gebhart/patrepeval huggingface dataset:
Crystal structure of the PB1 domain of NBR1 (2005)

The scaffold protein NBR1 is involved in signal transmission downstream of the serine/protein kinase from the giant muscle protein titin. Its N-terminal Phox and Bem1p (PB1) domain plays a critical role in mediating protein-protein interactions with both titin kinase and with another scaffold protein, p62. We have determined the crystal structure of the PB1 domain of NBR1 at 1.55A resolution. It reveals a type-A PB1 domain with two negatively charged residue clusters. We provide a structural perspective on the involvement of NBR1 in the titin kinase signalling pathway.
Finding Structure in Time (1990)

Time underlies many interesting human behaviors. Thus, the question of how to represent time in connectionist models is very important. One approach is to represent time implicitly by its effects on processing rather than explicitly (as in a spatial representation). The current report develops a proposal along these lines first described by Jordan (1986) which involves the use of recurrent links in order to provide networks with a dynamic memory. In this approach, hidden unit patterns are fed back to themselves: the internal representations which develop thus reflect task demands in the context of prior internal states. A set of simulations is reported which range from relatively simple problems (temporal version of XOR) to discovering syntactic/semantic features for words. The networks are able to learn interesting internal representations which incorporate task demands with memory demands: indeed, in this approach the notion of memory is inextricably bound up with task processing. These representations reveal a rich structure, which allows them to be highly context‐dependent, while also expressing generalizations across classes of items. These representations suggest a method for representing lexical categories and the type/token distinction.
Quantitative Measurement of Short-Range Chemical Bonding Forces (2001)

We report direct force measurements of the formation of a chemical bond. The experiments were performed using a low-temperature atomic force microscope, a silicon tip, and a silicon (111) 7x7 surface. The measured site-dependent attractive short-range force, which attains a maximum value of 2.1 nanonewtons, is in good agreement with first-principles calculations of an incipient covalent bond in an analogous model system. The resolution was sufficient to distinguish differences in the interaction potential between inequivalent adatoms, demonstrating the ability of atomic force microscopy to provide quantitative, atomic-scale information on surface chemical reactivity.
Diffractive exit-pupil expander for spherical light guide virtual displays designed for near-distance viewing (2009)

In this paper the use of diffractive exit-pupil expanders (EPEs) for implementation of compact and ergonomically friendly head-worn virtual displays is studied. We show that exit-pupil expansion of a virtual display designed for near-distance viewing is possible with a diffractive EPE having spherical shape. An analytical model for ray propagation through the proposed EPE is derived. The resulting expressions are used to characterize the geometrical distortions and the lateral color introduced in the pupil expansion process. Moreover, the resolution properties of the EPE are calculated using numerical simulations and compared with the acuity of the human eye. The results show that pupil expansion ratios enabling natural eye movements in typical near-to-eye display applications can be achieved while maintaining the information content of a virtual display.
The rôle of chlorhexidine in the one‐stage full‐mouth disinfection treatment of patients with advanced adult periodontitis (2000)

These findings suggest that the benefits of a "one-stage full-mouth disinfection" in the treatment of patients suffering from severe adult periodontitis probably results from the full-mouth scaling and root planing within 24 h rather than the beneficial effect of chlorhexidine. The raise in body temperature the second day after the full-mouth scaling and root planing seems to indicate a Shwartzman reaction.
Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells (2013)

