gebhart/patrepeval huggingface dataset:
A Novel Mechanism of Carbohydrate Recognition by the C-type Lectins DC-SIGN and DC-SIGNR (2001)

DC-SIGN and DC-SIGNR are cell-surface receptors that mediate cell-cell interactions within the immune system by binding to intercellular adhesion molecule-3. The receptor polypeptides share 77% amino acid sequence identity and are type II transmembrane proteins. The extracellular domain of each comprises seven 23-residue tandem repeats and a C-terminal C-type carbohydrate-recognition domain (CRD). Cross-linking, equilibrium ultracentrifugation, and circular dichroism studies of soluble recombinant fragments of DC-SIGN and DC-SIGNR have been used to show that the extracellular domain of each receptor is a tetramer stabilized by an alpha-helical stalk. Both DC-SIGN and DC-SIGNR bind ligands bearing mannose and related sugars through the CRDs. The CRDs of DC-SIGN and DC-SIGNR bind Man(9)GlcNAc(2) oligosaccharide 130- and 17-fold more tightly than mannose, and affinity for a glycopeptide bearing two such oligosaccharides is increased by a further factor of 5- to 25-fold. These results indicate that the CRDs contain extended or secondary oligosaccharide binding sites that accommodate mammalian-type glycan structures. When the CRDs are clustered in the tetrameric extracellular domain, their arrangement provides a means of amplifying specificity for multiple glycans on host molecules targeted by DC-SIGN and DC-SIGNR. Binding to clustered oligosaccharides may also explain the interaction of these receptors with the gp120 envelope protein of human immunodeficiency virus-1, which contributes to virus infection.
Efficient Autoscaling in the Cloud Using Predictive Models for Workload Forecasting (2011)

Large-scale component-based enterprise applications that leverage Cloud resources expect Quality of Service(QoS) guarantees in accordance with service level agreements between the customer and service providers. In the context of Cloud computing, auto scaling mechanisms hold the promise of assuring QoS properties to the applications while simultaneously making efficient use of resources and keeping operational costs low for the service providers. Despite the perceived advantages of auto scaling, realizing the full potential of auto scaling is hard due to multiple challenges stemming from the need to precisely estimate resource usage in the face of significant variability in client workload patterns. This paper makes three contributions to overcome the general lack of effective techniques for workload forecasting and optimal resource allocation. First, it discusses the challenges involved in auto scaling in the cloud. Second, it develops a model-predictive algorithm for workload forecasting that is used for resource auto scaling. Finally, empirical results are provided that demonstrate that resources can be allocated and deal located by our algorithm in a way that satisfies both the application QoS while keeping operational costs low.
The equilibrium partition function and base pair binding probabilities for RNA secondary structure (1990)

A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure. The pair binding probabilities, the computation of which depends on the partition function, are visually summarized in a "box matrix" display and this provides a useful tool for examining the full ensemble of probable alternative equilibrium structures. The calculation of this ensemble representation allows a proper application and assessment of the predictive power of the secondary structure method, and yields important information on alternatives and intermediates in addition to local information about base pair opening and slippage. The results are illustrated for representative tRNA, 5S RNA, and self-replicating and self-splicing RNA molecules, and allow a direct comparison with enzymatic structure probes. The effect of changes in the thermodynamic parameters on the equilibrium ensemble provides a further sensitivity check to the predictions.
Chronicle (2010)

We describe Chronicle, a new system that allows users to explore document workflow histories. Chronicle captures the entire video history of a graphical document, and provides links between the content and the relevant areas of the history. Users can indicate specific content of interest, and see the workflows, tools, and settings needed to reproduce the associated results, or to better understand how it was constructed to allow for informed modification. Thus, by storing the rich information regarding the document's history workflow, Chronicle makes any working document a potentially powerful learning tool. We outline some of the challenges surrounding the development of such a system, and then describe our implementation within an image editing application. A qualitative user study produced extremely encouraging results, as users unanimously found the system both useful and easy to use.
Inhibitors of Acyl-CoA:Cholesterol Acyltransferase. 1. Synthesis and Hypocholesterolemic Activity of Dibenz[b,e]oxepin-11-carboxanilides (1994)

