gebhart/patrepeval huggingface dataset:
Expression of a novel chitinase by the fungal endophyte in Poa ampla. (2012)

Many wild and cultivated cool-season grass species are naturally infected with fungal endophytes of the genera Neotyphodium and Epichloë. These associations generally are considered mutualistic with the plants benefiting from reduced herbivory and the fungi benefiting from nutrients supplied by the plants. The fungi secrete proteins that might have a role in the interspecies symbiosis. In the interaction between Poa ampla Merr. and the endophyte Neotyphodium sp., a fungal chitinase was detected in the apoplastic protein fraction. The chitinase was also the major protein secreted in culture. Sequence analysis of the chitinase revealed it has a low level of amino acid sequence identity to other fungal chitinases and one of the conserved active site residues is altered. DNA gel-blot analysis indicated the chitinase was encoded by a single gene. Expression of similar chitinases also was detected in endophyte-infected tall fescue (Festuca arundinacea Schreb.), perennial ryegrass (Lolium perenne L.) and Chewings fescue (Festuca rubra L. subsp. fallax [Thuill] Nyman). This is the first report of an endophyte chitinase expressed in the infected host grass. As a secreted hydrolytic enzyme, the chitinase might have roles in the nutrition, growth or defense of the endophyte.
CD8 independence and specificity of cytotoxic T lymphocytes restricted by HLA-Aw68. 1 (1991)

The crystal structure of the HLA-Aw68.1 antigen binding site revealed a negatively charged pocket centred on aspartic acid 74 (Garrett et al. 1989). Access to this '74 pocket' is blocked in HLA-Aw68.2 and HLA-Aw69 by two substitutions at positions 97 and 116. This key feature suggests that the Aw68.1-peptide-specific interactions may involve salt bridges between oppositely charged residues. In this paper, the influenza epitope recognized by virus-specific HLA-Aw68.1-restricted cytotoxic T lymphocytes (CTL) has been defined in vitro with a synthetic peptide corresponding to residues 89-101 of the nucleoprotein (NP). Amino acid substitutions of the peptide NP 89-101 showed that the arginine at position 99 is an anchor point of the peptide within the Aw68.1 antigen binding site. Consistent with this we find that neither HLA-Aw68.2 nor HLA-Aw69 positive cells can present peptide NP 89-101 to Aw68.1-restricted CTL. Our results therefore suggest a model in which presentation of NP 89-101 by HLA-Aw68.1 is dependent upon interaction of the positively charged arginine residue at position 99 of the peptide, with the negatively charged aspartic acid in the '74 pocket' of HLA-Aw68.1. We also show that influenza-virus-specific HLA-Aw68.1-restricted CTL are CD8 independent. This result is consistent with the low affinity of HLA-Aw68.1 for CD8 (Salter et al. 1989) and reveals a unique example of CD8-independent priming of CTL by natural infection with a common pathogen in humans.
From ab initio quantum mechanics to molecular neurobiology: A cation–π binding site in the nicotinic receptor (1998)

The nicotinic acetylcholine receptor is the prototype ligand-gated ion channel. A number of aromatic amino acids have been identified as contributing to the agonist binding site, suggesting that cation-pi interactions may be involved in binding the quaternary ammonium group of the agonist, acetylcholine. Here we show a compelling correlation between: (i) ab initio quantum mechanical predictions of cation-pi binding abilities and (ii) EC50 values for acetylcholine at the receptor for a series of tryptophan derivatives that were incorporated into the receptor by using the in vivo nonsense-suppression method for unnatural amino acid incorporation. Such a correlation is seen at one, and only one, of the aromatic residues-tryptophan-149 of the alpha subunit. This finding indicates that, on binding, the cationic, quaternary ammonium group of acetylcholine makes van der Waals contact with the indole side chain of alpha tryptophan-149, providing the most precise structural information to date on this receptor. Consistent with this model, a tethered quaternary ammonium group emanating from position alpha149 produces a constitutively active receptor.
Fiber Bragg grating cavity sensor for simultaneous measurement of strain and temperature (1999)

A novel and short (5 mm long) fiber grating based sensor with a fiber grating Fabry-Perot cavity (GFPC) structure was fabricated and tested for simultaneous measurement of strain and temperature. The sensor exhibits unique properties that it possesses two spectral peaks within its main reflection band and the normalized peak power difference, in addition to its peak wavelength shift, changes linearly with strain or temperature. The accuracy of this particular sensor in measuring strain and temperature are estimated to be /spl plusmn/30 μs in a range from 0 to 3000 μs and /spl plusmn/0.4/spl deg/C from 20/spl deg/C to 60/spl deg/C, respectively.
Pitch strength decreases as F0 and harmonic resolution increase in complex tones composed exclusively of high harmonics (2008)

