gebhart/patrepeval huggingface dataset:
List decoding of polar codes (2011)

We describe a successive-cancellation list decoder for polar codes, which is a generalization of the classic successive-cancellation decoder of Arikan. In the proposed list decoder, up to L decoding paths are considered concurrently at each decoding stage. Simulation results show that the resulting performance is very close to that of a maximum-likelihood decoder, even for moderate values of L. Thus it appears that the proposed list decoder bridges the gap between successive-cancellation and maximum-likelihood decoding of polar codes. The specific list-decoding algorithm that achieves this performance doubles the number of decoding paths at each decoding step, and then uses a pruning procedure to discard all but the L “best” paths. In order to implement this algorithm, we introduce a natural pruning criterion that can be easily evaluated. Nevertheless, straightforward implementation still requires O(L · n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) time, which is in stark contrast with the O(n log n) complexity of the original successive-cancellation decoder. We utilize the structure of polar codes to overcome this problem. Specifically, we devise an efficient, numerically stable, implementation taking only O(L · n log n) time and O(L · n) space.
Blind channel identification based on second-order statistics: a frequency-domain approach (1995)

In this communication, necessary and sufficient conditions are presented for the unique blind identification of possibly nonminimum phase channels driven by cyclostationary processes. Using a frequency domain formulation, it is first shown that a channel can be identified by the second-order statistics of the observation if and only if the channel transfer function does not have special uniformly spaced zeros. This condition leads to several necessary and sufficient conditions on the observation spectra and the channel impulse response. Based on the frequency-domain formulation, a new identification algorithm is proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Integrating Microseismic Monitoring With Well Completions, Reservoir Behavior, and Rock Mechanics (2009)

Abstract Microseismic monitoring has proved to be a valuable technology for assessing and optimizing hydraulic fracturing in a host of tight sand and gas shale reservoirs. Parameters such as fracture length, height, azimuth, and asymmetry are readily identified, but this technology can also be useful for understanding staging effectiveness, stimulated volume, complexity and network growth, natural fractures, stress azimuth and changes in that azimuth, fault interactions, and reservoir behavior as a result of the treatment. Various published data sets are examined to show how both quantitative and qualitative information about the fracturing behavior, completion effectiveness, and reservoir behavior can be usefully extracted from the microseismic data. Examples will include both vertical and horizontal wells, relatively planar and network fracture systems, various staging and diversion techniques, and faulted and naturally fractured reservoir response.
Arginase Is Inoperative in Developing Soybean Embryos1 (1999)

Arginase (EC 3.5.3.1) transcript level and activity were measured in soybean (Glycine max L.) embryos from the reserve deposition stage to postgermination. Using a cDNA probe for a small soybean arginase gene family, no transcript was detected in developing embryos. However, arginase transcripts increased sharply on germination, reaching a maximum at 3 to 5 d after germination. There was low but measurable in vitro arginase specific activity in developing embryos (less than 6% of seedling maximum). During germination arginase specific activity increased in parallel with the sharply increasing arginase transcript level. Seedling arginase activity was largely localized in cotyledons. Arginase activity was assayed in vivo by measuring urea accumulation in a urease-deficient mutant. No urea was detected in developing embryos, whereas accumulated urea paralleled arginase specific activity and transcript level in germinating seedlings. As in planta embryos, cultured cotyledons did not accumulate urea when arginine (Arg) was provided with other amino acids in a "mock" seed-coat exudate. Arg as the sole nitrogen source was converted to urea but did not support cotyledon growth. There appeared to be a lack of recruitment of the low-level arginase activity to hydrolyze free Arg in developing embryos, thus avoiding a futile urea cycle.
Microencapsulation selection for isolation of yeast mutants with increased secretion of Aspergillus awamori glucoamylase (1993)

We have developed a microencapsulation selection method which allows the rapid and quantitative screening of >10(6) yeast cells for enhanced secretion of Aspergillus awamori glucoamylase. The method provides a 400-fold single-pass enrichment for high-secreting mutants, and can be straightforwardly adapted for application to growth-based selection schemes with other microorganisms and enzymes.
Parameterized modeling and recognition of activities (2002)

A framework for modeling and recognition of temporal activities is proposed. The modeling of sets of exemplar activities is achieved by parameterizing their representation in the form of principal components. Recognition of spatio-temporal variants of modeled activities is achieved by parameterizing the search in the space of admissible transformations that the activities can undergo. Experiments on recognition of articulated and deformable object motion from image motion parameters are presented.
Characterization of excitatory prostanoid receptors in the human umbilical artery in vitro (1999)