A series of N-phenyl-6,11-dihydrodibenz[b,e]oxepin-11-carboxamides and related derivatives were prepared on the basis of structures of the reported inhibitors of acyl-CoA:cholesterol acyltransferase (ACAT). These compounds were tested for their ability to inhibit ACAT (liver microsomes from cholesterol-fed rabbits) in vitro and to decrease serum total cholesterol in cholesterol-fed golden hamsters in vivo. The structure-activity relationships in vitro were as follows. Substitution at positions 2 and 6 in the anilide resulted in potent inhibitory activity, and the potency increased with increasing size of the substituents, with maximum potency being obtained with a 2,6-diisopropyl substitution. The position of the substituent on the dibenz[b,e]oxepin ring system influenced the activity, and substitution at position 2 was critical for potent activity. The electronic effect of the substituent at position 2 does not influence activity, but bulkiness seems to be a significant factor. The lipophilicity of the compounds also plays an important role in determining ACAT inhibitory activity. Among the compounds tested, 2-bromo-N-(2,6-diisopropylphenyl)-6,11-dihydrodibenz-[b,e]++ +oxepin-11- carboxamide (33, KF17828) showed significant in vitro activity (rabbit liver microsomes IC50 = 23 nM) and the most potent in vivo activity (complete reduction in elevated serum total cholesterol levels at a dose of 10 mg/kg in hamsters).
Development of 3‐D shape measurement system using fiber grating (1987)

Abstract There is an increasing demand in industry and medicine for the noncontact measurement of the shape of a 3‐D object. Various studies are being made to develop highly accurate and simple means of such measurements. When a laser light is incident to the fiber grating in the vertical direction, a square spot array is produced. When the array is projected on a 3‐D object with a general shape, the array is distorted. By using the distortion as the data for the processing, the 3‐D shape can be measured strictly. This paper reports on the 3‐D shape measurement using an optical fiber grating. No particular application is considered in the design of the system. The projector of the spot array can be constructed with a lightweight and small size, and it is suitable as a built‐in device for the endoscopy, or a visual device to be installed directly on the industrial robot arm.
Possible Antituberculous Compounds. Part XIV. Condensation Products of Hydrazides and lsonitroso Ketones (1962)

Twentynight new compounds have been synthesised by condensing different hydrazidee and isonitroso acetones with a view to studying their tuberculnstatie activity.
Poxviral modifiers of cytokine responses to infection. (1995)

Poxviruses include some of the most virulent of all human pathogens. In part, the virulence of these viruses stems from their abilities to counter host defenses against infection. A family of cytokine-response modifiers encoded by the poxviruses contribute to these countermeasures. The poxviral cytokine-response modifiers appear to affect cytokine responses in at least four different ways: (a) by inhibiting the synthesis and release of cytokines from infected cells; (b) by interfering with the interaction between a cytokine and its receptor; (c) by inhibiting cytokine signal transmission; and (d) by synthesizing virus-encoded cytokines that antagonize the effects of host cytokines mediating antiviral processes. Known poxviral, cytokine-response modifiers include CrmA, an inhibitor of the interleukin-1 beta converting enzyme; several secreted soluble receptors for tumor necrosis factor, interleukin-1, and interferon-gamma; and poxvirus-encoded growth factors resembling epidermal growth factor. Collectively, these and other as yet unidentified cytokine-response modifiers contribute to the inhibition of a variety of nonspecific and virus-specific immune defenses against virus infection. Information gained on the mechanisms used by poxviruses to modify cytokine-mediated processes should assist the development of novel therapies for a variety of diseases.
Regulation of isthmic Fgf8 signal bysprouty2 (2004)