A melodic pitch experiment was performed to demonstrate the importance of time-interval resolution for pitch strength. The experiments show that notes with a low fundamental (75 Hz) and relatively few resolved harmonics support better performance than comparable notes with a higher fundamental (300 Hz) and more resolved harmonics. Two four note melodies were presented to listeners and one note in the second melody was changed by one or two semitones. Listeners were required to identify the note that changed. There were three orthogonal stimulus dimensions: F0 (75 and 300 Hz); lowest frequency component (3, 7, 11, or 15); and number of harmonics (4 or 8). Performance decreased as the frequency of the lowest component increased for both F0's, but performance was better for the lower F0. The spectral and temporal information in the stimuli were compared using a time-domain model of auditory perception. It is argued that the distribution of time intervals in the auditory nerve can explain the decrease in performance as F0, and spectral resolution increase. Excitation patterns based on the same time-interval information do not contain sufficient resolution to explain listener's performance on the melody task.
ChemInform Abstract: Synthesis of Substituted Benzo(b)thiophenes by Acid‐Catalyzed Cyclization of Phenylthio Acetals and Ketones. (1989)

Abstract The phenylthioacetaldehyde acetals (I) and the phenylthioacetones (III) are cyclized upon heating with polyphosphoric acid, forming the benzothiophenes (II) and (IV).
Deep Continuous Fusion for Multi-Sensor 3D Object Detection (2020)

In this paper, we propose a novel 3D object detector that can exploit both LIDAR as well as cameras to perform very accurate localization. Towards this goal, we design an end-to-end learnable architecture that exploits continuous convolutions to fuse image and LIDAR feature maps at different levels of resolution. Our proposed continuous fusion layer encode both discrete-state image features as well as continuous geometric information. This enables us to design a novel, reliable and efficient end-to-end learnable 3D object detector based on multiple sensors. Our experimental evaluation on both KITTI as well as a large scale 3D object detection benchmark shows significant improvements over the state of the art.
Reversal of elastase-induced pulmonary emphysema and promotion of alveolar epithelial cell proliferation by simvastatin in mice (2008)

Besides lowering cholesterol, statins exert multiple effects, such as anti-inflammatory activity and improvement of endothelial cell function. We examined whether simvastatin (SS) protects against the development of elastase-induced pulmonary emphysema in mice by using mean linear intercepts of alveoli (Lm) as a morphometric parameter of emphysema. After injection of intratracheal elastase on day 0, C57BL/6 mice were treated daily with SS (SS+ group) or PBS (SS- group) for 2 wk. A 21% decrease in Lm on day 7 was observed in the SS+ group vs. the SS- group. Anti-inflammatory effects of SS were observed as a decrease in percentage of neutrophils up to day 3, and in hydroxyproline concentration on day 3, in bronchoalveolar lavage fluid (BALF). SS also increased the number of proliferating cell nuclear antigen (PCNA)-positive alveolar epithelial cells between days 3 and 14. To confirm the role of statins in promoting proliferation of alveolar cells, mice were treated with SS (SS+) vs. PBS (SS-) for 12 days, starting 3 wk after elastase administration. After SS treatment, Lm decreased by 52% and PCNA-positive alveolar epithelial cells increased compared with the SS- group. Concentrations of vascular endothelial growth factor in BALF and endothelial nitric oxide synthase protein expression in pulmonary vessels tended to be higher in the SS+ group vs. the SS- group in this protocol. In conclusion, SS inhibited the development of elastase-induced pulmonary emphysema in mice. This therapeutic effect was due not only to anti-inflammation but also to the promotion of alveolar epithelial cell regeneration, partly mediated by restoring endothelial cell functions.
Side Effects of Long-Term Treatment with Human Leukocyte Interferon (1979)

Twenty-nine patients, 27 of them with osteosarcoma and two with juvenile laryngeal papilloma, were followed for an aggregate period of 365 months, during which time they received long-term treatment with human leukocyte interferon. The interferon was given by intramuscular injection either daily or three times a week; the dose was 3 x 10(6) standard units. During the course of the treatment, 12 distinct symptoms were recognized as possible side effects of the drug; the three most frequent symptoms occurring after injection were fever, local pain, and shivering. All but three of the patients reported between one and five symptoms. Partial purification of the interferon reduced or eliminated some, but not all, of the symptoms. All of the patients were treated on an ambulatory basis, and none had to discontinue the interferon therapy because of the side effects.
Stratospheric temperature trends: Observations and model simulations (2001)

