gebhart/patrepeval huggingface dataset:
De novo amyloid proteins from designed combinatorial libraries (1999)

Amyloid deposits are associated with several neurodegenerative diseases, including Alzheimer's disease and the prion diseases. The amyloid fibrils isolated from these different diseases share similar structural features. However, the protein sequences that assemble into these fibrils differ substantially from one disease to another. To probe the relationship between amino acid sequence and the propensity to form amyloid, we studied a combinatorial library of sequences designed de novo. All sequences in the library were designed to share an identical pattern of alternating polar and nonpolar residues, but the precise identities of these side chains were not constrained and were varied combinatorially. The resulting proteins self-assemble into large oligomers visible by electron microscopy as amyloid-like fibrils. Like natural amyloid, the de novo fibrils are composed of beta-sheet secondary structure and bind the diagnostic dye, Congo red. Thus, binary patterning of polar and nonpolar residues arranged in alternating periodicity can direct protein sequences to form fibrils resembling amyloid. The model amyloid fibrils assemble and disassemble reversibly, providing a tractable system for both basic studies into the mechanisms of fibril assembly and the development of molecular therapies that interfere with this assembly.
Adaptive Algorithms for Estimating and Suppressing Narrow-Band Interference in PN Spread-Spectrum Systems (1982)

Results of an investigation of algorithms for estimating and suppressing narrow-band interference in pseudonoise (PN) spread-spectrum digital communication systems are presented. Techniques for determining the coefficients of a linear, interference suppression filter are described, which are based on linear prediction and conventional spectral analysis methods. Numerical results are presented on the characteristics of the linear filter and on its effectiveness in suppressing the interference. The error rate performance of a receiver that employs the interference suppression filter followed by a PN correlator is determined based on the assumption that the combined noise and residual interference at the output of the PN correlator is Gaussian distributed. Performance results obtained by Monte Carlo simulation are also presented and compared with theoretical results.
Ligand Design and Bioconjugation of Colloidal Gold Nanoparticles (2002)

An ambitious goal in the area of nanobiosciences is to combine the functionality and stability of nanostructured inorganic solids with the structural variety and the self-organizing abilities of biochemical molecules. How the ligand shell of nanoparticles needs to be built up to achieve a stable and specific conjugation with biological molecules and to coordinate the chemical properties of nanoparticles and biomolecules is exemplified for gold nanoparticles conjugated with avidin (see picture). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2002/z18961_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Confirming Target Engagement for Reversible Inhibitors in Vivo by Kinetically Tuned Activity-Based Probes (2012)

The development of small-molecule inhibitors for perturbing enzyme function requires assays to confirm that the inhibitors interact with their enzymatic targets in vivo. Determining target engagement in vivo can be particularly challenging for poorly characterized enzymes that lack known biomarkers (e.g., endogenous substrates and products) to report on their inhibition. Here, we describe a competitive activity-based protein profiling (ABPP) method for measuring the binding of reversible inhibitors to enzymes in animal models. Key to the success of this approach is the use of activity-based probes that show tempered rates of reactivity with enzymes, such that competition for target engagement with reversible inhibitors can be measured in vivo. We apply the competitive ABPP strategy to evaluate a newly described class of piperazine amide reversible inhibitors for the serine hydrolases LYPLA1 and LYPLA2, two enzymes for which selective, in vivo active inhibitors are lacking. Competitive ABPP identified individual piperazine amides that selectively inhibit LYPLA1 or LYPLA2 in mice. In summary, competitive ABPP adapted to operate with moderately reactive probes can assess the target engagement of reversible inhibitors in animal models to facilitate the discovery of small-molecule probes for characterizing enzyme function in vivo.
Efficient type I blue second-harmonic generation in periodically segmented KTiOPO4 waveguides (1990)