HIV-infected individuals currently cannot be completely cured because existing antiviral therapy regimens do not address HIV provirus DNA, flanked by long terminal repeats (LTRs), already integrated into host genome. Here, we present a possible alternative therapeutic approach to specifically and directly mediate deletion of the integrated full-length HIV provirus from infected and latently infected human T cell genomes by using specially designed zinc-finger nucleases (ZFNs) to target a sequence within the LTR that is well conserved across all clades. We designed and screened one pair of ZFN to target the highly conserved HIV-1 5'-LTR and 3'-LTR DNA sequences, named ZFN-LTR. We found that ZFN-LTR can specifically target and cleave the full-length HIV-1 proviral DNA in several infected and latently infected cell types and also HIV-1 infected human primary cells in vitro. We observed that the frequency of excision was 45.9% in infected human cell lines after treatment with ZFN-LTR, without significant host-cell genotoxicity. Taken together, our data demonstrate that a single ZFN-LTR pair can specifically and effectively cleave integrated full-length HIV-1 proviral DNA and mediate antiretroviral activity in infected and latently infected cells, suggesting that this strategy could offer a novel approach to eradicate the HIV-1 virus from the infected host in the future.
Split-beam Fourier filter and its application in a gain-flattened EDFA (1995)

Erbium-doped fiber amplifiers (EDFAs) used in long wavelength-division-multiplexed (WDM) systems will require flat gain over the wavelength range of the WDM channels,1 A recent theoretical study2 showed that a Mach-Zehnder filter characteristic with appropriate parameters gives good gain equalization in the 1540-1560-nm wavelength range. In this paper we describe a novel filter, called the split-beam Fourier filter, that has a Mach-Zehnder characteristic with an easily designed wavelength period that offers simplicity and extremely low excess loss as well as tunability of the center wavelength and extinction.
Therapeutic effects of anti-HMGB1 monoclonal antibody on pilocarpine-induced status epilepticus in mice (2017)

Inflammatory processes in brain tissue have been described in human epilepsy of various etiologies and in experimental models of seizures. High mobility group box-1 (HMGB1) is now recognized as representative of damage-associated molecular patterns (DAMPs). In the present study, we focused on whether anti-HMGB1 antibody treatment could relieve status epilepticus- triggered BBB breakdown and inflammation response in addition to the seizure behavior itself. Pilocarpine and methyl-scopolamine were used to establish the acute seizure model. Anti-HMGB1 mAb showed inhibitory effects on leakage of the BBB, and on the HMGB1 translocation induced by pilocarpine. The expression of inflammation-related factors, such as MCP-1, CXCL-1, TLR-4, and IL-6 in hippocampus and cerebral cortex were down-regulated by anti-HMGB1 mAb associated with the number of activated astrocytes, microglial cells as well as the expression of IL-1β. Both hematoxylin & eosin and TUNEL staining showed that the apoptotic cells could be reduced after anti-HMGB1 mAb treatment. The onset and latency of Racine stage five were significantly prolonged in the anti-HMGB1 mAb group. These results suggested that anti-HMGB1 mAb prevented the BBB permeability, reduced HMGB1 translocation while inhibiting the expression of inflammation-related factors, protected against neural cell apoptosis and prolonged Racine stage 5 seizure onset and latency.
C2-ceramide exhibits antiproliferative activity and potently induces apoptosis in endometrial carcinoma (2005)

The purpose of the present study was to investigate the effects of an exogenously administered cell-permeable synthetic ceramide analogue, C(2)-ceramide (N-acetyl-sphingosine) on the growth, cell cycle, and death of Ishikawa human endometrial carcinoma cells. We investigated the effects of C(2)-ceramide on Ishikawa endometrial cancer cell lines in vitro. The cells were treated with C(2)-ceramide, and its effects on cell growth, cell cycle, apoptosis, and related measurements were investigated. MTT assays showed that C(2)-ceramide, a cell-permeable analogue of ceramide, significantly induced dose- and time-dependent death in human endometrial carcinoma Ishikawa cells. Cell-cycle analysis indicated that their exposure to C(2)-ceramide decreased the proportion of cells in S phase and increased the proportion in G0/G1 and/or G2/M phases of the cell cycle. Induction of apoptosis was confirmed by annexin V staining of externalized phosphatidylserine and loss of the transmembrane potential of mitochondria. This induction occurred in concert with the altered expression of genes related to cell growth, malignant phenotype, and apoptosis, including cleavage of poly-ADP ribose polymerase. Furthermore, we demonstrated that the amount of phosphorylated Akt was decreased by C(2)-ceramide. These results raise the possibility that C(2)-ceramide may prove particularly effective in the treatment of endometrial cancers.
[Effect of basic FGF on the proliferation of rat neuroblasts in culture]. (1986)