Fgf8 functions as an organizer at the mes/metencephalic boundary (isthmus). We showed that a strong Fgf8 signal activates the Ras-ERK signaling pathway to organize cerebellar differentiation. Sprouty2 is expressed in an overlapping manner to Fgf8, and is induced by Fgf8. Its function, however, is indicated to antagonize Ras-ERK signaling. Here, we show the regulation of Fgf8 signaling in relation to Sprouty2. sprouty2 expression was induced very rapidly by Fgf8b, but interfered with ERK activation. sprouty2 misexpression resulted in a fate change of the presumptive metencephalon to the mesencephalon. Misexpression of a dominant negative form of Sprouty2 augmented ERK activation, and resulted in anterior shift of the posterior border of the tectum. The results indicate that Fgf8 activates the Ras-ERK signaling pathway to differentiate the cerebellum, and that the hyper- or hypo-signaling of this pathway affects the fate of the brain vesicles. Sprouty2 may regulate the Fgf8-Ras-ERK signaling pathway for the proper regionalization of the metencephalon and mesencephalon.
Crystal Growth and Characterization of Ca3NbGa3Si2O14 Single Crystal (2006)

Single crystals of Ca3NbGa3Si2O14 (CNGS) with ordered Ca3Ga2Ge4O14 (CGG) structure were successfully grown from stoichiometric melts by conventional Czochralski technique along the a-axis and two large (001) facets and two small (100) facets appear in every crystal. An arrangement of parallel steps and a clear height change were observed in (001) facet by atomic force microscopy (AFM). High-resolution X-ray diffraction (HRXRD) results indicate that CNGS crystals have good quality and free low-angle boundaries. The crystals also exhibit good optical quality and high optical transmittance in c-direction.
Polythiophene Hybrids of Transition-Metal Bis(salicylidenimine)s:  Correlation between Structure and Electronic Properties (1999)

The synthesis, electrochemistry, and spectroscopic behavior of tetradentate bis(salicylidenimine) transition metal complexes 5−9 are reported. Appending these complexes with 3,4-ethylenedioxythiophene (EDOT) moieties allows for electrochemical polymerization at much lower potentials than the parent salen complexes. The resulting polymers display well-defined organic-based electrochemistry at potentials <0.5 V vs Fc/Fc+. The EDOT-modified N,N‘-ethylene bis(salicylidene), N,N‘-o-phenylene bis(salicylidene), and N,N‘-trans-cyclohexylene bis(salicylidene) complexes 5a−b, 6a−b, and 8a−b display cyclic voltammograms with four organic-based redox waves. Increasing the interchain separation through the use of nonplanar bis(salicylidene) ligands results in only two redox waves. The conductivity of the copper-based polymers decreases with increasing interchain spacing, with the maximum conductivity being 92 S cm-1 for poly(5a) and 16 S cm-1 for poly(7a). The nickel complexes were less sensitive to increased interchain separation and showed conductivities greater than 48 S cm-1 regardless of the interchain spacing and near 100 S cm-1 in the case of poly(6b). In situ spectroelectrochemistry was consistent with the segmented electronic nature of these polymers. Cyclic voltammetry of an analogous uranyl complex, 5c, revealed that two electrons per repeat unit were removed during oxidation. Consideration of our collective investigations, which also included in situ EPR spectroscopic studies, led to a postulation that π-aggregation processes are occurring in those polymers which are allowed to have close interchain spacing.
Shock-induced fast reactions of zinc nanoparticles and RDX (2008)