Trends and variations in global stratospheric temperatures are an integral part of the changes occurring in the Earth's climate system. Data sets for analyzing long‐term (a decade and more) changes in the stratospheric temperatures consist of radiosonde, satellite, lidar, and rocketsonde measurements; meteorological analyses based on radiosonde and/or satellite data; and products based on assimilating observations using a general circulation model. Each of these contain varying degrees of uncertainties that influence the interpretation and significance of trends. We review the long‐term trends from approximately the mid‐1960s to the mid‐1990s period. The stratosphere has, in general, undergone considerable cooling over the past 3 decades. At northern midlatitudes the lower stratosphere (∼16–21 km) cooling over the 1979–1994 period is strikingly coherent among the various data sets with regard to magnitude and statistical significance. A substantial cooling occurs in the polar lower stratosphere during winter‐spring; however, there is a large dynamical variability in the northern polar region. The vertical profile of the annual‐mean stratospheric temperature change in the northern midlatitudes over the 1979–1994 period is robust among the different data sets, with ∼0.75 K/decade cooling in the ∼20‐ to 35‐km region and increasing cooling above (e.g., ∼2.5 K/decade at 50 km). Model investigations into the cause or causes of the observed temperature trends are also reviewed. Simulations based on the known changes in species' concentrations indicate that the depletion of lower stratospheric ozone is the major radiative factor in accounting for the 1979–1990 cooling trend in the global, annual‐mean lower stratosphere (∼0.5 to 0.6 K/decade), with a substantially lesser contribution by the well‐mixed greenhouse gases. Ozone loss is also an important causal factor in the latitude‐month pattern of the lower stratospheric cooling trend. Uncertainties arise due to incomplete knowledge of the vertical profile of ozone loss near the tropopause. In the middle and upper stratosphere, both well‐mixed greenhouse gases and ozone changes contribute in an important manner to the cooling, but model simulations underestimate the observed decadal‐scale trend. While there is a lack of reliable information on water vapor changes over the 1980s decade, satellite measurements in the early to middle 1990s indicate increases in water vapor that could be a significant contributor to the cooling of the global lower stratosphere.
Treating Anemia in the Preanesthesia Assessment Clinic: Results of a Retrospective Evaluation (2018)

An anemia clinic within the preanesthesia assessment clinic is a feasible and effective approach to treat preoperative anemia. The IVI supplementation was safe but was associated with decreased RBC transfusions in gynecology/obstetric patients only. The conclusions from this retrospective analysis have to be tested in prospective, controlled trials.
Inhibition of Macroautophagy Triggers Apoptosis (2005)

Mammalian cells were observed to die under conditions in which nutrients were depleted and, simultaneously, macroautophagy was inhibited either genetically (by a small interfering RNA targeting Atg5, Atg6/Beclin 1-1, Atg10, or Atg12) or pharmacologically (by 3-methyladenine, hydroxychloroquine, bafilomycin A1, or monensin). Cell death occurred through apoptosis (type 1 cell death), since it was reduced by stabilization of mitochondrial membranes (with Bcl-2 or vMIA, a cytomegalovirus-derived gene) or by caspase inhibition. Under conditions in which the fusion between lysosomes and autophagosomes was inhibited, the formation of autophagic vacuoles was enhanced at a preapoptotic stage, as indicated by accumulation of LC3-II protein, ultrastructural studies, and an increase in the acidic vacuolar compartment. Cells exhibiting a morphology reminiscent of (autophagic) type 2 cell death, however, recovered, and only cells with a disrupted mitochondrial transmembrane potential were beyond the point of no return and inexorably died even under optimal culture conditions. All together, these data indicate that autophagy may be cytoprotective, at least under conditions of nutrient depletion, and point to an important cross talk between type 1 and type 2 cell death pathways.
Z-Selective Olefin Metathesis Reactions Promoted by Tungsten Oxo Alkylidene Complexes (2011)