Cultures highly enriched in neuronal cells, derived from brain hemispheres of 13-day-old rat embryo, were used. In these cultures, neuroblasts proliferate during the first 3 days in vitro. The addition of the astroglial growth factor (AGF2), also known as basic fibroblast growth factor (bFGF), 4 hrs. after seeding, induces a strong increase of [125I]-deoxyuridine incorporation. We checked by autoradiography combined with specific immunocytochemical staining of the neurones, using an anti-neurofilament antibody, that the number of proliferating neuroblasts is increased after the treatment. These results demonstrate that AGF2, or bFGF, is a mitogenic factor for rat neuroblasts in culture.
Towards a testbed for malicious code detection (2002)

An environment for detecting many types of malicious code, including computer viruses, Trojan horses, and time/logic bombs, is proposed. The malicious code testbed (MCT) is based upon both static and dynamic analysis tools developed at the University of California, Davis, which have been shown to be effective against certain types of malicious code. The testbed extends the usefulness of these tools by using them in a complementary fashion to detect more general cases of malicious code. Perhaps more importantly, the MCT allows administrators and security analysts to check a program before installation, thereby avoiding any damage a malicious program might inflict.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sclerostin Is an Osteocyte-expressed Negative Regulator of Bone Formation, But Not a Classical BMP Antagonist (2004)

Sclerosteosis, a skeletal disorder characterized by high bone mass due to increased osteoblast activity, is caused by loss of the SOST gene product, sclerostin. The localization in bone and the mechanism of action of sclerostin are not yet known, but it has been hypothesized that it may act as a bone morphogenetic protein (BMP) antagonist. We show here that SOST/sclerostin is expressed exclusively by osteocytes in mouse and human bone and inhibits the differentiation and mineralization of murine preosteoblastic cells (KS483). Although sclerostin shares some of the actions of the BMP antagonist noggin, we show here that it also has actions distinctly different from it. In contrast to noggin, sclerostin did not inhibit basal alkaline phosphatase (ALP) activity in KS483 cells, nor did it antagonize BMP-stimulated ALP activity in mouse C2C12 cells. In addition, sclerostin had no effect on BMP-stimulated Smad phosphorylation and direct transcriptional activation of MSX-2 and BMP response element reporter constructs in KS483 cells. Its unique localization and action on osteoblasts suggest that sclerostin may be the previously proposed osteocyte-derived factor that is transported to osteoblasts at the bone surface and inhibits bone formation.
Acoustic concentration of particles in piezoelectric tubes: Theoretical modeling of the effect of cavity shape and symmetry breaking (2004)

A new class of simple, highly efficient, cylindrical acoustic concentration devices has been developed based upon cylindrical (or near cylindrical) geometries [Kaduchak et al., Rev. Sci. Instrum. 73, 1332–1336 (2002)] for aerosol concentration applications. The concentrators are constructed from single PZT tubes driven at or near the breathing mode resonance. Acoustic concentration of aerosols is performed within the tube cavity. It has been found that slight modifications to the cylindrical cavity geometry can significantly increase the collection efficiency and assist in precise particle positioning. This paper analyzes the theoretical framework for the acoustic concentration of particles in these devices for various geometrical perturbations. The cavity geometries studied are (1) hollow cylindrical piezoelectric tube, (2) hollow piezoelectric tube with an inner concentric solid cylinder insert, (3) a hollow piezoelectric tube with a concentric elliptic insert which breaks the circular-cylindrical symmetry, and (4) a hollow elliptic cylindrical piezoelectric tube. It is shown that breaking the circular symmetry within the cavity localizes the particles in small spatial regions within the cavity. This localization of particles may be very useful in applications requiring aerosol collection or particle stream positioning.
Learning speaker representation for neural network based multichannel speaker extraction (2017)