Fast reactions of zinc nanoparticles and RDX were investigated in normal incident shock waves. The emergence time and emission spectra intensity of partial products such as NO2, H, C2, O, CO, CH2O, CO2, H2O and ZnO were observed by a TDS5054 oscilloscope. The results indicate that NO2 appears first in each experiment, which is in agreement with the theoretical results. The addition of zinc nanoparticles to RDX can not only shorten the ignition delay time by 20% but also double the shockwave diffusion velocity to 2180 ± 50 m s−1 and triple the temperature to 2020 ± 60 K. The emergence time of products shortens by around 10–40% and the emission spectra intensity of H2O and CH2O rises by about three times and one times, respectively. CO2, H2O and O2 in various concentrations were introduced into the zinc–RDX reaction, respectively, which indicate that O2 made the ignition delay time shorten by over 30%, the effect of H2O was not prominent while CO2 made the ignition delay time lag by around 30%. The results indicate that the Zn–O2 reaction mainly occurs in O2, CO2 and H2O.
Antagonistic effects of intestinal Lactobacillus isolates on pathogens of chicken (1996)

Twelve Lactobacillus strains isolated from chicken intestine, which demonstrated a strong and moderate capacity to adhere to the ileal epithelial cells in vitro, were used to investigate their inhibitory ability against five strains of salmonella, i.e. Salmonella enteritidis 935/79, Salm. pullorum, Salm. typhimurium, Salm. blockley and Salm. enteritidis 94/448, and three serotypes of Escherichia coli, viz. E. coli O1:K1, O2:K1 and O78:K80. The results showed that all the 12 Lactobacillus isolates were able to inhibit the growth of the five strains of salmonella, and the three strains of E. coli in varying degrees. Generally, they were more effective in inhibiting the growth of salmonella than E. coli. Inhibition of the pathogenic bacteria was probably due to the production of organic acids by the Lactobacillus isolates.
Catalytic, Enantioselective, Conjugate Alkyne Addition (2005)

We document a copper-catalyzed, enantioselective, conjugate addition involving the direct use of a terminal acetylene, which undergoes in situ metalation. The addition reactions of phenylacetylene to Meldrum's acid derived acceptors take place in aqueous media, without recourse to inert atmosphere. The success of the enantioselective process was enabled by the use of a new class of conveniently accessed P,N-ligands, which we have termed PINAP. These modular ligands are responsive to numerous electronic and steric modifications that permit optimization of the reaction.
Transparent optical packet switching: the European ACTS KEOPS project approach (1998)

This paper reviews the work carried out under the European ACTS KEOPS (KEys to Optical Packet Switching) project, centering on the definition, development and assessment of optical packet switching and routing networks capable of providing transparency to the payload bit rate. The adopted approach uses optical packets of fixed duration with low bit rate headers to facilitate processing at the network/node interfaces. The paper concentrates on the networking concepts developed in the KEOPS project through a description of the implementation issues pertinent to optical packet switching nodes and network/node interfacing blocks, and consideration of the network functionalities provided within the optical packet layer. The implementation, from necessity, relies on advanced optoelectronic components specifically developed within the project, which are also briefly described.
Shepherding AKT and androgen receptor by Ack1 tyrosine kinase (2010)

Ack1 (also known as ACK, TNK2, or activated Cdc42 kinase) is a structurally unique non-receptor tyrosine kinase that is expressed in diverse cell types. It integrates signals from plethora of ligand-activated receptor tyrosine kinases (RTKs), for example, MERTK, EGFR, HER2, PDGFR and insulin receptor to initiate intracellular signaling cascades. Ack1 transduces extracellular signals to cytosolic and nuclear effectors such as the protein kinase AKT/PKB and androgen receptor (AR), to promote cell survival and growth. While tyrosine phosphorylation of AR at Tyr267 regulates androgen-independent recruitment of AR to the androgen-responsive enhancers and transcription of AR target genes to drive prostate cancer progression, phosphorylation of an evolutionarily conserved Tyrosine 176 in the kinase domain of AKT is essential for mitotic progression and positively correlates with breast cancer progression. In contrast to AR and AKT, Ack1-mediated phosphorylation of the tumor suppressor Wwox at Tyr287 lead to rapid Wwox polyubiquitination followed by degradation. Thus, by its ability to promote tumor growth by negatively regulating tumor suppressor such as Wwox and positively regulating pro-survival factors such as AKT and AR, Ack1 is emerging as a critical player in cancer biology. In this review, we discuss recent advances in understanding the physiological functions of Ack1 signaling in normal cells and the consequences of its hyperactivation in various cancers.
Developmental activation of an episomic hsp70 gene promoter in two-cell mouse embryos by transcription factor Sp1 (1997)

