gebhart/patrepeval huggingface dataset:
Quantitative Structure-Activity Relationships of Selective Antagonists of Glucagon Receptor Using QuaSAR Descriptors (2006)

In the present paper, quantitative structure activity relationship (QSAR) approach was applied to understand the affinity and selectivity of a novel series of triaryl imidazole derivatives towards glucagon receptor. Statistically significant and highly predictive QSARs were derived for glucagon receptor inhibition by triaryl imidazoles using QuaSAR descriptors of molecular operating environment (MOE) employing computer-assisted multiple regression procedure. The generated QSAR models revealed that factors related to hydrophobicity, molecular shape and geometry predominantly influences glucagon receptor binding affinity of the triaryl imidazoles indicating the relevance of shape specific steric interactions between the molecule and the receptor. Further, QSAR models formulated for selective inhibition of glucagon receptor over p38 mitogen activated protein (MAP) kinase of the compounds in the series highlights that the same structural features, which influence the glucagon receptor affinity, also contribute to their selective inhibition.
Implementation of H.264 decoder on general-purpose processors with media instructions (2003)

As emerging video coding standards, e.g. H.264, aim at high-quality video contents at low bit-rates, the encoding and decoding processes require much more computation than most existing standards do. This paper analyzes software implementation of a real-time H.264 decoder on general-purpose processors with media instructions. Specifically, we discuss how to optimize the speed of H.264 decoders on Intel Pentium 4 processors. This paper first analyzes the reference implementation to identify the time-consuming modules. Our study shows that a number of components, e.g., motion compensation and inverse integer transform, are the most time-consuming modules in the H.264 decoder. Second, we present a list of performance optimization methods using media instructions to improve the efficiency of these modules. After appropriate optimizations, the decoder speed improved by more than 3x---it can decode a 720&times;480 resolution video sequence at 48 frames per second on 2.4GHz Intel Pentium 4 processors compared to reference software’s 12 frames per second. The optimization techniques demonstrated in this paper can also be applied to other video/image processing applications. Additionally, after presenting detailed application behavior on general-purpose processors, this paper discusses a few recommendations on how to design future efficient/powerful video/image applications/standards with given hardware implications.
New Taxanes fromTaxus chinensis (1990)

Two new taxane diterpenes, decinnamoyltaxagifine ( 3) and decinnanioyltaxagifine acetate ( 2), have been isolated from the leaves and stems of TAXUS CHINENSIS. Their structures were elucidated by spectroscopic methods. Their (13)C-NMR chemical shifts were assigned.
A stable complex between integrase and viral DNA ends mediates human immunodeficiency virus integration in vitro. (1994)

Retroviral replication depends on integration of the viral genome into a chromosome of the host cell. The steps in this process are orchestrated in vivo by a large nucleoprotein complex and are catalyzed by the retroviral enzyme integrase. Several biochemical properties of the in vivo nucleoprotein complex were reproduced in vitro with purified integrase of human immunodeficiency virus type 1 and model viral DNA substrates. A stable complex between integrase and viral DNA was detected as an early intermediate in the integration reaction. After formation of this initial complex, the enzyme processively catalyzed the 3' end processing and strand transfer steps in the reaction. Complexes containing only purified integrase and the model viral DNA end were stable under a variety of conditions and efficiently used nonviral DNA molecules as integration targets. These complexes required a divalent cation for their formation, and their stability was highly dependent on the 5'-terminal dinucleotide of the viral DNA, for which no functional role has previously been defined. Thus, interactions between integrase and the extreme ends of the viral DNA molecule may be sufficient to account for the stability of the in vivo integration complex.
Learning-based configuration estimation of a multi-segment continuum robot (2012)

In this paper, we present a visual learning algorithm for estimating the configuration of a multisegment continuum robot designed for surgery. Our algorithm interpolates a stereo visual feature descriptor manifold using Radial Basis Functions (RBFs) to estimate configuration pose angles. Results are shown on a 3-segment snake robot, where rotational accuracy in the range of 1° -2° is achieved.
Using emulation to understand and improve wireless networks and applications (2005)

