gebhart/patrepeval huggingface dataset:
The TGF-beta family mediator Smad1 is phosphorylated directly and activated functionally by the BMP receptor kinase. (1997)

Bone morphogenetic proteins (BMPs) are members of the TGF-beta family that regulate cell proliferation, apoptosis, and differentiation, and participate in the development of most tissues and organs in vertebrates. Smad proteins function downstream of TGF-beta receptor serine/threonine kinases and undergo serine phosphorylation in response to receptor activation. Smad1 is regulated in this fashion by BMP receptors, and Smad2 and Smad3 by TGF-beta and activin receptors. Here, we report that BMP receptors phosphorylate and activate Smad1 directly. Phosphorylation of Smad1 in vivo involves serines in the carboxy-terminal motif SSXS. These residues are phosphorylated directly by a BMP type I receptor in vitro. Mutation of these carboxy-terminal serines prevents several Smad1 activation events, namely, Smad1 association with the related protein DPC4, accumulation in the nucleus, and gain of transcriptional activity. Similar carboxy-terminal serines in Smad2 are required for its phosphorylation and association with DPC4 in response to TGF-beta, indicating the generality of this process of Smad activation. As a direct physiological substrate of BMP receptors, Smad1 provides a link between receptor serine/threonine kinases and the nucleus.
Two-Microphone Generalized Sidelobe Canceller with Post-Filter Based Speech Enhancement in Composite Noise (2015)

This paper describes an algorithm to suppress composite noise in a two-microphone speech enhancement system for robust hands-free speech communication. The proposed algorithm has four stages. The first stage estimates the power spectral density of the residual stationary noise, which is based on the detection of nonstationary signal-dominant time-frequency bins (TFBs) at the generalized sidelobe canceller output. Second, speech-dominant TFBs are identified among the previously detected nonstationary signal-dominant TFBs, and power spectral densities of speech and residual nonstationary noise are estimated. In the final stage, the bin-wise output signal-to-noise ratio is obtained with these power estimates and a Wiener post-filter is constructed to attenuate the residual noise. Compared to the conventional beamforming and post-filter algorithms, the proposed speech enhancement algorithm shows significant performance improvement in terms of perceptual evaluation of speech quality.
Developing a Design System into an Intelligent Tutoring System (1997)

As the techniques of artificial intelligence become more widely used, an increasing number of knowledge-based design systems has been developed to handle problems that cannot be solved by traditional computational-based systems. Knowledge-based design systems are embedded with a wealth of design rules and heuristics. In addition, the architecture of knowledge-based system has features such as symbolic and structured programming, objects, rules manipulation, and ruletracing and explanation. Therefore, they are ideal candidates for development into intelligent tutoring systems (ITS). This paper explains how a knowledge-based design prototype system for progressive die design is developed into an ITS that can be used to teach authentic design activities both in the classroom and on-the-job. It illustrates how the flexibility offered in the trainee-system interaction facilitates the exploration of design alternatives and case studies to tackle open-ended design problems. The ITS uses a computer-aided design and drafting (CADD) system as the frontend and automates many of the tedious drafting, measurement, shape recognition and manipulation tasks associated with progressive die planning and design. Therefore, it promises to be a more effective training aid which can help shorten the traditionally long period of apprenticeship training program which a trainee has to follow.
Size and voltage dependence of effective anisotropy in sub-100-nm perpendicular magnetic tunnel junctions (2016)

Magnetic tunnel junctions with perpendicular magnetic anisotropy are investigated using a conductive atomic force microscope. The $1.23\ensuremath{-}\mathrm{nm}$ ${\mathrm{Co}}_{40}{\mathrm{Fe}}_{40}{\mathrm{B}}_{20}$ recording layer coercivity exhibits a size dependence which suggests single-domain behavior for diameters $\ensuremath{\le}\phantom{\rule{0.16em}{0ex}}100$ nm. Focusing on devices with diameters smaller than 100 nm, we determine the effect of voltage and size on the effective device anisotropy ${K}_{\text{eff}}$ using two different techniques. ${K}_{\text{eff}}$ is extracted both from distributions of the switching fields of the recording and reference layers and from measurement of thermal fluctuations of the recording layer magnetization when a field close to the switching field is applied. The results from both sets of measurements reveal that ${K}_{\text{eff}}$ increases monotonically with decreasing junction diameter, consistent with the size dependence of the demagnetization energy density. We demonstrate that ${K}_{\text{eff}}$ can be controlled with a voltage down to the smallest size measured, 64 nm.
Multiple sclerosis. I. The immune pathogenetic hypothesis. (1990)