Addition of LiOHMT (OHMT = O-2,6-dimesitylphenoxide) to W(O)(CH-t-Bu)(PMe(2)Ph)(2)Cl(2) led to WO(CH-t-Bu)Cl(OHMT)(PMe(2)Ph) (4). Subsequent addition of Li(2,5-Me(2)C(4)H(2)N) to 4 yielded yellow W(O)(CH-t-Bu)(OHMT)(Me(2)Pyr)(PMe(2)Ph) (5). Compound 5 is a highly effective catalyst for the Z-selective coupling of selected terminal olefins (at 0.2% loading) to give product in >75% yield with >99% Z configuration. Addition of 2 equiv of B(C(6)F(5))(3) to 5 afforded a catalyst activated at the oxo ligand by B(C(6)F(5))(3). 5·B(C(6)F(5))(3) is a highly active catalyst that produces thermodynamic products (~20% Z).
Concentration-Dependent Processivity of Multiple Glutamate Ligations Catalyzed by Folylpoly-γ-glutamate Synthetase (2008)

Folylpoly-gamma-glutamate synthetase (FPGS, EC 6.3.2.17) is an ATP-dependent ligase that catalyzes formation of poly-gamma-glutamate derivatives of reduced folates and antifolates such as methotrexate and 5,10-dideaza-5,6,7,8-tetrahydrofolate (DDAH 4PteGlu 1). While the chemical mechanism of the reaction catalyzed by FPGS is known, it is unknown whether single or multiple glutamate residues are added following each folate binding event. A very sensitive high-performance liquid chromatography method has been used to analyze the multiple ligation reactions onto radiolabeled DDAH 4PteGlu 1 catalyzed by FPGS to distinguish between distributive or processive mechanisms of catalysis. Reaction time courses, substrate trapping, and pulse-chase experiments were used to assess folate release during multiple glutamate additions. Together, the results of these experiments indicate that hFPGS can catalyze the processive addition of approximately four glutamate residues to DDAH 4PteGlu 1. The degree of processivity was determined to be dependent on the concentration of the folate substrate, thus suggesting a mechanism for the regulation of folate polyglutamate synthesis in cells.
Macrophages in Tumor Microenvironments and the Progression of Tumors (2012)

Macrophages are widely distributed innate immune cells that play indispensable roles in the innate and adaptive immune response to pathogens and in-tissue homeostasis. Macrophages can be activated by a variety of stimuli and polarized to functionally different phenotypes. Two distinct subsets of macrophages have been proposed, including classically activated (M1) and alternatively activated (M2) macrophages. M1 macrophages express a series of proinflammatory cytokines, chemokines, and effector molecules, such as IL-12, IL-23, TNF-α, iNOS and MHCI/II. In contrast, M2 macrophages express a wide array of anti-inflammatory molecules, such as IL-10, TGF-β, and arginase1. In most tumors, the infiltrated macrophages are considered to be of the M2 phenotype, which provides an immunosuppressive microenvironment for tumor growth. Furthermore, tumor-associated macrophages secrete many cytokines, chemokines, and proteases, which promote tumor angiogenesis, growth, metastasis, and immunosuppression. Recently, it was also found that tumor-associated macrophages interact with cancer stem cells. This interaction leads to tumorigenesis, metastasis, and drug resistance. So mediating macrophage to resist tumors is considered to be potential therapy.
Solution Structure of the N-terminal Domain of the Human TFIIH MAT1 Subunit (2001)

The human MAT1 protein belongs to the cyclin-dependent kinase-activating kinase complex, which is functionally associated to the transcription/DNA repair factor TFIIH. The N-terminal region of MAT1 consists of a C3HC4 RING finger, which contributes to optimal TFIIH transcriptional activities. We report here the solution structure of the human MAT1 RING finger domain (Met(1)-Asp(65)) as determined by (1)H NMR spectroscopy. The MAT1 RING finger domain presents the expected betaalphabetabeta topology with two interleaved zinc-binding sites conserved among the RING family. However, the presence of an additional helical segment in the N-terminal part of the domain and a conserved hydrophobic central beta strand are the defining features of this new structure and more generally of the MAT1 RING finger subfamily. Comparison of electrostatic surfaces of RING finger structures shows that the RING finger domain of MAT1 presents a remarkable positively charged surface. The functional implications of these MAT1 RING finger features are discussed.
Enhancement of Interleukin-2-Induced Lymphokine-Activated Killer Activity by Interleukin 7 against Autologous Human Renal Cell Carcinoma (1998)