Researchers have long faced a fundamental tension between the experimental realism of wireless testbeds on one hand, and the control and repeatability of simulation on the other hand. To overcome the stark tradeoff of these traditional alternatives, we are developing a wireless emulator that enables both realistic and repeatable experimentation by leveraging physical layer emulation.We discuss the design and implementation of a prototype wireless emulator, and show how this emulator can be leveraged to provide insight into wireless network and application behaviour. Our experience shows that, compared to simulation, our emulator-based approach provides us with a better understanding of real-world wireless network performance, and enables us to quickly deploy our research into an operational wireless network, while still allowing us to enjoy the benefits of a controlled experimental environment.
Effect of Translational Signals on mRNA Decay in Bacillus subtilis (2003)

A 254-nucleotide model mRNA, designated deltaermC mRNA, was used to study the effects of translational signals and ribosome transit on mRNA decay in Bacillus subtilis. DeltaermC mRNA features a strong ribosome-binding site (RBS) and a 62-amino-acid-encoding open reading frame, followed by a transcription terminator structure. Inactivation of the RBS or the start codon resulted in a fourfold decrease in the mRNA half-life, demonstrating the importance of ternary complex formation for mRNA stability. Data for the decay of deltaermC mRNAs with stop codons at positions increasingly proximal to the translational start site showed that actual translation--even the formation of the first peptide bond--was not important for stability. The half-life of an untranslated 3.2-kb deltaermC-lacZ fusion RNA was similar to that of a translated deltaermC-lacZ mRNA, indicating that the translation of even a longer RNA was not required for wild-type stability. The data are consistent with a model in which ribosome binding and the formation of the ternary complex interfere with a 5'-end-dependent activity, possibly a 5'-binding endonuclease, which is required for the initiation of mRNA decay. This model is supported by the finding that increasing the distance from the 5' end to the start codon resulted in a 2.5-fold decrease in the mRNA half-life. These results underscore the importance of the 5' end to mRNA stability in B. subtilis.
Terfenadine, an H 1 Antihistamine, Inhibits Histamine Release In Vivo in the Human (1990)

A double-blind, placebo-controlled clinical trial was performed on 12 subjects with allergic rhinitis to evaluate the effect of 1-wk pretreatment with terfenadine (60 mg twice daily or 300 mg twice daily) on the response to sequential nasal challenges with allergen and histamine. The response to allergen challenge was monitored by counting sneezes and by quantifying the levels of histamine, kinins, TAME-esterase activity, and albumin in recovered nasal lavages. Following histamine challenges, sneezing and the levels of albumin were recorded. Terfenadine significantly reduced sneezing and the levels of histamine, kinins, TAME-esterase activity, and albumin seen after antigen challenge. In addition, terfenadine reduced the increase in sneezing and vascular permeability, as measured by albumin levels, following challenge with histamine. No significant differences were found between the two doses of terfenadine. Our data suggest that terfenadine not only antagonizes the H1 activity of released histamine during the immediate allergic reaction but also, at currently prescribed doses, inhibits the release of histamine.
Testosterone Therapy For Human Immunodeficiency Virus-Positive Men With and Without Hypogonadism (1999)

This study was designed to evaluate the safety and effectiveness of testosterone therapy for clinical symptoms of hypogonadism (low libido, low mood, low energy, loss of appetite/weight) in human immunodeficiency virus-positive men with CD4 cell counts less than 400 cells/mm3 and deficient or low normal serum testosterone levels. The trial consisted of 8 weeks of open treatment with 400 mg of intramuscular testosterone cypionate biweekly. Responders were maintained at this dosage for another 4 weeks and then were randomized in a double-blind, placebo-controlled, 6-week discontinuation trial. Of the 112 men who completed at least 8 weeks of treatment, 102 (91%) were rated as responders on a global assessment of sexual desire/function. Of the 34 study completers with major depressive disorder and/or dysthymia, 79% reported significant improvement in mood at week 8. Average weight change was a gain of 3.7 pounds, with 45% gaining more than 5 pounds. Eighty-four men entered and 77 completed the double-blind phase; of these, 78% of completers randomized to testosterone and 13% randomized to placebo maintained their response. No significant medical or immunologic adverse effects were identified. Testosterone therapy was well tolerated and effective in ameliorating symptoms of clinical hypogonadism, and equally so for men with and without testosterone deficiency. For patients with major depression and/or dysthymia, improvement was equal to that achieved with standard antidepressants.
Effect of Aging on Regulation of Brain Stem Circulation During Hypotension (1997)

