gebhart/patrepeval huggingface dataset:
A Negative Cofactor Containing Dr1/p19 Modulates Transcription with TFIIA in a Promoter-specific Fashion (1996)

An activity that modulated the relative levels of transcription from the adenovirus major late promoter (MLP), and the immunoglobulin heavy chain mu promoter (mu) was purified as a 90-kDa factor. This factor is suggested to be a heterotetramer of two subunits: a 20-kDa polypeptide identical to the previously described Dr1/p19 and a novel 30-kDa polypeptide. The Dr1/p19 protein has been characterized as a repressor of transcription, and the 30-kDa protein is related to a recently identified yeast gene proposed to encode a repressor of transcription. The 90-kDa factor forms a complex with TATA-binding protein on DNA and at high concentrations of both factors protects over a 150-base pair region around the promoter from DNase I cleavage. The conformation of this complex as assayed by footprinting analysis is altered by the transcription factor TFIIA on the MLP but not on the mu promoter. Similarly, TFIIA reverses the repression of transcription by the 90-kDa factor on the MLP but not on the mu promoter. Thus, the interactions of TATA-binding protein, TFIIA, and the 90-kDa factor are promoter-specific.
Elastic Properties and Short‐to Medium‐Range Order in Glasses (2007)

Very different materials are named “Glass,” with Young's modulus ( E ) and Poisson's ratio (ν) extending from 5 to 180 GPa and from 0.1 to 0.4, respectively, in the case of bulk inorganic glasses. Although glasses have in common the lack of long‐range order in the atomic organization, they offer a wide range of structural features at the nanoscale and we show in this analysis that beside the essential role of elastic properties for materials selection in mechanical design, the elastic characteristics ( E , ν) at the continuum scale allow to get insight into the short‐ and medium‐range orders existing in glasses. In particular, ν, the atomic packing density ( C g ) and the glass network dimensionality appear to be strongly correlated. Maximum values for ν and C g are observed for metallic glasses (ν∼0.4 and C g &gt;0.7), which are based on cluster‐like structural units. Atomic networks consisting primarily of chains and layers units (chalcogenides, low Si‐content silicate, and phosphate glasses) correspond to ν&gt;0.25 and C g &gt;0.56. On the contrary, ν&lt;0.25 is associated with a highly cross‐linked network, such as in a‐SiO 2 , with a tri‐dimensional organization resulting in a low packing density. Moreover, the temperature dependence of the elastic moduli brings a new light on the structural changes occurring above the glass transition temperature and on the depolymerization rate in the supercooled liquid. The softening rate depends on the level of cooperativity of atomic movements at the source of the deformation process, with an obvious correlation with the “fragility” of the liquid.
Stem Cell Therapy in Articular Cartilage Injury (2012)

The natural history after articular cartilage injury is unclear. However, it is generally accepted that once articular cartilage is injured, its ability to regenerate is limited and that injury progresses to arthritis with time. Over the years various treatments have been developed and are used, such as arthroscopic debridement, microfracture, multiple drilling, osteochondral transfer, and Autologous Chondrocyte Implantation (ACI). These can be divided into treatment methods which apply cells and those which apply tissue. The former include abrasion chondroplasty, microfracture, multiple drilling, and ACI. The latter include osteochondral transfer and allograft. Combination treatments using both cells and tissues are new-generation ACI and microfracture with biomaterials. The clinical applications of stem cell therapy is still at an early stage, but shows much promise, particularly in the management of cartilage defects.
26.3: Multidirectional Asymmetrical Microlens‐Array Light Control Films for High Performance Reflective Liquid Crystal Displays (2002)

Abstract The multidirectional asymmetrical microlens array light control film (MAMA‐LCF) is developed to enhance the image brightness and contrast ratio of reflective liquid crystal displays. Through optimized designs and optical alignments, the MAMA‐LCF which is constructed with asymmetrical microlens arrays, leads to a ∼5× gain in brightness over the MgO standard white and 12:1 contrast ratio for color STN‐LCDs, 10× gain and 11.5:1 contrast ratio for PDLC, and 9× gain over the conventional Ch‐LCD. In each display, the light control film does not induce visible surface diffusion, moiré patterns and parallax.
Low-Complexity Method For Papr Reduction In Ofdm Based On Frame Expansion Parameter Selection (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
Anthrax toxin-mediated delivery of a cytotoxic T-cell epitope in vivo. (1996)