Adjuvant immunotherapy with interferons and/or interleukin 2 (IL-2) is widely used for advanced kidney cancer. However, the results are not satisfactory so far. The purpose of this study is to evaluate the inducible activity of lymphokine-activated killer (LAK) cells against autologous human renal cell carcinoma. The effect of interleukin 7 (IL-7) on IL-2-induced LAK activity was assessed by the autologous assay system which we have established. Peripheral blood lymphocytes from patients with renal cell carcinoma were stimulated with IL-2 and/or IL-7, and tested for antitumor activity against autologous renal cell carcinoma. In all 10 cases tested, IL-7 alone induced LAK activity. Moreover, IL-2-induced LAK activity was augmented by the concomitant addition of IL-7. Flow cytometry revealed an increase in IL-2-receptor-positive lymphocytes following incubation with IL-7. These results suggest that combination therapy using IL-2 and IL-7 may be a useful treatment for patients with advanced renal cell carcinoma.
PERMEABILITY OF THE FOETAL GUINEA-PIG PLACENTA TO ARGININE-VASOPRESSIN (1977)

Departments of Physiology, *The Middlesex Hospital Medical School, Cleveland Street, London, W1P 6DB, and St Mary's Hospital Medical School, Praed Street, London, W2 1PG (Received 13 October 1976) Recently there has been increasing interest in the possible role of foetal neurohypophysial hormones in parturition (Alexander, Bashore, Britton & Forsling, 1974; Burton, Illingworth, Challis & McNeilly, 1974). The significance of plasma levels in the mother and foetus depends on the placental permeability to the hormone. It has been suggested that in the sheep there is no placental transfer of oxytocin (Forsling, Jack & Nathanielsz, 1975) or arginine-vasopressin (AVP) (Alexander et al. 1974). Burton and her co-workers, however, reported that the guinea-pig placenta allows passage of oxytocin. It is therefore of interest to know whether this placenta which is haemochorial in nature is also permeable to AVP. The placentae of nine guinea-pigs in the third trimester of pregnancy were perfused by recirculation
Active Defense of a Computer System using Autonomous Agents (1995)

This report presents a prototype architecture for an active defense mechanism for computer systems. The intrusion detection problem is introduced and some of the key aspects of any solution are explained. Previous attempts to use similar techniques are discussed, and their shortcomings are explained. A new architecture is proposed which uses Genetic Programming to evolve programs to detect anomalous behaviour in a system. This architecture is developed and evaluated. A sample genetic program is used to discuss some of the design aspects of the agents. Cooperative monitoring of NFS requests shows how the approach can be generalised. The discussion details some issues to be addressed and future research directions. 1 Introduction Because of increased network connectivity, computer systems are becoming increasingly vulnerable to attack. These attacks often exploit flaws in either the operating system or application programs. The general goal of such intrusions is to subvert the traditi...
Bladder cancer xenografts: a model of tumor cell heterogeneity. (1986)

Twenty bladder biopsies from patients with primary transitional cell carcinoma were inoculated into nude mice. To date, eleven of these have grown as primary implants and three serially transplantable xenograft lines (UCRU-BL-12, UCRU-BL-13, UCRU-BL-14) have been established. The histological and ultrastructural features of human transitional cell carcinoma have been maintained in each line. Despite a relatively uniform histological appearance, several indices of occult tumor heterogeneity have been revealed. Immunocytochemical staining was negative for beta-subunit human chorionic gonadotrophin but positive for carcinoembryonic antigen only in areas of squamous differentiation. All three tumors bound peanut lectin. Flow cytometric DNA analysis of UCRU-BL-13 showed multiple aneuploid peaks, separate populations being demonstrated in different xenografts of the same generation. However, the morphologies of these tumors remained identical. On initial implantation UCRU-BL-12 and UCRU-BL-14 were near diploid but aneuploid populations became apparent with increasing passage number. Each xenograft line caused cachexia in the host mice. Treatment with the cisplatin analogue, isopropyl platinum, ameliorated the cachexia displayed by mice carrying UCRU-BL-14 but did not cause tumor regression. UCRU-BL-12, when tested with cisplatin, isopropyl platinum, and carboplatin, showed equivalent growth retardation with each drug. These xenografted human bladder cancers may be useful models for the study of heterogeneity of the tumor populations in bladder cancer and for the evaluation of new approaches to treatment.
Effect of tofacitinib, a Janus kinase inhibitor, on haematological parameters during 12 weeks of psoriasis treatment (2013)

Tofacitinib conferred tolerable, dose-dependent changes in haematological parameters during short-term administration in patients with psoriasis. The effects did not appear to be progressive, and were often transient or reversible.