This study was designed to determine age related changes in autoregulatory responses of the brain stem circulation in vivo. In anesthetized adult (4 to 6 months, n = 8) and aged (24 to 26 months, n = 7) Sprague-Dawley rats, local CBF to the brain stem was determined with laser-Doppler flowmetry and diameters of the basilar artery and its branches were measured through an open cranial window during stepwise hemorrhagic hypotension. In aged rats, the lower limit of CBF autoregulation shifted upward to 60 to 75 mm Hg from 30 to 45 mm Hg in adult rats. Dilator responses of the basilar artery (baseline diameter: 254 +/- 15 microns), large branch (109 +/- 23 microns), and small branch (44 +/- 10 microns) to hypotension were much smaller in aged rats than in adult rats. The maximum change in diameter of the basilar artery during profound hypotension was significantly smaller in aged rats (11 +/- 8%) than that in adult ones (23 +/- 12%, P < 0.05); that of the large branch was 12 +/- 8% versus 33 +/- 17% (P < 0.005); and that of the small branch was 17 +/- 7% versus 40 +/- 13% (P < 0.0005), suggesting greater attenuation of the responses in the smaller vessels. Thus, this study provides direct evidence that aging diminishes the compensatory dilatation of brain stem arterioles and arteries during hypotension and modifies the autoregulatory plateau of CBF, which seems to increase the risk of the brain stem ischemia during hypotensive conditions.
Crystallinity of inorganic films grown by atomic layer deposition: Overview and general trends (2013)

Atomic layer deposition (ALD) is gaining attention as a thin film deposition method, uniquely suitable for depositing uniform and conformal films on complex three-dimensional topographies. The deposition of a film of a given material by ALD relies on the successive, separated, and self-terminating gas–solid reactions of typically two gaseous reactants. Hundreds of ALD chemistries have been found for depositing a variety of materials during the past decades, mostly for inorganic materials but lately also for organic and inorganic–organic hybrid compounds. One factor that often dictates the properties of ALD films in actual applications is the crystallinity of the grown film: Is the material amorphous or, if it is crystalline, which phase(s) is (are) present. In this thematic review, we first describe the basics of ALD, summarize the two-reactant ALD processes to grow inorganic materials developed to-date, updating the information of an earlier review on ALD [R. L. Puurunen, J. Appl. Phys. 97, 121301 (2005)], and give an overview of the status of processing ternary compounds by ALD. We then proceed to analyze the published experimental data for information on the crystallinity and phase of inorganic materials deposited by ALD from different reactants at different temperatures. The data are collected for films in their as-deposited state and tabulated for easy reference. Case studies are presented to illustrate the effect of different process parameters on crystallinity for representative materials: aluminium oxide, zirconium oxide, zinc oxide, titanium nitride, zinc zulfide, and ruthenium. Finally, we discuss the general trends in the development of film crystallinity as function of ALD process parameters. The authors hope that this review will help newcomers to ALD to familiarize themselves with the complex world of crystalline ALD films and, at the same time, serve for the expert as a handbook-type reference source on ALD processes and film crystallinity.
Cell-based and antibody-mediated immunotherapies directed against leukemic stem cells in acute myeloid leukemia: Perspectives and open issues (2020)