Animal models indicate that chronic relapsing demyelinating diseases of the central nervous system (CNS) can be induced both by certain viruses and by sensitization to myelinic antigens. Epidemiological data (studies on emigrants and on so-called "Multiple Sclerosis (MS) epidemics") suggest that an environmental transmissible agent, acting on a genetic substrate, could play a role in the pathogenesis of the disease. The transmissible agent could be a virus. Data to this effect are insufficiently indicative, but the hypothesis has been recently put forward that it could be antigenically related to the lymphotropic viruses (HTLV). The transmissible agent could act either by desegregating myelinic antigens or by inducing an alteration of the immune system with a reduction of T lymphocyte suppressor activity. There appears to be rapid and intense activated T lymphocyte "traffic" across the blood-brain barrier in patients affected with MS. Cells specifically sensitized to the unknown antigen find within the CNS other cells able to perpetuate presentation of the antigen (HLA-DR+ astrocytes and endothelial cells, not present in normal brain) and then activate the macrophages which in turn begin immuno-mediated phagocytosis of the healthy myelin. Aspecific immune cells are also recruited into CNS where seem to abnormally proliferate (possibly owing to reduced suppressor activity) producing antibodies against various viral or cerebral antigens which are not clearly related to the pathogenesis of the disease (production of intra-CNS "nonsense" antibodies and synthesis of the oligoclonal immunoglobulin bands seen at the cerebrospinal fluid electrophoresis.)
Reproducibility of Retinal Nerve Fiber Thickness Measurements Using the Stratus OCT in Normal and Glaucomatous Eyes (2005)

Reproducibility of RNFL measurements using the Stratus OCT is excellent in normal and glaucomatous eyes. The nasal quadrant appears to be the most variable measurement. Standard RNFL and Fast RNFL scans are equally reproducible and yield comparable measurements. These findings have implications for the diagnosis of glaucoma and glaucomatous progression.
Stimulator design and subsequent stimulation parameter optimization for controlling micturition and reducing urethral resistance (1996)

An implantable computerized electrical stimulation system designed to induce bladder evacuation in animal models (dogs) after spinal cord transection has been realized and evaluated. This fully programmable system is based on a handheld device and generates a wide range of stimuli through multichannel implantable miniaturized stimulator. Using the new bladder stimulator and inducing reversible fatigue to the external sphincter via the pudendal nerve enables us to reduce the bladder outlet resistance, resulting in the proper emptying of the bladder during stimulation without the need for sacral nerve rhizotomies and the pudendal nerve neurectomies. Four chronically affected dogs were studied to determine the optimal stimulation parameters for inducing a sphincter fatigue that would reliably empty the bladder for the duration of the experiment. These parameters were: maximum amplitude of 1.5 mA +/- 0.5 SD, stimuli composed of a high frequency signal of 200 Hz +/- 50 SD modulated by a low frequency signal of 10 Hz +/- 5 SD, pulse width controlled by a duty-cycle of 20% +/- 10 SD, sacral nerve stimulation of 50 s +/- 25 SD and fatiguing duration of 20 s +/- 5 SD.
High-power pulsed light for microbial decontamination of some fruits and vegetables with different surfaces (2012)