The protective antigen (PA) component of anthrax toxin mediates entry of the toxin's lethal factor (LF) and edema factor into the cytosolic compartment of mammalian cells. The amino-terminal domain of LF (LFn; 255 amino acids) binds LF to PA, and when fused to heterologous proteins, the LFn domain delivers such proteins to the cytoplasm in the presence of PA. In the current study, we fused a 9-amino acid cytotoxic T-lymphocyte (CTL) epitope (LLO91-99) from an intracellular pathogen, Listeria monocytogenes, to LFn and measured the ability of the resulting LFn-LLO91-99 fusion protein to stimulate a CTL response against the epitope in BALB/c mice. As little as 300 fmol of fusion could stimulate a response. The stimulation was PA-dependent and occurred with the peptide fused to either the amino terminus or the carboxyl terminus of LFn. Upon challenge with L. monocytogenes, mice previously injected with LFn-LLO91-99 and PA showed a reduction of colony-forming units in spleen and liver, relative to nonimmunized control mice. These results indicate that anthrax toxin may be useful as a CTL-peptide delivery system for research and medical applications.
Bragg grating performance in Er–Sn-doped germanosilicate fiber for simultaneous measurement of wide range temperature (to 500 °C) and strain (2003)

A fiber-optic sensing scheme for the simultaneous measurement of strain and a wide range of temperatures has been investigated by combining the properties of the fiber Bragg grating (FBG) and the fluorescence from a rare-earth-doped photosensitive fiber. The temperature-dependent fluorescence peak power ratio of the two peaks occurring around 1535 nm and 1552 nm from the amplified spontaneous emission due to the I13/24↔4I15/2 transitions in Er3+-doped tin–germanosilicate fiber, with 980 nm pumping, and the dual functionality of the FBG were exploited in this scheme. The sensor is based on a single FBG written in a small length (∼10 cm) of the above fiber, which can be used for the simultaneous measurement of strain and temperature over ranges of 0–1150 με and 22–500 °C, with root-mean-square errors of 36 με and 6 °C, respectively.
Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters (2006)

Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current state-of-the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time. We have also developed numerical techniques that maintain high accuracy while using single precision computation in order to exploit processor-level vector instructions. These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. Our results suggest that Desmond's parallel performance substantially surpasses that of any previously described code. For example, on a standard benchmark, Desmond's performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM's Blue Gene/L machine with 32K processors running its Blue Matter MD code.
Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens (2015)

A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1.
Strong blue photoluminescence from single-crystalline bismuth oxychloride nanoplates (2008)

Single-crystalline bismuth oxychloride (BiOCl) nanoplates with in-plane sizes of 200-500 nm and a thickness of 15-25 nm are synthesized by a simple solution route. Strong blue photoluminescence centred at 455 nm (∼2.72 eV) with very high quantum yields (Φ(PL)∼0.4) has been observed at room temperature, representing the first report of strong room temperature photoluminescence from bismuth oxyhalide nanomaterials. It is envisaged that bismuth oxychloride could join the family of non-cadmium based high-efficiency emitters; it has promising applications in various fields, especially in light emitting diodes, lasers and solar cells.
Effect of phthalates on the stability and performance of AgBF4-PVP membranes for olefin/paraffin separation. (2001)

The presence of a phthalate in dry polymer membranes consisting of polyvinylpyrrolidone (PVP) and AgBF4, AgBF4-PVP, provides long-term stability and better performance for the separation of propylene/propane gas mixtures.
Frequency Division Duplex Time Reversal (2011)

This paper proposes a new pre-coding technique called Frequency Division Duplex Time Reversal (FDD TR) for FDD Multiple Input Multiple Output (MIMO) wireless communications which relies on unquantized uncoded channel feedback. This technique is compared in terms of performance and overhead to Time Reversal (TR), 1bit Time Reversal (1bit TR). The performance assessment of a 16x2 MIMO system, is based on post receiver Signal To Noise Ratio (SINR) formulas and simulated indoor propagation channels. Results show that FDD TR outperforms 1bit TR in terms of overhead and throughput.
Characterization of Soluble, Disulfide Bond-Stabilized, Prokaryotically Expressed Human Thyrotropin Receptor Ectodomain* (1997)