Despite new insights in molecular features of leukemic cells and the availability of novel treatment approaches and drugs, acute myeloid leukemia (AML) remains a major clinical challenge. In fact, many patients with AML relapse after standard therapy and eventually die from progressive disease. The basic concept of leukemic stem cells (LSC) has been coined with the goal to decipher clonal architectures in various leukemia-models and to develop curative drug therapies by eliminating LSC. Indeed, during the past few years, various immunotherapies have been tested in AML, and several of these therapies follow the strategy to eliminate relevant leukemic subclones by introducing LSC-targeting antibodies or LSC-targeting immune cells. These therapies include, among others, new generations of LSC-eliminating antibody-constructs, checkpoint-targeting antibodies, bi-specific antibodies, and CAR-T or CAR-NK cell-based strategies. However, responses are often limited and/or transient which may be due to LSC resistance. Indeed, AML LSC exhibit multiple forms of resistance against various drugs and immunotherapies. An additional problems are treatment-induced myelotoxicity and other side effects. The current article provides a short overview of immunological targets expressed on LSC in AML. Moreover, cell-based therapies and immunotherapies tested in AML are discussed. Finally, the article provides an overview about LSC resistance and strategies to overcome resistance.
Haptoglobin Phenotypes in Dementia of the Alzheimer Type (1986)

Previous investigations of the association of haptoglobin (Hp) with dementia of the Alzheimer type (DAT) have reported contradictory results. In the present study, we phenotyped 69 patients clinically diagnosed as having DAT and, for comparison, 64 cognitively intact individuals. We failed to find a significant association between either of the Hp alleles and DAT. Instead, we observed a nonsignificant decrease in the Hp-1 gene frequency in the DAT population (0.34) as compared to our normal elderly comparison group (0.41).
Clinical Supervision: Findings from an Australian Research Study (2010)

The findings from a ground-breaking state-wide randomized controlled trial (RCT) of clinical supervision (CS) of nurses working in 17 mental health facilities in Queensland are discussed. Recommendations based on the study are also highlighted.
The Fc-region of a new class of intact bispecific antibody mediates activation of accessory cells and NK cells and induces direct phagocytosis of tumour cells (2000)

Bispecific antibodies (bsAb) are considered as promising tools for the elimination of disseminated tumour cells in a minimal residual disease situation. The bsAb-mediated recruitment of an immune effector cell in close vicinity of a tumour cell is thought to induce an antitumoural immune response. However, classical bispecific molecules activate only a single class of immune effector cell that may not yield optimal immune responses. We therefore constructed an intact bispecific antibody, BiUII (anti-CD3 x anti-EpCAM), that not only recognizes tumour cells and T lymphocytes with its two binding arms, but also binds and activates Fcgamma-receptor positive accessory cells through its Fc-region. We have demonstrated recently that activated accessory cells contribute to the bsAb-induced antitumoural activity. We now analyse this stimulation in more detail and demonstrate here the BiUII-induced upregulation of activation markers like CD83 and CD95 on accessory cells and the induction of neopterin and biopterin synthesis. Experiments with pure cell subpopulations revealed binding of BiUII to CD64+ accessory cells and CD16+ NK cells, but not to CD32+ B lymphocytes. We provide further evidence for the importance of the Fc-region in that this bispecific molecule stimulates Fcgamma-R-positive accessory cells to eliminate tumour cells in vitro by direct phagocytosis.
On the advantages of polar and log-polar mapping for direct estimation of time-to-impact from optical flow (1993)

The application of an anthropomorphic retina-like visual sensor and the advantages of polar and log-polar mapping for visual navigation are investigated. It is demonstrated that the motion equations that relate the egomotion and/or the motion of the objects in the scene to the optical flow are considerably simplified if the velocity is represented in a polar or log-polar coordinate system, as opposed to a Cartesian representation. The analysis is conducted for tracking egomotion but is then generalized to arbitrary sensor and object motion. The main result stems from the abundance of equations that can be written directly that relate the polar or log-polar optical flow with the time to impact. Experiments performed on images acquired from real scenes are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A phase 2 clinical trial of nab‐paclitaxel in previously treated and chemotherapy‐naive patients with metastatic melanoma (2009)

nab-Paclitaxel was found to be well tolerated and demonstrated activity in both previously treated and chemotherapy-naive patients with MM. The response rate, PFS, and survival compared favorably with current standard dacarbazine therapy and combination therapies for melanoma. nab-Paclitaxel therapy of MM should be investigated further in controlled clinical trials. Cancer 2010. (c) 2010 American Cancer Society.
Docetaxel (Taxotere) as monotherapy in the treatment of hormone-refractory prostate cancer: preliminary results. (1999)