1. 5-HT and the prostanoid TP receptor agonists, U46619 and I-BOP, constricted the human umbilical artery with pEC50 values of 7.3+/-0. 2, 6.7+/-0.1, and 7.3+/-0.2, respectively. The selective TP receptor antagonist, GR32191 (0.1 microM), shifted the concentration-effect curves to U46619 and I-BOP to the right, but had no effect on the response to 5-HT. 2. The natural prostaglandins, PGF2alpha and PGE2, caused concentration-dependent contraction with pEC50 values of 5.2+/-0.2 and 4.9+/-0.2, respectively. PGD2 was a partial agonist with a pEC50 of 5.24+/-0.03. GR32191 (0.1 microM) inhibited the responses to all of these compounds suggesting that they produce contraction by acting at TP receptors. 3. Sulprostone failed to elicit contraction in the human umbilical artery at concentrations up to 4.4 microM suggesting the absence of EP1 and EP3 receptors. Despite this, 17-phenyltrinor PGE2 and GR63799 both induced contraction at concentrations above 1 microM, but the effects were sensitive to GR32191 (0.1 microM). 4. Fluprostenol had no effect on the human umbilical artery at concentrations up to 17 microM suggesting the absence of FP receptors. Cloprostenol was ineffective in two tissues, but caused contraction in one tissue at the highest concentration tested (1.7 microM). However, this response was abolished in the presence of GR32191 (0.1 microM). 5. The effects of four TP receptor antagonists were assessed by global non-linear regression analysis. GR32191, SQ29548, SQ30741, and ICI192605 competitively inhibited responses to U46619 with pKb values of 8.0+/-0.1, 7.6+/-0.1, 7.0+/-0. 2 and 8.1+/-0.1, respectively. 6 These results suggest that the human umbilical artery functionally expresses TP receptors, but not EP1, EP2 or FP receptors.
Inhibition of malignant cell growth by 311, a novel iron chelator of the pyridoxal isonicotinoyl hydrazone class: effect on the R2 subunit of ribonucleotide reductase. (2001)

The key roles of iron and iron proteins in cell proliferation make them potential targets for cancer therapy. However, clinical trials directed toward perturbation of tumor iron homeostasis by iron chelation have been limited to the use of deferoxamine (DFO). There is thus a need to develop agents with greater efficacy. In the present study, we investigated the mechanism of cytotoxicity of 311 (2-hydroxy-1-naphthylaldehyde benzoyl hydrazone), a novel iron chelator of the pyridoxal isonicotinoyl class. We found that 311 inhibited the growth of CCRF-CEM cells in a time- and concentration-dependent fashion with an IC(50) that was approximately 20-fold lower than that of DFO. 311 also inhibited the growth of breast, bladder, and head and neck cancer cell lines. Using electron spin resonance (ESR) spectroscopy analysis, we found that a 12-h exposure of CCRF-CEM cells to 311 inhibited the tyrosyl radical ESR signal of the R2 subunit of ribonucleotide reductase. However, overproduction of the R2 subunit in hydroxyurea-resistant CCRF-CEM cells was associated with a decrease in sensitivity of cells to 311 but not to DFO. Our studies show that 311 is a more potent cytotoxic agent than DFO, with activity against both hematopoietic and nonhematopoietic cell lines regardless of their p53 status. Furthermore, the ESR studies suggest that inhibition of the R2 subunit of ribonucleotide reductase is at least one mechanism by which 311 blocks cell proliferation.
TNFα as Therapeutic Target: New Drugs, More Applications (2002)

TNFalpha is a crucial cytokine in the establishment and maintenance of inflammation in multiple autoimmune diseases. With the introduction of infliximab and etanercept, two injectable biologic TNFalpha blocking drugs are now available. Both are effective in the treatment of rheumatoid arthritis, reducing clinical inflammation and damage to bones. In addition, infliximab is FDA-approved for the treatment of Crohn's disease. More recent controlled trials have shown effectiveness for TNFalpha blockers in psoriasis, psoriatic arthritis, and ankylosing spondylitis. Further trials are underway in diverse inflammatory conditions including including uveitis, sarcoidosis, Behcet's syndrome, and graft versus host disease. Although the safety profile has been generally excellent, the rare development of reactivation tuberculosis, anti double-stranded DNA antibodies, or a demyelination syndrome point out the need for further close follow-up of treated patients. New formulations of recombinant anti-TNFalpha biologics undergoing clinical trials use modifications to reduce antigenicity, increase the half-life, and maintain or extend the efficacy of these agents. Future development of TNFalpha antagonists is turning to small molecule inhibitors. The inhibition of the TNFalpha signaling cascade is under study using blockers of the p38, JNK, and ERK kinases, and by antagonists of transcription factor NF-kappaB activation. The goal of this approach is to develop compounds that are orally available, have increased selectivity compared to generalized blockade of TNFalpha, yet are therapeutically useful for a range of chronic inflammatory diseases.
Cloning and characterization of a novel human histone deacetylase, HDAC8 (2000)