We report type I phase-matched blue second-harmonic generation from periodically segmented channel ion-exchanged waveguides in KTiOPO4 with output wavelengths from 0.38 to 0.48 μm and efficiencies exceeding 50%/W cm2. Evidence is presented suggesting that these efficiencies result from ferroelectric domain reversals induced by waveguide fabrication. Waveguide structure, wavelength, and output power characteristics are presented.
Virus Envelope Protein of HTLV-III Represents Major Target Antigen for Antibodies in AIDS Patients (1985)

In this study, two glycoproteins (gp160 and gp120) that are encoded by human T-cell lymphoma virus type III (HTLV-III) were the antigens most consistently recognized by antibodies found in patients with the acquired immune deficiency syndrome (AIDS) and with the AIDS-related complex (ARC) and in healthy homosexual males. The techniques used to detect the glycoproteins were radioimmunoprecipitation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (RIP/SDS-PAGE). Although most antibody-positive samples from ARC patients and from healthy homosexual males also reacted with the virus core protein p24, less than half of the AIDS patients revealed a positive band with p24 under the same conditions. The ability to detect antibodies against a profile of both the major env gene encoded antigens and the gag gene encoded antigens suggests that the RIP/SDS-PAGE may be a valuable confirmatory assay for establishing the presence or absence of antibodies to HTLV-III in human serum samples.
Role of Testosterone, Estradiol, and Insulin in Diet- and Exercise-Induced Reductions in Serum-Stimulated Prostate Cancer Cell Growth In Vitro (2002)

Prostate cancer risk is associated with a high-fat diet and a sedentary lifestyle. Placing men on a low-fat diet-and-exercise intervention reduces serum hormones, including estradiol, insulin, and free testosterone, that may play a role in prostate cancer growth. Eight men participated in a low-fat diet-and-exercise program for a mean of 14.2 yr, and LNCaP cell growth in culture was measured in medium supplemented with 10% of each subject's serum as well as with testosterone, estradiol, and insulin added singly or in combination. These results were compared in the fetal bovine serum (FBS)-stimulated growth and cell growth in serum obtained from a control group of 14 overweight men. In separate tissue culture experiments, LNCaP and PC-3 cell growth was also measured in response to the addition of testosterone, estradiol, or insulin to steroid-stripped FBS. LNCaP cell growth in medium with subject serum was 40% less than in FBS-stimulated medium and 49% less than in medium with serum from control, overweight men. Addition of testosterone, estradiol, and insulin to serum from diet-and-exercise subjects significantly stimulated LNCaP cell growth in vitro but accounted for only about half of the difference between the control and diet-and-exercise subjects. Thus other serum changes must also account for the significant reduction in LNCaP cell growth observed using medium with serum from the diet-and-exercise subjects in the cell culture assay.
Cellular digital packet data networks (2002)

Cellular digital packet data (CDPD) is the first wide area wireless data network with open interfaces to enter the wireless services market. Operating in the 800-MHz cellular bands, CDPD offers native support of transmission control protocol/Internet protocol (TCP/IP) and connectionless network protocol (CLNP). This paper presents an overview of CDPD's network architecture, its network performance issues, and wireless data applications that take advantage of CDPD's seamless support of IP and CLNP data.
Decentralizing the economic dispatch problem using a two-level incremental cost consensus algorithm in a smart grid environment (2011)

In a smart grid, effective distributed control algorithms could be embedded in distributed controllers to properly allocate electrical power among connected buses autonomously. By selecting the incremental cost of each generation unit as the consensus variable, the Incremental Cost Consensus (ICC) algorithm can solve the economic dispatch problem in a distributed manner instead of using conventional centralized approaches. In this paper, we further decrease the requirement of the communication network by using an average consensus algorithm to acquire the system power mismatch information. The mathematical formulation of the algorithms is also presented in this paper. In addition, the results of several case studies are presented to show the convergence rate of the ICC algorithm and the comparison between the previous ICC and the new two-level ICC algorithm.
The Effect of Superpulsed Carbon Dioxide Laser Energy on Keloid and Normal Dermal Fibroblast Secretion of Growth Factors: A Serum-Free Study (2000)

