gebhart/patrepeval huggingface dataset:
Inhibition of protein geranylgeranylation requires p27kip1 to induce human breast cancer cell death (2007)

AACR Annual Meeting-- Apr 14-18, 2007; Los Angeles, CA

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Decreased levels of the CDK inhibitor p27Kip1 are associated with poor prognosis in breast cancer patients. We designed a novel tetrapeptide mimic inhibitor of geranylgeranyltransferase I (GGTase I), GGTI-2418, that significantly induces breast tumor cell death by increasing the protein levels of p27Kip1. GGTI-2418, inhibits GGTase I competitively (Ki = 4.4 ± 1.6nM) and selectively (5600 fold) over farnesyltransferase. In human breast cancer cell lines, GGTI-2417 a methyl ester prodrug of GGTI-2418 induces p27Kip1 levels, tumor cell death and G/G1 accumulation. p27Kip1 knockout cells and p27kip1 siRNA experiments demonstrated that GGTI-2417-induced breast tumor cell death requires p27Kip1. In nude mouse xenografts, GGTI-2418 suppresses the growth of human breast tumors. In transgenic mice where breast tumors are driven by the oncogene ErbB2, GGTI-2418 induces significant tumor regression.
12-O-Tetradecanoylphorbol-13-acetate stimulation of DNA synthesis in cultured preneoplastic familial polyposis colonic epithelial cells but not in normal colonic epithelial cells. (1984)

We have developed a method for the routine primary culture of human colonic epithelial cells. Cultured cells exhibited characteristic epithelial structures, including a brush border and junctional complexes. Flask-like goblet cells containing mucus were also seen within the epithelial monolayer. [3H]Thymidine labeling indices were used to distinguish between cultured cells from familial polyposis patients, other patients at high risk to develop colon cancer, and low-risk control subjects. 12-O-Tetradecanoylphorbol-13-acetate (TPA) at 10 ng/ml enhanced DNA synthesis an average of 8-fold when assayed by labeling index in colonic epithelial cells from five of six familial polyposis patients. No such stimulation by TPA was seen in cells from 13 high-risk patients without familial polyposis or in cells from five low-risk subjects. Hundreds of benign polyps can be found in the colons of familial polyposis patients. One such benign tubular adenoma exhibited the same enhancement of DNA synthesis by TPA as normal-appearing epithelial cells from a biopsy adjacent to that polyp. Mitogenic response to TPA had been seen earlier in cells from each of four tubular adenomas (Friedman, E. Cancer Res., 41: 4588-4599, 1981). Both familial polyposis epithelial cells and adenoma cells are considered preneoplastic, but they are not identical because their patterns of actin cytoskeletal organization differ. These results imply that familial polyposis epithelial cells are precursors of tubular adenoma cells, and their transition to the more advanced preneoplastic cells of this benign tumor is influenced by endogeneous tumor promoters.
Automatic Detection of Squats in Railway Infrastructure (2014)

This paper presents an automatic method for detecting railway surface defects called “squats” using axle box acceleration (ABA) measurements on trains. The method is based on a series of research results from our group in the field of railway engineering that includes numerical simulations, the design of the ABA prototype, real-life implementation, and extensive field tests. We enhance the ABA signal by identifying the characteristic squat frequencies, using improved instrumentation for making measurements, and using advanced signal processing. The automatic detection algorithm for squats is based on wavelet spectrum analysis and determines the squat locations. The method was validated on the Groningen-Assen track in The Netherlands and accurately detected moderate and severe squats with a hit rate of 100%, with no false alarms. The methodology is also sensitive to small rail surface defects and enables the detection of squats at their earliest stage. The hit rate for small rail surface defects was 78%.
New Method Developed to Measure Contact Angles of a Sessile Drop (2002)

The spreading of an evaporating liquid on a solid surface occurs in many practical processes and is of importance in a number of practical situations such as painting, textile dyeing, coating, gluing, and thermal engineering. Typical processes involving heat transfer where the contact angle plays an important role are film cooling, boiling, and the heat transfer through heat pipes. The biological phenomenon of cell spreading also is analogous to a drop spreading (ref. 1). In the study of spreading, the dynamic contact angle describes the interfacial properties on solid substrates and, therefore, has been studied by physicists and fluid mechanics investigators. The dynamic contact angle of a spreading nonvolatile liquid drop provides a simple tool in the study of the free-boundary problem, but the study of the spreading of a volatile liquid drop is of more practical interest because the evaporation of common liquids is inevitable in practical processes. The most common method to measure the contact angle, the contact radius, and the height of a sessile drop on a solid surface is to view the drop from its edge through an optical microscope. However, this method gives only local information in the view direction. Zhang and Yang (ref. 2) developed a laser shadowgraphy method to investigate the evaporation of sessile drop on a glass plate. As described here, Zhang and Chao (refs. 3 and 4) improved the method and suggested a new optical arrangement to measure the dynamic contact angle and the instant evaporation rate of a sessile drop with much higher accuracy (less than 1 percent). With this method, any fluid motion in the evaporating drop can be visualized through shadowgraphy without using a tracer, which often affects the field under investigation.
Angelic debugging (2011)