Previous chemotherapy trials in hormone refractory prostate cancer have resulted in low response rates and minimal survival impact. Clearly, better agents are needed to improve outcomes in such patients. Microtubule inhibitors have been a recent focus of investigation as chemotherapeutic agents in prostate cancer; in tissue culture, docetaxel (Taxotere; Rhône-Poulenc Rorer, Collegeville, PA) appears to be the most active of these drugs. Patients enrolled in this trial had hormone refractory prostate cancer and were required to have progressive disease despite hormonal therapy and, if previously treated with antiandrogens, have progressive disease despite antiandrogen withdrawal. Patients had not been exposed to any prior chemotherapy. Testosterone suppression was continued during the trial when patients received docetaxel at 75 mg/m2 every 21 days. Thirty-five patients with ages ranging from 49 to 85 years (median age, 70 years) were enrolled in the trial. Three hundred twelve treatments have been given (median, six treatments), with a minimum follow-up of 4 months. The median prostate-specific antigen (PSA) at the time of entry was 96 ng/mL (range, 24 to 2,070 ng/mL). Seven patients (20%) have had a more than 80% decline in PSA and 16 (46%) have had a more than 50% decline. Six additional patients have had a PSA decline of 40% to 50%. Soft tissue disease was seen in 25 of 35 patients. One patient had a complete response; three others had a nearly complete response. Three patients met criteria for a partial response, yielding a 28% response rate with measurable disease. Three additional patients had substantial shrinkage and 12 had prolonged stable disease. Combining both PSA and soft tissue responses, one complete response and five partial responses were seen. Substantial responses, defined as a more than 40% PSA decline and a more than 50% reduction of bidimensional cross-products in patients with measurable disease, were seen in 17 of 35 patients enrolled. Responses were maintained for a median of 9 months (range, 2 to 24 months). The median overall survival was 27 months. Three patients remain under therapy. Toxicity remained tolerable throughout the treatment. Grade 4 toxicities requiring discontinuation of treatment included stomatitis, small bowel obstruction, and a gluteal abscess. There were two deaths during the study: one due to lung toxicity/pneumonia and one due to pulmonary embolus. The patient with lung toxicity had markedly elevated transaminases with marked involvement of the liver with tumor. Six patients stopped voluntarily due to fatigue or edema Other common toxicities were neutropenia, anemia, mild edema and hyperglycemia (due to steroids), anorexia, myalgias, and mild alopecia The responses seen in this population are very encouraging and suggest substantial durable activity for docetaxel as single-agent therapy for hormone refractory prostate cancer.
Chromosome structure and function : impact of new concepts (1988)

A Historical Perspective on the Study of Chromosome Structure and Function R. Appels Division of Plant Industry CSIRO P.O. Box 1600 A.C.T. AUSTRALIA Modern physical science gives us no model to explain the re duplication of the gene-string in each cell generation, or to ex plain the production of effective quantities of specific enzymes or other agents by specific genes. precise pairing and inter change of segments by homologous gene-strings at meiosis also suggest novel physical properties of this form of matter. Stadler (1954) very strong influence of reductionism in the history of understanding chromosome structure and function is evident in the above quotation from Stadler's 1954 paper, The gene. Earlyob servations on the constancy of the cytological appearance of chromo somes and their regular behaviour in cell division led to specula tion on their biological importance. As genetics became more refined in the early decades of the 20th century the genes-on-a string model of chromosomes developed and greater emphasis was placed on the further dissection of these structures. As a result, in the 1980's the reductionist approach is reaching a crest as extensive regions of the genetic material are being sequenced.