An in vitro model was used to determine the effect of superpulsed CO2 laser energy on normal dermal and keloid-producing fibroblast proliferation and release of growth factors. Growth factors assayed included basic fibroblast growth factor (bFGF) and transforming growth factor beta1 (TGF-beta1). bFGF is mitogenic, inhibits collagen production, and stabilizes cellular phenotype. TGF-beta1 stimulates growth and collagen secretion and is thought to be integral to keloid formation. Growth in a serum-free medium allowed measurement of these growth factors without confounding variables. Keloid and normal dermal fibroblasts cell lines were established from facial skin samples using standard explant techniques. Samples consisted of three separate keloid and three separate normal dermal fibroblast cell lines. Cells were used at passage 4 to seed 24-well trays at a concentration of 6 x 10(4) cells per milliliter in serum-free medium. At 48 hours, 18.8 percent of each cell well was exposed to a fluence of 2.4, 4.7, and 7.3 J/cm2 using the superpulsed CO2 laser. Cell viability and counts were established at four time points: 0 (time of superpulsed CO2 laser treatment), 24, 72, and 120 hours. Supernatants were collected and assessed for bFGF and TGF-beta1 using a sandwich enzyme immunoassay. All cell lines demonstrated logarithmic growth through 120 hours (conclusion of experiment), with a statistically significant shorter population doubling time for keloid fibroblasts (p < 0.05). Use of the superpulsed CO2 laser shortened population doubling times relative to that of controls; the differences were statistically significant in keloid dermal fibroblasts when fluences of 2.4 and 4.7 J/cm2 were used (p < 0.05 and 0.01, respectively). bFGF was present in greater levels in normal dermal fibroblasts than in keloid dermal fibroblasts. Application of superpulsed CO2 demonstrated a trend toward increased bFGF secretion in both fibroblast types; the increase was significant in the keloid group at 4.7J/cm2. A consistent trend in suppression of TGF-beta1 was seen in both groups exposed to superpulsed CO2, with the maximal effect occurring at 4.7 J/cm2. Serum-free culture sustains logarithmic cell growth and allows growth factor measurement without confounding variables from serum-containing media. Superpulsed CO2 enhances fibroblast replication and seems to stimulate bFGF secretion and to inhibit TGF-beta1 secretion. Given the function of these growth factors, the application of superpulsed CO2 may support normalized wound healing. These findings may explain the beneficial effects of laser resurfacing on a cellular level and support the use of superpulsed CO2 in the management of keloid scar tissue.
Natural methods for robot task learning (2003)

Among humans, teaching various tasks is a complex process which relies on multiple means for interaction and learning, both on the part of the teacher and of the learner. Used together, these modalities lead to effective teaching and learning approaches, respectively. In the robotics domain, task teaching has been mostly addressed by using only one or very few of these interactions. In this paper we present an approach for teaching robots that relies on the key features and the general approach people use when teaching each other: first give a demonstration, then allow the learner to refine the acquired capabilities by practicing under the teacher's supervision, involving a small number of trials. Depending on the quality of the learned task, the teacher may either demonstrate it again or provide specific feedback during the learner's practice trial for further refinement. Also, as people do during demonstrations, the teacher can provide simple instructions and informative cues, increasing the performance of learning. Thus, instructive demonstrations, generalization over multiple demonstrations and practice trials are essential features for a successful human-robot teaching approach. We implemented a system that enables all these capabilities and validated these concepts with a Pioneer 2DX mobile robot learning tasks from multiple demonstrations and teacher feedback.
Plasma Levels of Adrenomedullin in Patients with Acute Myocardial Infarction (1998)