This study focused on the evaluation of possibility to use high-power pulsed light (HPPL) for microbial control of fruits and vegetables (FV) with different irregular surfaces. FV were treated with HPPL and afterwards analyzed in terms of microbial contamination, nutritional quality, colour and texture. Results indicated that the decontamination of FV by HPPL was significant compared to control. Naturally distributed mesophilic bacteria were inactivated by 1.0-1.3 log depending on FV surface characteristics. Inoculated Bacillus cereus was more susceptible to pulsed light treatment and its inactivation reached 1.3-2.0 log depending on surface. The increase of temperature on the surface of fruit never exceeded 42°C. No significant changes in vitamin C, total phenolics, antioxidant capacity, firmness and colour were observed in all treated FV. In conclusion, HPPL is effective, non-thermal and environmentally friendly technique which can be applied for microbial control of fruits and vegetables with different irregular surfaces.
Effect of ac on current-induced domain wall motion (2007)

Saitoh et al. [Nature (London) 432, 203 (2004)] have reported the experimental result showing the interplay of a transverse domain wall with an electrical ac of megahertz-range frequencies. They observed a single peak of resistance in the frequency range and interpreted it with a nonadiabatic spin torque. It was argued that an ac current can induce a micrometer-range displacement of domain wall. We reconstructed the experiment in micromagnetic simulations considering the local nonzero nonadiabatic spin torque. We could not observe either an explicit single peak in the frequency-dependent resistance or an eventual displacement of domain wall by use of an ac. It indicates the local nonadiabatic torque is inappropriate to explain the experimental results of ac-induced domain wall motion. Other approaches such as the nonlocal nonadiabatic spin torque may be needed.
Predictive Value of Serum Carbohydrate Antigen 19‐9 in Malignant Intraductal Papillary Mucinous Neoplasms (2011)

Serum CA 19-9 level has good predictive value for malignant or invasive IPMNs. Patients with CA 19-9 > 63.60 U/ml had poor postoperative prognosis in IPMNs. Preoperative abnormal serum CA 19-9 might be predictive for an aggressive surgical intervention in IPMNs.
Redirected Lysis of Human Melanoma Cells by a MCSP/CD3-bispecific BiTE Antibody That Engages Patient-derived T Cells (2011)

Melanoma-associated chondroitin sulfate proteoglycan (MCSP; also called HMW-MAA, CSPG4, NG2, MSK16, MCSPG, MEL-CSPG, or gp240) is a well characterized melanoma cell-surface antigen. In this study, a new bispecific T-cell engaging (BiTE) antibody that binds to MCSP and human CD3 (MCSP-BiTE) was tested for its cytotoxic activity against human melanoma cell lines. When unstimulated peripheral mononuclear blood cells (PBMCs) derived from healthy donors were cocultured with melanoma cells at effector:target ratios of 1:1, 1:5, or 1:10, and treated with MCSP-BiTE antibody at doses of 10, 100, or 1000 ng/mL, all MCSP-expressing melanoma cell lines (n=23) were lysed in a dose-dependent and effector:target ratio-dependent manner, whereas there was no cytotoxic activity against MCSP-negative melanoma cell lines (n=2). To investigate whether T cells from melanoma patients could act as effector cells, we cocultured unstimulated PBMCs with allogeneic melanoma cells from 13 patients (4 stage I/II, 3 stage III, and 6 stage IV) or with autologous melanoma cells from 2 patients (stage IV). Although cytotoxic activity varied, all 15 PBMC samples mediated significant redirected lysis by the BiTE antibody. When PBMC or CD8 T cells were prestimulated by anti-CD3 antibody OKT-3 and interleukin-2, the MCSP-BiTE concentrations needed for melanoma cell lysis decreased up to 1000-fold. As MCSP is expressed on most human melanomas, immunotherapy with MCSP/CD3-bispecific antibodies merits clinical investigation.
A simple model host for identifying Gram-positive virulence factors (2001)