Recently, schemes employing deep neural networks (DNNs) for extracting speech from noisy observation have demonstrated great potential for noise robust automatic speech recognition. However, these schemes are not well suited when the interfering noise is another speaker. To enable extracting a target speaker from a mixture of speakers, we have recently proposed to inform the neural network using speaker information extracted from an adaptation utterance from the same speaker. In our previous work, we explored ways how to inform the network about the speaker and found a speaker adaptive layer approach to be suitable for this task. In our experiments, we used speaker features designed for speaker recognition tasks as the additional speaker information, which may not be optimal for the speaker extraction task. In this paper, we propose a usage of a sequence summarizing scheme enabling to learn the speaker representation jointly with the network. Furthermore, we extend the previous experiments to demonstrate the potential of our proposed method as a front-end for speech recognition and explore the effect of additional noise on the performance of the method.
Biochemistry, molecular biology, and genetics of the oligosaccharyltransferase (1996)

Asparagine-linked glycosylation is a highly conserved protein modification reaction that occurs in all eukaryotes. The initial stage in the biosynthesis of N-linked glycoproteins, catalyzed by the enzyme oligosaccharyltransferase (OST), involves the transfer of a preassembled high-mannose oligosaccharide from a dolichol-linked oligosaccharide donor onto asparagine acceptor sites in nascent proteins in the lumen of the rough endoplasmic reticulum. Biochemical, molecular biological, and genetic studies conducted during the past 5 years have resulted in an explosive growth in our knowledge concerning the OST. Although the basic biochemical properties of the enzyme were determined more than a decade ago using intact microsomal membranes, recent studies provide novel insight into the catalytic mechanism of the enzyme. The OST was recently purified as a large heteroligomeric membrane protein complex; the sequences of many of the subunits have been determined from both fungal and vertebrate sources. Consistent with the evolutionary conservation of N-linked glycosylation, protein sequence comparisons reveal significant homologies between vertebrate, invertebrate, plant, and fungal OST subunits. Yeast molecular genetic methods have been instrumental in the functional characterization of the OST subunits, and have proven to be powerful tools for the identification of novel gene products that influence oligosaccharide transfer in vivo.
The Technology Behind Personal Digital Assistants: An overview of the system architecture and key components (2017)

We have long envisioned that one day computers will understand natural language and anticipate what we need, when and where we need it, and proactively complete tasks on our behalf. As computers get smaller and more pervasive, how humans interact with them is becoming a crucial issue. Despite numerous attempts over the past 30 years to make language understanding (LU) an effective and robust natural user interface for computer interaction, success has been limited and scoped to applications that were not particularly central to everyday use. However, speech recognition and machine learning have continued to be refined, and structured data served by applications and content providers has emerged. These advances, along with increased computational power, have broadened the application of natural LU to a wide spectrum of everyday tasks that are central to a user's productivity. We believe that as computers become smaller and more ubiquitous [e.g., wearables and Internet of Things (IoT)], and the number of applications increases, both system-initiated and user-initiated task completion across various applications and web services will become indispensable for personal life management and work productivity. In this article, we give an overview of personal digital assistants (PDAs); describe the system architecture, key components, and technology behind them; and discuss their future potential to fully redefine human?computer interaction.
Magnetic Resonance Imaging Contrast Agents and the Nuclear Pharmacist (1989)

The nuclear pharmacist works with a very specific group of drugs. These drugs generally exhibit no toxic effects and are used almost exclusively for diagnosis. In the past these have been the radioactive drugs used in nuclear medicine and the iodinated contrast agents used in radiology. However, with the advent of magnetic resonance imaging (MRI), there is an additional class of drugs used in radiology, the magnetopharmaceuticals. These drugs are designed especially for increasing diagnostic sensitivity with MRI. This article is intended to provide topical insight into the basics of MRI and magnetopharmaceuticals.
Food proteins : properties and characterization (1996)