1. Adrenomedullin, a newly identified vasorelaxant peptide, participates in the regulation of the cardiovascular system. To investigate the pathophysiological significance of adrenomedullin in patients with acute myocardial infarction, we measured plasma levels of adrenomedullin. 2. Cardiac catheterization was performed on admission, after 1 day, and after 4 weeks in 36 patients with acute myocardial infarction. We measured plasma levels of adrenomedullin, atrial natriuretic peptide and brain natriuretic peptide in the right atrium, pulmonary artery and aorta. 3. Plasma levels of adrenomedullin in the right atrium (mean +/- SEM) were significantly increased on admission (4.2 +/- 2.6 h) in patients with acute myocardial infarction (10.6 +/- 1.0 pmol/l) compared with controls (5.2 +/- 0.3 pmol/l, P < 0.01). In addition, plasma levels of adrenomedullin were further elevated in patients with congestive heart failure (12.3 +/- 1.4 pmol/l) compared with patients without congestive heart failure (7.8 +/- 0.6 pmol/l, P < 0.01). In patients with congestive heart failure, plasma adrenomedullin on admission significantly correlated with atrial natriuretic peptide and brain natriuretic peptide. 4. These results suggest that plasma adrenomedullin increases in the early phase of acute myocardial infarction and that volume expansion may be one of the additional stimuli for the release of adrenomedullin in patients with acute myocardial infarction complicated by congestive heart failure.
Singularity analysis of closed-loop kinematic chains (1990)

The different kinds of singularities encountered in closed-loop kinematics chains are analyzed. A general classification of these singularities in three main groups, which is based on the properties of the Jacobian matrices of the chain, is described. The identification of the singular configurations is particularly relevant for hard automation modules or robotic devices based on closed kinematic chains, such as linkages and parallel manipulators. Examples are given to illustrate the application of the method to these mechanical systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On-Line Monitoring of Apoptosis in Insulin-Secreting Cells (2003)

Apoptosis was monitored in intact insulin-producing cells both with microfluorometry and with two-photon laser scanning microscopy (TPLSM), using a fluorescent protein based on fluorescence resonance energy transfer (FRET). TPLSM offers three-dimensional spatial information that can be obtained relatively deep in tissues. This provides a potential for future in vivo studies of apoptosis. The cells expressed a fluorescent protein (C-DEVD-Y) consisting of two fluorophores, enhanced cyan fluorescent protein (ECFP) and enhanced yellow fluorescent protein (EYFP), linked by the amino acid sequence DEVD selectively cleaved by caspase-3-like proteases. FRET between ECFP and EYFP in C-DEVD-Y could therefore be monitored on-line as a sensor of caspase-3 activation. The relevance of using caspase-3 activation to indicate beta-cell apoptosis was demonstrated by inhibiting caspase-3-like proteases with Z-DEVD-fmk and thereby showing that caspase-3 activation was needed for high-glucose-and cytokine-induced apoptosis in the beta-cell and for staurosporine-induced apoptosis in RINm5F cells. In intact RINm5F cells expressing C-DEVD-Y and in MIN6 cells expressing the variant C-DEVD-Y2, FRET was lost at 155 +/- 23 min (n = 9) and 257 +/- 59 min (n = 4; mean +/- SE) after activation of apoptosis with staurosporine (6 micromol/l), showing that this method worked in insulin-producing cells.
Histological Evaluation of Human Intraosseous Healing Responses to the Placement of Tricalcium Phosphate Ceramic Implants (1986)

Eight intrabony lesions in four patients were removed en bloc 3 to 8 months after periodontal flap debridement. At the time of debridement, the position of the gingival margin and the most apically located calculus were notched to serve as reference points. All lesions received "Synthograft" implants and lesions healed uneventfully. Even though these were severely involved periodontal sites, clinical measurements at time of block removal demonstrated gingival recession (average = 2.9 mm) and a gain in clinical closure (average = 2.6 mm). Histologically, graft particles were present in each specimen. They were walled off by collagen and did not appear to enhance new attachment nor did they induce an inflammatory infiltrate. Thus, they seemed to act as nonirritating fillers. Microscopically, closure of the lesions demonstrated repair with limited evidence of new connective tissue attachment. Histologic expression of the clinical gain in closure was the result of closure by long epithelial adhesion (long junctional epithelium) and possible linkage of dentinal collagen with gingival fibers at areas of dentinal resorption. These variations in closure were often seen within the same clinical site.
Role of renal nerves in onset and maintenance of spontaneous hypertension (1982)