We demonstrate the use of the nematode Caenorhabditis elegans as a facile and inexpensive model host for several Gram-positive human bacterial pathogens. Enterococcus faecalis, Streptococcus pneumoniae, and Staphylococcus aureus, but not Bacillus subtilis, Enterococcus faecium, or Streptococcus pyogenes, kill adult C. elegans. Focusing our studies on the enterococcal species, we found that both E. faecalis and E. faecium kill C. elegans eggs and hatchlings, although only E. faecalis kills the adults. In the case of adults, a low inoculum of E. faecalis grows to a high titer in the C. elegans intestine, resulting in a persistent infection that cannot be eradicated by prolonged feeding on E. faecium. Interestingly, a high titer of E. faecium also accumulates in the nematode gut, but does not affect the longevity of the worms. Two E. faecalis virulence-related factors that play an important role in mammalian models of infection, fsr, a putative quorum-sensing system, and cytolysin, are also important for nematode killing. We exploit the apparent parallels between Gram-positive infection in simple and more complex organisms by using the nematode to identify an E. faecalis virulence factor, ScrB, which is relevant to mammalian pathogenesis.
Doping of chemically deposited intrinsic CdS thin films to n type by thermal diffusion of indium (1995)

CdS thin films deposited from chemical bath containing citratocadmium(II) and thiourea are intrinsic and highly photosensitive. In the present letter, we discuss the conversion of such films to n type by thermal diffusion of indium from an evaporated 50 nm indium film deposited on the CdS thin film. The process which takes place in the temperature range of 250 °C–350 °C involves the formation of an In2O3 surface layer which acts as a barrier preventing the outdiffusion of indium. This allows indium to diffuse into the CdS film and results in an indium-doped CdS thin film. The electrical conductivity of such films is about 300 Ω−1 cm−1. All beneficial optical properties of chemically deposited CdS thin films for application as a window material in heterojunction optoelectronic devices are retained.
Nano‐ and Micropatterning of Optically Transparent, Mechanically Robust, Biocompatible Silk Fibroin Films (2008)

Regular nanometer-scale patterning down to a few tens of nanometers and the manufacturing of diffractive optical elements in silk by using the ideas of soft lithography is reported. The unique processing of silk films makes them an ideal substrate to incorporate biological matter (such as small organics, enzymes, proteins, cells). Unprecedented definition in the transverse direction, with features down to few tens of nanometers, is reported.
Internet Communications Using SIP: Delivering VoIP and Multimedia Services with Session Initiation Protocol (2006)

The Session Initialion Protocol has received tremendous market acceptance since it became an official IETF Internet communications standard in 1999. SIP is the technology that makes possible multimedia communications sessions on the Web—ones that allow voice, video, chat, interactive games, and others to run all at the same time. Now that the deployment of real SIP networks is about to take off, two leaders of the commercial rollout deliver complete guidance on this exciting new technology. Geared to IT and networking professionals and decision-makers at Internet service providers (ISPs), as well as networking (NSPs) and application (ASPs) service providers, this book helps readers sort through the available vendor offerings and services to discover how to integrate and maximize SIP's power across their networks.
Flexible support for multiple access control policies (2001)

Although several access control policies can be devised for controlling access to information, all existing authorization models, and the corresponding enforcement mechanisms, are based on a specific policy (usually the closed policy). As a consequence, although different policy choices are possible in theory, in practice only a specific policy can actually be applied within a given system. In this paper, we present a unified framework that can enforce multiple access control policies within a single system. The framework is based on a language through which users can specify security policies to be enforced on specific accesses. The language allows the specification of both positive and negative authorizations and incorporates notions of authorization derivation, conflict resolution, and decision strategies. Different strategies may be applied to different users, groups, objects, or roles, based on the needs of the security policy. The overall result is a flexible and powerful, yet simple, framework that can easily capture many of the traditional access control policies as well as protection requirements that exist in real-world applications, but are seldom supported by existing systems. The major advantage of our approach is that it can be used to specify different access control policies that can all coexist in the same system and be enforced by the same security server.
Subthalamic nucleus deep brain stimulus evoked potentials: Physiological and therapeutic implications (2002)