Histone deacetylases (HDACs) are a growing family of enzymes implicated in transcriptional regulation by affecting the acetylation state of core histones in the nucleus of cells. HDACs are known to have key roles in the regulation of cell proliferation [Brehm, Miska, McCance, Reid, Bannister and Kouzarides (1998) Nature (London) 391, 597-600], and aberrant recruitment of an HDAC complex has been shown to be a key step in the mechanism of cell transformation in acute promyelocytic leukaemia [Grignani, De Matteis, Nervi, Tomassoni, Gelmetti, Cioce, Fanelli, Ruthardt, Ferrara, Zamir et al. (1998) Nature (London) 391, 815-818; Lin, Nagy, Inoue, Shao, Miller and Evans (1998), Nature (London) 391, 811-814]. Here we present the complete nucleotide sequence of a cDNA clone, termed HDAC8, that encodes a protein product with similarity to the RPD3 class (I) of HDACs. The predicted 377-residue HDAC8 product contains a shorter C-terminal extension relative to other members of its class. After expression in two cell systems, immunopurified HDAC8 is shown to possess trichostatin A- and sodium butyrate-inhibitable HDAC activity on histone H4 peptide substrates as well as on core histones. Expression profiling reveals the expression of HDAC8 to various degrees in every tissue tested and also in several tumour lines. Mutation of two adjacent histidine residues within the predicted active site severely decreases activity, confirming these residues as important for HDAC8 enzyme activity. Finally, linkage analysis after radiation hybrid mapping has localized HDAC8 to chromosomal position Xq21.2-Xq21.3. These results confirm HDAC8 as a new member of the HDAC family.
Role of FGF1, FGF2 and FGF7 in the development of the pancreas from control and streptozotocin‐treated hamsters (2006)

Although progress has been made with respect to the growth and transcription factors implicated in pancreatic development, many questions remain unsolved. It has been established that during embryonic life, both endocrine and acinar cells are derived from pancreatic epithelial precursor cells. Growth factors control the proliferation of precursor cells and their ability to differentiate into mature cells, both in pre-natal and in early post-natal life. Pancreatic development during the early post-natal period is an area of great interest for many scientists. In this study we have examined the structure characteristics, functional and proliferative activity of control and diabetic hamster pancreatic ductal, exocrine and beta cells, following treatment with FGFs 1, 2 and 7 in vitro. Light and electron microscopic studies indicated active synthetic processes in these cells under the influence of the investigated FGFs. In our experimental model of diabetes, the labelling index of the cells was significantly higher than in corresponding control groups of hamsters. We established that FGF2 at a concentration of 10 ng/l was responsible for the most prominent effect on ductal cells and beta cells in the diabetic groups. FGF1 at a concentration of 10 ng/l displayed the highest stimulatory effect on exocrine cells in the diabetic groups at post-natal day 10. Taken together these data strongly suggest that FGF1 and FGF2 induce proliferation of pancreatic epithelial cells during the early post-natal period whereas FGF7 is not strictly specific for pancreatic cell proliferation.
Long-Term Risk Factors for Stroke (2006)

High blood pressure and diabetes retain their importance as stroke risk factors also over an extended follow-up into old age. A family history of cardiovascular disease was not significantly related to outcome. Transient ischemic attacks, atrial fibrillation, stress, smoking, and a history of chest pain were associated with outcome only for the first or the first 2 periods. High body mass index and antihypertensive medication at baseline emerged as risk factors in the second and third decades.
Methods for Fatigue Strength Improvement of the Weld Structure (II) - Post Weld Improvement Methods - (2012)