Renal denervation has been reported to delay development of hypertension in Okamoto spontaneously hypertensive rats (SHR) but to have no effect on the final hypertensive state. However, functional reinnervation begins to occur about 1 mo after renal denervation. The arterial pressure of SHR undergoing repeated bilateral renal denervations at the age of 4, 7, 10, 13, and 16 wk was compared with that in sham-operated SHR. In addition, the effect of successive renal denervations at 4, 7, and 10 wk of age in Wistar-Kyoto (WKY) control rats was determined. Both indirect measurement of pressure by the tail-cuff technique and mean arterial pressure (MAP) measurement indicated that renal denervation prevents full expression of hypertension in SHR. MAP in 19-wk-old renal-denervation SHR averaged 159 +/- 5.1 mmHg (SE) vs. 178 +/-0 4.2 mmHg in sham-operated SHR. Renal denervation had no effect on arterial pressure of WKY rats. Renal norepinephrine content in the renal-denervated WKY rats and SHR was less than 20% of that in the sham-operated groups. Successive bilateral renal denervations every 3 wk blocks 30-40% of the expected progressive elevation of arterial pressure in aging SHR.
MPI-LAPI: an efficient implementation of MPI for IBM RS/6000 SP systems (2001)

The IBM RS/6000 SP system is one of the most cost-effective commercially available high performance machines. IBM RS/6000 SP systems support the Message Passing Interface standard (MPI) and LAPI. LAPI is a low level, reliable and efficient one-sided communication API library implemented on IBM RS/6000 SP systems. This paper explains how the high performance of the LAPI library has been exploited in order to implement the MPI standard more efficiently than the existing MPI. It describes how to avoid unnecessary data copies at both the sending and receiving sides for such an implementation. The resolution of problems arising from the mismatches between the requirements of the MPI standard and the features of LAPI is discussed. As a result of this exercise, certain enhancements to LAPI are identified to enable an efficient implementation of MPI on LAPI. The performance of the new implementation of MPI is compared with that of the underlying LAPI itself. The latency (in polling and interrupt modes) and bandwidth of our new implementation is compared with that of the native MPI implementation on RS/6000 SP systems. The results indicate that the MPI implementation on LAPI performs comparably to or better than the original MPI implementation in most cases. Improvements of up to 17.3 percent in polling mode latency, 35.8 percent in interrupt mode latency, and 20.9 percent in bandwidth are obtained for certain message sizes. The implementation of MPI on top of LAPI also outperforms the native MPI implementation for the NAS Parallel Benchmarks.
Parkinson disease: an update. (2013)

Parkinson disease is a progressive neurologic disorder afflicting approximately 1 percent of Americans older than 60 years. The cardinal features of Parkinson disease are bradykinesia, rigidity, tremor, and postural instability. There are a number of neurologic conditions that mimic the disease, making it difficult to diagnose in its early stages. Physicians who rarely diagnose Parkinson disease should refer patients suspected of having it to physicians with more experience in making the diagnosis, and should periodically reevaluate the accuracy of the diagnosis. Treatment is effective in reducing motor impairment and disability, and should be started when a patient begins to experience functional impairment. The combination of carbidopa and levodopa is the most effective treatment, but dopamine agonists and monoamine oxidase-B inhibitors are also effective, and are less likely to cause dyskinesias. For patients taking carbidopa/levodopa who have motor complications, adjunctive therapy with a dopamine agonist, a monoamine oxidase-B inhibitor, or a catechol O-methyltransferase inhibitor will improve motor symptoms and functional status, but with an increase in dyskinesias. Deep brain stimulation is effective in patients who have poorly controlled symptoms despite optimal medical therapy. Occupational, physical, and speech therapy improve patient function. Fatigue, sleep disturbances, dementia, and depression are common in patients with Parkinson disease. Although these conditions are associated with significantly lower quality of life, they may improve with treatment.