Physical and chemical properties of amino acids and proteins denaturation of proteins functional properties of proteins chemical and enzymatic modifications of proteins nutritional value of proteins from different food sources protein analysis - quantification and physical characterization thermal analysis separation and purification biotechnology.
Detection of telomerase, its components, and human papillomavirus in cervical scrapings as a tool for triage in women with cervical dysplasia (2002)

Neither detection of telomerase or its components, nor detection of high risk HPV seem suitable for the triage of women with borderline, mild, and moderate cytological dyskaryosis.
Proteoglycan-Specific Molecular Switch for RPTPσ Clustering and Neuronal Extension (2011)

Heparan and chondroitin sulfate proteoglycans (HSPGs and CSPGs, respectively) regulate numerous cell surface signaling events, with typically opposite effects on cell function. CSPGs inhibit nerve regeneration through receptor protein tyrosine phosphatase sigma (RPTPσ). Here we report that RPTPσ acts bimodally in sensory neuron extension, mediating CSPG inhibition and HSPG growth promotion. Crystallographic analyses of a shared HSPG-CSPG binding site reveal a conformational plasticity that can accommodate diverse glycosaminoglycans with comparable affinities. Heparan sulfate and analogs induced RPTPσ ectodomain oligomerization in solution, which was inhibited by chondroitin sulfate. RPTPσ and HSPGs colocalize in puncta on sensory neurons in culture, whereas CSPGs occupy the extracellular matrix. These results lead to a model where proteoglycans can exert opposing effects on neuronal extension by competing to control the oligomerization of a common receptor.
Isolation and functional characterization of TIF-IB, a factor that confers promoter specificity to mouse RNA polymerase I (1990)

The murine ribosomal gene promoter contains two cis-acting control elements which operate in concert to promote efficient and accurate transcription initiation by RNA polymerase I. The start site proximal core element which is indispensable for promoter recognition by RNA polymerase I (pol I) encompasses sequences from position -39 to -1. An upstream control element (UCE) which is located between nucleotides -142 and -112 stimulates the efficiency of transcription initiation both in vivo and in vitro. Here we report the isolation and functional characterization of a specific rDNA binding protein, the transcription initiation factor TIF-IB, which specifically interacts with the core region of the mouse ribosomal RNA gene promoter. Highly purified TIF-IB complements transcriptional activity in the presence of two other essential initiation factors TIF-IA and TIF-IC. We demonstrate that the binding efficiency of purified TIF-IB to the core promoter is strongly enhanced by the presence in cis of the UCE. This positive effect of upstream sequences on TIF-IB binding is observed throughout the purification procedure suggesting that the synergistic action of the two distant promoter elements is not mediated by a protein different from TIF-IB. Increasing the distance between both control elements still facilitates stable factor binding but eliminates transcriptional activation. The results demonstrate that TIF-IB binding to the rDNA promoter is an essential early step in the assembly of a functional transcription initiation complex. The subsequent interaction of TIF-IB with other auxiliary transcription initiation factors, however, requires the correct spacing between the UCE and the core promoter element.
Multi-label Classification Using Ensembles of Pruned Sets (2008)

This paper presents a pruned sets method (PS) for multi-label classification. It is centred on the concept of treating sets of labels as single labels. This allows the classification process to inherently take into account correlations between labels. By pruning these sets, PS focuses only on the most important correlations, which reduces complexity and improves accuracy. By combining pruned sets in an ensemble scheme (EPS), new label sets can be formed to adapt to irregular or complex data. The results from experimental evaluation on a variety of multi-label datasets show that [E]PS can achieve better performance and train much faster than other multi-label methods.