일반적으로 용접 구조물의 피로강도는 용접부와 같은 기하학적 불연속부에 있어서의 응력집중에 의해 결정된다. 이때 응력집중은 구조적 형상에 의한 전체적인 요인 및 용접부 비드 등의 국부적인 요인의 의해 영향을 받는 것으로 알려져 있으며, 기계 및 구조물의 80% 이상이 피로에 의해서 여러 가지 형태의 원인으로 파손되고 있다고 알려져 있다. 좀 더 구체적으로 구분하면, 용접부의 피로 수명을 저하시키는 원인으로는 앞서 설명한 바와 같이 구조적 불연속 및 용접변형에 의한 부정합(misalignment), 국부적 응력 집중의 영향, 언더컷, 블로우 홀, 개재물 등에 의한 용접결함 그리고 용접 인장 잔류응력의 영향 등 크게 네 가지로 구분될 수 있다. 피로파괴는 때때로 매우 위험한 결과를 초래하기 때문에 이를 방지하고 높은 수명시간을 확보하기 위해서는 설계-시공-후처리 각각의 단계에서 다음과 같은 사항들이 고려되어야 한다. 첫째로 용접연결부의 설계 단계에서는 진동 및 공명(resonance)이 발생하는 위치를 되도록 피하여 피로하중이 최소화될 수 있게 이뤄져야 하며, 부식 환경의 노출 최소화 및 응력집중계수를 낮게 설계하여야 한다. 둘째로 시공단계에서는 모재와 용가재, 용접공정의 올바른 선택, 시공 전 그루브 형상 및 표면 준비 등의 철저한 준수 및 작업자의 숙련도 검증 등의 사항이 요구된다. 마지막으로 시공이 끝나면 적절한 후처리(post weld improvement)를 거쳐 최종적으로 피로강도를 향상시킬 수 있는데, 본회에서는 앞서 기고한 용접 연결부의 설계 방안에 이어 그 두 번째로 용접후처리 단계에서 실시할 수 있는 용접부 피로수명 연장기법에 대해 IIW Recommendation
Evaluation of a rapid method of extracting DNA from stool samples for use in hybridization assays (1989)

The ability of the Extractor system (Molecular Biosystems, Inc., San Diego, Calif.) to isolate nucleic acid (NA) from stool samples for use in hybridization assays was investigated. Crude NA was recovered from 45 of 50 stool samples by using this system. The amount of NA recovered varied considerably depending on the microbial flora present in the sample (mean +/- standard deviation, 50.2 +/- 46.7 micrograms; range, 2 to 228 micrograms) but did not correlate with the consistency of the sample. Samples containing primarily gram-positive organisms or yeast cells gave lower yields of NA (less than 10 micrograms) than those containing gram-negative bacilli. The five samples which did not yield NA were sterile when cultured aerobically on blood agar plates. Samples of the 45 stools yielding NA were inoculated into broth and grown overnight, and a 10-microliters sample of broth was spotted onto nitrocellulose filters. The NA samples recovered from the Extractor column were applied to nylon membranes by using the Centri-dot system. The NA on the broth blots and the NA on the Centri-dot filters were hybridized with a 310-base-pair probe specific for the 2"-O-aminoglycoside adenylyltransferase [ANT(2")] resistance gene. The Extractor-Centri-dot system demonstrated 61.9% sensitivity and 95.8% specificity in detecting the ANT(2") gene in stool samples containing colonies demonstrating the ANT(2") phenotype. The positive and negative predictive values of the NA blot were 92.8 and 74.2%, respectively.
The Taxoids (1997)

Paclitaxel and docetaxel belong to the taxoid family, a new class of antineoplastic drugs. The name taxoids refers to compounds, natural or modified, having a taxane skeleton.
The Effect of Recombinant Factor VIIa on Coagulopathic Pigs with Grade V Liver Injuries (2002)

rFVIIa reduces blood loss in hypothermic, dilutionally coagulopathic pigs with grade V injuries when used as an adjunct to packing. Increasing the dose does not enhance the hemostatic effect.
Enhancement of cellular and humoral immune responses to hepatitis C virus core protein using DNA-based vaccines augmented with cytokine-expressing plasmids (1997)

