nearest-neighbor rules (1999)

The edited nearest neighbor classification rules constitute a valid alternative to k-NN rules and other nonparametric classifiers. Experimental results with synthetic and real data from various domains and from different researchers and practitioners suggest that some editing algorithms (especially, the optimal ones) are very sensitive to the total number of prototypes considered. This paper investigates the possibility of modifying optimal editing to cope with a broader range of practical situations. Most previously introduced editing algorithms are presented in a unified form and their different properties (acid not just their asymptotic behavior) are intuitively analyzed. The results show the relative limits in the applicability of different editing algorithms.
PCR Sequencing with the Aid of Detergents (2003)

The polymerase chain reaction (PCR) allows the rapid detection of infectious viruses or other microorganisms as well as the cause of genetic defects. By performing sequence analysis afterward, important additional information on the PCR products is obtained. Often direct sequencing of the PCR products is preferred over the more time-consuming and expensive procedure of cloning prior to sequencing.
Multiple isoforms of guinea pig decay-accelerating factor (DAF) generated by alternative splicing (1995)

Human decay-accelerating factor (DAF, CD55), which is one of the regulators of complement activation (RCA), prevents complement activation on homologous cell membranes, resulting in a functional discrimination between self cells and invading microorganisms. DAF is a glycosylphosphatidylinositol (GPI)-anchored glycoprotein and has been identified at the molecular level only in primates. We have isolated guinea pig DAF cDNA clones from a spleen library and identified six different classes. All encode the same four short consensus repeat domains with 58% amino acid sequence identity to human DAF, but show variability in the C-terminal region. Alternative splicing of two optional exons generates transmembrane, GPI-anchored, and secreted forms of guinea pig DAF, and differential usage of splice sites in the single exon composed of internally quintuplicated sequences generates variable Ser/Thr-rich regions. Multiple isoforms were expressed ubiquitously in all tissues and cells tested. Similar variability in the Ser/Thr-rich region has been reported in human membrane cofactor protein (MCP), another membrane inhibitor of the RCA family. There seems to be a common ancestral sequence in DAF and MCP consisting of a Ser/Thr-rich region, but obviously multiplication occurred independently, indicating the importance of variability of the Ser/Thr-rich region for the effective regulation of complement activation.
Focussing over the edge: adaptive subsurface laser fabrication up to the sample face (2012)

Direct laser writing is widely used for fabrication of subsurface, three dimensional structures in transparent media. However, the accessible volume is limited by distortion of the focussed beam at the sample edge. We determine the aberrated focal intensity distribution for light focused close to the edge of the substrate. Aberrations are modelled by dividing the pupil into two regions, each corresponding to light passing through the top and side facets. Aberration correction is demonstrated experimentally using a liquid crystal spatial light modulator for femtosecond microfabrication in fused silica. This technique allows controlled subsurface fabrication right up to the edge of the substrate. This can benefit a wide range of applications using direct laser writing, including the manufacture of waveguides and photonic crystals.
C-MYB and C/EBP Family Transcription Factors Regulate the Gfi-1 Promoter. (2006)

Abstract Gfi-1 −/− mice generate abnormal immature myeloid cells exhibiting characteristics of both monocytes and granulocytes. One of Gfi-1’s critical functions is to downregulate monocyte specific genes in order for granulocytes to develop properly. Since the transcription factors C/EBP alpha and C/EBP epsilon are needed for granulocyte development we hypothesized that these factors may regulate Gfi-1 expression. The Gfi-1 promoter contains several putative C/EBP binding sites and we show by electrophoretic mobility shift and chromatin immunoprecipitation that C/EBP family members can bind to some of these sites. However we were unable to see activation of the Gfi-1 promoter by C/EBP proteins in transient transfection reporter assays. Other groups have shown that C/EBP proteins can synergize with the transcription factor c-myb. We observed that the Gfi-1 promoter contains sites for the hematopoietic transcription factor c-myb. Sevral of these c-myb binding sites are adjacent to C/EBP binding sites. In reporter assays in non-hematopoietic cells c-myb activated the Gfi-1 promoter by itself and this activity was enhanced when we included either C/EBP alpha or epsilon in the transfection. Our data suggests that C/EBP proteins and c-myb regulate the transcription of Gfi-1 in myeloid cells.
Acute<i>Chlamydia pneumoniae</i>and<i>Mycoplasma pneumoniae</i>Infections in Community-Acquired Pneumonia and Exacerbations of COPD or Asthma: Therapeutic Considerations (2004)

Rates of acute Chlamydia pneumoniae and Mycoplasma pneumoniae infections were determined in 115 adults hospitalized for community-acquired pneumonia (CAP), purulent exacerbations of COPD and acute exacerbations of bronchial asthma, by means of serology and molecular methods. Results were compared with those obtained in a matched control group. Common respiratory pathogens were isolated by cultures in 22.5% and 22.2% of CAP and exacerbated COPD patients, respectively. Cultures from exacerbated asthma patients were always negative. Serological and molecular evidence of current C. pneumoniae infection was obtained in 10.0%, 8.9% and 3.3% of CAP, COPD and asthma cases. The corresponding rates of acute M. pneumoniae infection were 17.5%, 6.7% and 3.3%, respectively. Finally, no difference was found between typical and atypical pathogen rates. These findings highlight the importance of taking into account C. pneumoniae and M. pneumoniae infections in guiding the choice of empirical antibacterial treatment for CAP and purulent exacerbations of COPD.
Isolation and characterization of a starchless mutant of <i>Chlorella pyrenoidosa</i> STL‐PI with a high growth rate, and high protein and polyunsaturated fatty acid content (2006)

SUMMARY The growth characteristics, biochemical composition and ultrastructure of a novel starchless mutant of Chlorella pyrenoidosa, designated as STL‐PI, are compared to the same characteristics of its parental strain, C. pyrenoidosa 82T. The STL‐PI mutant had a 22 ± 5% higher growth rate, and 24.5 ± 4.2% more protein than the parental strain, 82T. Furthermore, the STL‐PI mutant accumulated 20.4% more polyunsaturated fatty acids and 18% less saturated fatty acids than the parental 82T. When the parental 82T was cultured in a nitrogen‐free media, their starch content increased from 6.8 ± 2.8% to 22.5 ± 3.1%. In contrast, the STL‐PI mutant produced no starch, regardless of the growth conditions. Instead, the mutant cells responded to nitrogen limitation by further increasing their lipid content from 25.2 ± 1.2% to 38.0 ± 2.3% per dry weight. Transmission electron micrography revealed that nitrogen limitation typically stimulates the formation of starch granules in the chloroplast of 82T cells. Yet no starch granules were observed in the STL‐PI cells. Instead, only the formation of large lipid globules was observed in the mutant cells. These results demonstrate that the starchless mutant STL‐P1 possesses novel physiological and phytochemical properties distinct from the 82T cells: their cells were deficient in starch synthesis and showed higher growth rates and productivity than 82T cells.