To study the interaction of TSH receptor (TSHR) autoantibodies with receptor protein; it is necessary first to express the receptor in the proper conformation including the formation of correct disulfide bridges. However, the reducing environment of the Escherichia coli (E. coli) cytoplasm prevents the generation of protein disulfide bonds and limits the solubility and immunoreactivity of recombinant human TSHR (hTSHR) products. To circumvent these limitations, hTSHR complementary DNA encoding the extracellular domain (hTSHR-ecd; amino acids 21-415) was inserted into the vector pGEX-2TK by directional cloning and used to transform the thioredoxin reductase mutant strain of E. coli (Ad494), which allowed formation of disulfide bonds in the cytoplasm. After induction, the expressed soluble hTSHR-ecd fusion protein was detected by Western blot analysis using a monoclonal antibody directed against hTSHR amino acids 21-35. This showed that over 50% of the expressed hTSHR-ecd was soluble in contrast to expression in a wild-type E. coli (strain alpha F'), where the majority of the recombinant receptor was insoluble. The soluble recombinant receptor was affinity purified and characterized. Under nonreducing SDS-PAGE conditions, the soluble hTSHR-ecd migrated as refolded, disulfide bond-stabilized, multimeric species, whose formation was independent of fusion partner protein. This product was found to be biologically active as evidenced by the inhibition of the binding of 125I-TSH to the full-length hTSHR expressed in transfected CHO cells and was used to develop a competitive capture enzyme-linked immunosorbent assay for mapping of hTSHR antibody epitopes. Hence, hTSHR-ecd produced in bacteria with a thioredoxin reductase mutation was found to be highly soluble and biologically relevant.
Partial splenic embolization using polyvinyl alcohol foam, dextran, polystyrene, or silicone. An experimental study in dogs. (1982)

Partial splenic arterial embolization (50% reduction in flow) was evaluated in dogs using polyvinyl alcohol foam or microspheres (20-500 mu) made of dextran, polystyrene, or silicone. Dextran and polystyrene were found to be superior for several reasons: they were easier to use, did not shatter when agitated, and produced permanent, homogeneous, peripheral occlusion with only one administration. Partial embolization with dextran or polystyrene increased platelet levels within 1 week and markedly reduced splenic size with minimal if any collateral filling within 6 weeks. Microscopically, no acute infarction or necrosis was seen at 6 weeks; there was some fibrosis, but the remaining parenchyma appeared normal.
Calculation of composition of dilute cosputtered multicomponent films (1973)

A method for calculating the composition of cosputtered films from calculated deposition profiles and measured film thicknesses has been shown to be applicable to high concentrations of each of the components. Four new modifications are described for concentrations ranging down to 0.1% or less, which employ alternate ways of determining deposition rates. Several examples of cosputtered Cu–Ni alloys show that the rms accuracy of the methods is about 25% of the amount of the solute. Cosputtered films of Al–Si so analyzed have been used as standards for instrumental methods of analysis.
Interpretation of interference signals in label free integrated interferometric biosensors (2006)

In the future fast, simple and reliable biosensors will be needed to detect various analytes from different biosamples. This is due to fact that the needs of traditional health care are changing. In the future homecare of patients and peoples' responsibility for their own health will increase. Also, different wellness applications need new parameters to be analysed, reducing costs of traditional health care, which are increasing rapidly. One fascinating and promising sensor type for these applications is an integrated optical interferometric immunosensor, which is manufactured using organic materials. The use of organic materials opens up enormous possibilities to develop different biochemical functions. In label free biosensors the measurement is based on detecting changes in refractive index, which typically are in the range of 10<sup>-6</sup>-10<sup>-8</sup> [1]. In this research, theoretically generated interferograms are used to compare various signal processing methods. The goal is to develop an efficient method to analyse the interferogram. Different time domain signal processing methods are studied to determine the measuring resolution and efficiency of these methods. A low cost CCD -element is used in detecting the interferogram dynamics. It was found that in most of the signal processing methods the measuring resolution was mainly limited by pixel size. With calculation of Pearson's correlation coefficient, subpixel resolution was achieved which means that nanometer range optical path differences can be measured. This results in the refractive index resolution of the order of 10<sup>-7</sup>.
Ribonuclease D is not essential for the normal growth of Escherichia coli or bacteriophage T4 or for the biosynthesis of a T4 suppressor tRNA. (1983)

Transposon Tn10-mediated rearrangement was used to isolate a strain of Escherichia coli carrying a deletion in the rnd region which is known to encode the structural gene for the putative 3' tRNA processing nuclease, RNase D. Genetic analysis indicated that about 0.4-0.5 min of the chromosome in the 39.5-40.0 min region was deleted. The mutant strain was devoid of RNase D activity, but other RNase activities were unaffected. The viability of the mutant strain and its normal growth characteristics indicate that RNase D is not essential for E. coli survival. The normal plating efficiency in this mutant host of wild type T4 and a T4 psu1+-amber double mutant indicates that RNase D is also not required for T4 growth or psu1+-tRNA processing. The implications of these findings for the role of RNase D in bacterial and bacteriophage tRNA metabolism, and the possible involvement of alternative enzymes, are discussed.
Multiple Genetic Loci for Bone Mineral Density and Fractures (2008)