To investigate the control of zygotic genome expression in two-cell mouse embryos, we studied transcription factors required for transient expression of microinjected DNA constructs driven by the promoter of one of the earliest genes activated after fertilization in this system, the heat shock gene hsp70. Cis-acting elements required for hsp70 activation were first investigated by mutational analysis. Mutation of the TATA box and a proximal GC box strongly inhibited construct expression, while that of a CCAAT box had no effect. Transcription factors binding the wild-type hsp70 promoter were then titrated in vivo by coinjecting the construct with double-stranded oligodeoxyribonucleotides containing definite consensus sequences. Wild-type GC box oligonucleotides strongly inhibited construct expression, while those containing mutated GC boxes,wild-type CCAAT boxes, and heat shock elements had no effects. Finally, construct expression was challenged by coinjecting antibodies to specific: transcription factors, Antibodies to factor Spl depressed construct expression in a dose-dependent manner, while those to Sp2, HSF1 and HSF2 were ineffective; These results pinpoint the Spl transcription factor as an absolute requirement for activation of the hsp70 gene promoter in two-cell mouse embryos, and make this factor a candidate for a major regulator of the onset of murine zygotic genome expression.
Quality-of-life benefit in chemotherapy patients treated with epoetin alfa is independent of disease response or tumor type: results from a prospective community oncology study. Procrit Study Group. (1998)

Epoetin alfa appears to have a beneficial impact on patient-reported functional capacity and quality of life in patients with cancer who received chemotherapy independent of tumor response. Concordantly, epoetin alfa appeared to increase hemoglobin levels and decrease transfusion use. Patients responded across all tumor types. The results suggest that epoetin alfa effectively improves functional outcomes in patients with cancer who receive chemotherapy.
Profiling and imaging proteins in the mouse epididymis by imaging mass spectrometry (2003)

Different aspects of matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) have been used as discovery tools to obtain global and time-correlated information on the local proteomic composition of the sexually mature mouse epididymis from both qualitative and semiquantitative points of view. Tissue sections and laser captured microdissected cells and secretory products were analyzed by MALDI-MS and from the recovered protein profiles, over 400 different proteins were monitored. Over 50 of these, some of which have been identified, displayed regionalized behavior from caput to cauda within the epididymis. Combining the information obtained from high-resolution imaging mass spectrometry and laser captured microdissection experiments, numerous proteins were localized within the epididymis at the cellular level. Furthermore, from the signal intensities observed in the different protein profiles organized in space, semiquantitative information for each protein was obtained.
Parkinson's disease (1997)

Parkinson's disease is a common disabling disease of old age. The diagnosis of idiopathic Parkinson's disease is based on clinical signs and has poor sensitivity, with about 25% of patients confidently diagnosed as having the disease actually having other conditions such as multi-system atrophy and other parkinsonism-plus syndromes. Benign essential tremor and arteriosclerotic pseudo-parkinsonism can easily be confused with Parkinson's disease. The cause of Parkinson's disease remains unknown. Speculative research highlights the role of oxidative stress and free radical mediated damage to dopaminergic cells. Parkinson's disease is the one neurodegenerative disorder in which drugs have been demonstrated to be of value. There is now a wide variety of drugs and formulations available, including anticholinergics, amantidine, L-dopa, dopamine agonists including apomorphine, selegiline and soon to be available catechol-O-methyltransferase inhibitors. Disabling side-effects of treatment, fluctuations, dyskinesias and psychiatric problems require strategic use of the drugs available. There is an increasing potential for neurosurgical intervention.