Development of a broad based cellular and humoral immune response to hepatitis C virus (HCV) structural proteins may be important for irradication of infection. DNA-based immunization is a promising approach to generate HCV-specific immune responses. Previous studies of DNA-based immunizations in mice using an HCV core DNA expression plasmid (pHCV2-2) demonstrated an efficient CTL response against HCV core epitopes; however, the humoral and Th cell proliferative responses were found to be weak. To enhance the immunogenicity of this nonsecreted viral structural protein at the B and T cell level, we coimmunized mice with pHCV2-2 and DNA expression constructs encoding for mouse IL-2, IL-4, and granulocyte-macrophage CSF proteins. Under these experimental conditions, a seroconversion frequency to anti-HCV core increased from 40 to 80% in immunized mice. The CD4+ inflammatory T cell proliferative responses as well as CD8+ CTL activity to HCV core protein were enhanced substantially after coimmunization with the IL-2 and granulocyte-macrophage CSF DNA expression constructs. In contrast, coimmunization with an IL-4-producing construct induced differentiation of Th cells toward a Th0 subtype and suppressed HCV core-specific CTL activity. Taken together, these studies emphasize that generation of antiviral immune responses using DNA-based immunization may be modified by local cytokine production at the site of Ag presentation.
Diffraction imaging by focusing-defocusing: An outlook on seismic superresolution (2004)

Abstract Diffractions always need more advertising. It is true that conventional seismic processing and migration are usually successful in using specular reflections to estimate subsurface velocities and reconstruct the geometry and strength of continuous and pronounced reflectors. However, correct identification of geological discontinuities, such as faults, pinch-outs, and small-size scattering objects, is one of the main objectives of seismic interpretation. The seismic response from these structural elements is encoded in diffractions, and diffractions are essentially lost during the conventional processing/migration sequence. Hence, we advocate a diffraction-based, data-oriented approach to enhance image resolution—as opposed to the traditional image-oriented techniques, which operate on the image after processing and migration. Even more: it can be shown that, at least in principle, processing of diffractions can lead to superresolution and the recovery of details smaller than the seismic wavelength. The so-called reflection stack is capable of effectively separating diffracted and reflected energy on a prestack shot gather by focusing the reflection to a point while the diffraction remains unfocused over a large area. Muting the reflection focus and defocusing the residual wavefield result in a shot gather that contains mostly diffractions. Diffraction imaging applies the classical (isotropic) diffraction stack to these diffraction shot gathers. This focusing-muting-defocusing approach can successfully image faults, small-size scattering objects, and diffracting edges. It can be implemented both in model-independent and model-dependent contexts. The resulting diffraction images can greatly assist the interpreter when used as a standard supplement to full-wave images.
The Role of Pyruvate Ferredoxin Oxidoreductase in Pyruvate Synthesis during Autotrophic Growth by the Wood-Ljungdahl Pathway (2000)

Pyruvate:ferredoxin oxidoreductase (PFOR) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA and CO(2). The catalytic proficiency of this enzyme for the reverse reaction, pyruvate synthase, is poorly understood. Conversion of acetyl-CoA to pyruvate links the Wood-Ljungdahl pathway of autotrophic CO(2) fixation to the reductive tricarboxylic acid cycle, which in these autotrophic anaerobes is the stage for biosynthesis of all cellular macromolecules. The results described here demonstrate that the Clostridium thermoaceticum PFOR is a highly efficient pyruvate synthase. The Michaelis-Menten parameters for pyruvate synthesis by PFOR are: V(max) = 1.6 unit/mg (k(cat) = 3.2 s(-1)), K(m)(Acetyl-CoA) = 9 micrometer, and K(m)(CO(2)) = 2 mm. The intracellular concentrations of acetyl-CoA, CoASH, and pyruvate have been measured. The predicted rate of pyruvate synthesis at physiological concentrations of substrates clearly is sufficient to support the role of PFOR as a pyruvate synthase in vivo. Measurements of its k(cat)/K(m) values demonstrate that ferredoxin is a highly efficient electron carrier in both the oxidative and reductive reactions. On the other hand, rubredoxin is a poor substitute in the oxidative direction and is inept in donating electrons for pyruvate synthesis.
Mechanisms of Cellular Uptake of Cell-Penetrating Peptides (2011)

Recently, much attention has been given to the problem of drug delivery through the cell-membrane in order to treat and manage several diseases. The discovery of cell penetrating peptides (CPPs) represents a major breakthrough for the transport of large-cargo molecules that may be useful in clinical applications. CPPs are rich in basic amino acids such as arginine and lysine and are able to translocate over membranes and gain access to the cell interior. They can deliver large-cargo molecules, such as oligonucleotides, into cells. Endocytosis and direct penetration have been suggested as the two major uptake mechanisms, a subject still under debate. Unresolved questions include the detailed molecular uptake mechanism(s), reasons for cell toxicity, and the delivery efficiency of CPPs for different cargoes. Here, we give a review focused on uptake mechanisms used by CPPs for membrane translocation and certain experimental factors that affect the mechanism(s).