The effect of subthalamic nucleus (STN) stimulation on cortical electroencephalographic activity was examined in 10 patients with Parkinson's disease and 4 patients with epilepsy. Evoked potentials were created by time-locking electroencephalography to the onset of electrical stimulation delivered through the lead implanted in the STN of patients who had previously undergone deep brain stimulation (DBS) surgery. The effect of different patterns of stimulation on the evoked response, including single- and paired-pulse as well as burst stimulation, was explored. Cortical evoked potentials to single pulses were observed with latencies as short as 1 to 2 msec after a single pulse of stimulation, with activity continuing, in some cases, for up to 400 msec. Paired-pulse experiments revealed refractory periods on the order of 0.5 msec, suggesting that stimulation of axons contributed to the generation of at least some portion of the evoked potential waveform. Evoked potentials were also present in response to 100-msec bursts of stimulation, with some evidence that the potential was initiated within the burst artifact. The potential implications of the types of responses observed as well as potential applications are discussed.
Rapamycin (AY-22,989), a new antifungal antibiotic. II. Fermentation, isolation and characterization. (1975)

Rapamycin is a new antifungal antibiotic produced by Streptomyces hygroscopicus NRRL 5491. It was isolated from the mycelium by solvent extraction, purified by silica gel column chromatography and crystallized as a colorless solid which melts at 183 approximately to 185 degrees C and has the empirical formula C56H89NO14. From its characteristic ultraviolet absorption spectrum rapamycin can be classified as a triene. It is highly active against various Candida species, especially Candida albicans. Its activity is compared with that of amphotericin B, candicidin and nystatin.
Analysis of host-cell proteins in biotherapeutic proteins by comprehensive online two-dimensional liquid chromatography/mass spectrometry (2012)

Assays for identification and quantification of host-cell proteins (HCPs) in biotherapeutic proteins over 5 orders of magnitude in concentration are presented. The HCP assays consist of two types: HCP identification using comprehensive online two-dimensional liquid chromatography coupled with high resolution mass spectrometry (2D-LC/MS), followed by high-throughput HCP quantification by liquid chromatography, multiple reaction monitoring (LC-MRM). The former is described as a "discovery" assay, the latter as a "monitoring" assay. Purified biotherapeutic proteins (e.g., monoclonal antibodies) were digested with trypsin after reduction and alkylation, and the digests were fractionated using reversed-phase (RP) chromatography at high pH (pH 10) by a step gradient in the first dimension, followed by a high-resolution separation at low pH (pH 2.5) in the second dimension. As peptides eluted from the second dimension, a quadrupole time-of-flight mass spectrometer was used to detect the peptides and their fragments simultaneously by alternating the collision cell energy between a low and an elevated energy (MSE methodology). The MSE data was used to identify and quantify the proteins in the mixture using a proven label-free quantification technique ("Hi3" method). The same data set was mined to subsequently develop target peptides and transitions for monitoring the concentration of selected HCPs on a triple quadrupole mass spectrometer in a high-throughput manner (20 min LC-MRM analysis). This analytical methodology was applied to the identification and quantification of low-abundance HCPs in six samples of PTG1, a recombinant chimeric anti-phosphotyrosine monoclonal antibody (mAb). Thirty three HCPs were identified in total from the PTG1 samples among which 21 HCP isoforms were selected for MRM monitoring. The absolute quantification of three selected HCPs was undertaken on two different LC-MRM platforms after spiking isotopically labeled peptides in the samples. Finally, the MRM quantitation results were compared with TOF-based quantification based on the Hi3 peptides, and the TOF and MRM data sets correlated reasonably well. The results show that the assays provide detailed valuable information to understand the relative contributions of purification schemes to the nature and concentrations of HCP impurities in biopharmaceutical samples, and the assays can be used as generic methods for HCP analysis in the biopharmaceutical industry.
Planar-integrated optical vector-matrix multiplier (2000)

We present the design of a planar-integrated optoelectronic vector-matrix multiplier. The inherent parallel-processing potential is fully exploited by optical implementation of multiplications and summations. Planar integration makes the free-space optical system compatible with electronic VLSI technologies. It is composed of phase-only diffractive optical elements, which implement lens and multiple-beam-splitter functions. A demonstrator version of the optical system for a matrix of size 10 x 10 was fabricated on quartz glass by means of multimask lithography and reactive ion etching. It shows low cross talk and good uniformity of the signals.