We have discovered common sequence variants that are consistently associated with bone mineral density and with low-trauma fractures in three populations of European descent. Although these variants alone are not clinically useful in the prediction of risk to the individual person, they provide insight into the biochemical pathways underlying osteoporosis.
Synthesis and characterization of novel fluorinated bistolane-type liquid crystals (2001)

Three series of fluorinated bistolane-type liquid crystals have been synthesized. Their mesomorphic properties were studied by optical polarizing microscopy and DSC. These compounds exhibit only a broad nematic phase with high clearing points, wide phase transition temperatures and low melting points. The effects of lateral fluoro-substitution and the introduction of the tetrafluorophenylene moiety are discussed in detail.
Time-varying management of data storage (2005)

The efficiency of large-scale applications is strongly de-pendent on good data management techniques. In this pa-per, we claim that the ability to specify data requirements in a time-varying manner facilitates data management and im-proves application efficiency. This is because requirements such as availability, bandwidth and latency can vary sig-nificantly with time. Consequently, the storage system can dynamically change the allocation of resources to data ob-jects. We describe how an application may specify these dynamic requirements using utility functions, and outline a strategy towards achieving an optimal allocation of re-sources to data objects. 1
Leukocytes Can Enhance Platelet-mediated Aggregation and Thromboxane Release via Interaction of P-selectin Glycoprotein Ligand 1 with P-selectin (2001)

Leukocytes can enhance platelet agonist--induced aggregation and thromboxane release in whole blood and platelet-rich plasma under shear conditions in vitro. Interaction of platelet P-selectin with leukocyte PSGL1 contributes substantially to these effects.
Speech and Language Processing: An Introduction to Natural Language Processing, Computational Linguistics, and Speech Recognition (2000)

This book takes an empirical approach to language processing, based on applying statistical and other machine-learning algorithms to large corpora.Methodology boxes are included in each chapter. Each chapter is built around one or more worked examples to demonstrate the main idea of the chapter. Covers the fundamental algorithms of various fields, whether originally proposed for spoken or written language to demonstrate how the same algorithm can be used for speech recognition and word-sense disambiguation. Emphasis on web and other practical applications. Emphasis on scientific evaluation. Useful as a reference for professionals in any of the areas of speech and language processing.
Early physiologic patterns in acute illness and accidents: toward a concept of circulatory dysfunction and shock based on invasive and noninvasive hemodynamic monitoring. (1996)

The aim of the present study was to explore methods, concepts, and techniques that provide recognition of circulatory deficiencies at the earliest possible time in the patient's illness. We used both the standard invasive pulmonary artery thermodilution catheter and noninvasive hemodynamic monitoring systems consisting of a new bioimpedance cardiac output device, pulse oximetry, transcutaneous oxygen (PtCO2) and carbon dioxide tensions as well as the transcutaneous oxygen tension/fraction of inspired oxygen ratio (PtCO2/FIO2). These three noninvasive systems were used to evaluate cardiac function, pulmonary function, and tissue perfusion, respectively. This approach to early noninvasive monitoring is based on recent evidence suggesting that poor tissue perfusion and oxygenation initiate circulatory dysfunction that leads to shock and organ failure. We studied 303 acute episodes of circulatory dysfunction and shock in 261 patients in a university-run county hospital; 75 were acute traumatic injuries and 109 acute nontrauma medical emergencies on admission to the emergency department, and 77 ICU patients with an acute illness or exacerbation of their current illness. The study was a prospective, descriptive study to identify early abnormal circulatory patterns reflecting the cardiac, pulmonary, and perfusion functions associated with death and with survival. We described noninvasively monitored patterns in individual illustrative cases, in common etiologic groups, and in physiologic categories representing various abnormal functional patterns. We found that hypotensive shock usually was preceded by episodes of high flow followed by low flow and inadequate tissue perfusion indicated by reduced PtCO2; this frequent pattern was modified by associated co-morbid conditions, especially hypovolemia, limited cardiac reserve capacity, age, hypertensive states, and increased body metabolism from infection, trauma, stress, exercise, temperature, and endocrine disorders. Reduced pulmonary function occurred in 18% of emergency patients; these were usually patients with thoracic trauma, severe hypovolemia, head injuries, chronic obstructive pulmonary disease, asthma, drug overdose, and central nervous system failure (massive stroke and coma). We concluded that noninvasive measurements identify early circulatory problems reliably and provide objective criteria for physiologic analysis as well as for definition of therapeutic goals and titration of therapy.