Software ships with known bugs because it is expensive to pinpoint and fix the bug exposed by a failing test. To reduce the cost of bug identification, we locate expressions that are likely causes of bugs and thus candidates for repair. Our symbolic method approximates an ideal approach to fixing bugs mechanically, which is to search the space of all edits to the program for one that repairs the failing test without breaking any passing test. We approximate the expensive ideal of exploring syntactic edits by instead computing the set of values whose substitution for the expression corrects the execution. We observe that an expression is a repair candidate if it can be replaced with a value that fixes a failing test and in each passing test, its value can be changed to another value without breaking the test. The latter condition makes the expression flexible in that it permits multiple values. The key observation is that the repair of a flexible expression is less likely to break a passing test. The method is called angelic debugging because the values are computed by angelically nondeterministic statements. We implemented the method on top of the Java PathFinder model checker. Our experiments with this technique show promise of its applicability in speeding up program debugging.
PTH-092 Discovery and quantitation of novel liver fibrosis biomarkers using proteomics (2015)

<h3>Introduction</h3> Liver biopsy is the reference standard for assessing liver fibrosis and serum biomarkers can be used as a less invasive approach. Various antibody-based assays for serum biomarkers are currently in use to help diagnose fibrosis stage. However, these immunoassays have potential disadvantages such as the inability to detect degraded proteins and often these assays are time consuming. We have developed an antibody-free method to detect and quantify novel liver fibrosis biomarkers in human plasma/serum which overcomes these disadvantages. <h3>Method</h3> Novel liver fibrosis biomarkers were identified by analysing proteins in plasma/serum samples from controls and patients with varying stages of liver fibrosis using a proteomics technique: two dimensional gel electrophoresis (2DE). For the most promising liver fibrosis biomarkers, an antibody-free assay (parallel reaction monitoring using mass spectrometry) was used which detects tryptic peptides of the biomarkers and their fragments. A calibration curve, established from known amounts of synthetic isotopically labelled peptides, was used to determine the concentrations of our biomarkers in serum/plasma samples from patients with varying stages of liver fibrosis. <h3>Results</h3> Several candidate biomarkers for hepatic fibrosis were identified using 2DE. Our best biomarkers were promising when compared by Western blotting to the proteins used in existing serum biomarker tests for liver fibrosis. Using parallel reaction monitoring, antibody-free assays were developed for our most promising biomarkers which were able to successfully discriminate between neighbouring stages of liver fibrosis. <h3>Conclusion</h3> We have developed a fast, sensitive and robust antibody-free method to detect and quantify novel liver fibrosis biomarkers in human plasma/serum. Unlike immunoassays which are restricted on the number of biomarkers due to antibody cost, our method can successfully detect and quantify more than 50 biomarkers in a single 30 min run. This novel assay may help clinicians to assess hepatic fibrosis and reduce the need for invasive liver biopsies. <h3>Disclosure of interest</h3> None Declared. <h3>References</h3> Bevin Gangadharan <i>et al</i>. Discovery of novel biomarker candidates for liver fibrosis in hepatitis C patients. PLoS One 2012;7:e39603 Bevin Gangadharan <i>et al</i>. Two dimensional gel electrophoresis using pH3-5.6 immobilised pH gradient strips identifies potential novel disease biomarkers. <i>Nature Protocol Exchange</i>, 2011:doi:10.1038/protex.2011.261 Bevin Gangadharan <i>et al</i>. New approaches for biomarker discovery: The search for liver fibrosis markers in hepatitis C patients. J Proteome Res 2011;10:2643 Bevin Gangadharan <i>et al</i>. Novel serum biomarker candidates for liver fibrosis in hepatitis C patients. Clin Chem 2007;53:1792
Adenosine Deaminase Inhibitors:  Synthesis and Biological Evaluation of Unsaturated, Aromatic, and Oxo Derivatives of (+)-<i>e</i><i>rythro</i>-9-(2‘<i>S</i>-Hydroxy-3‘<i>R</i>-nonyl)adenine [(+)-EHNA] (2000)

The synthesis and biological evaluation of three classes of chain-modified derivatives of (+)-EHNA are described. Among the 5', 6'-unsaturated derivatives, the Z-isomer was the most potent inhibitor of adenosine deaminase (ADA) but 3-fold less active than (+)-EHNA. Several 9-aralkyladenines (ARADs) have been prepared, and their inhibitory activity was determined. A minimum of two carbon atoms separating the aromatic ring from the adenine-bearing carbon (C-3') was found to be essential for ADA activity equal to or slightly greater than that of (+)-EHNA. Finally, replacement of the C-5' carbon with an oxygen resulted in reduced potency.
Distral: Robust Multitask Reinforcement Learning (2025)

Neural information processing systems foundation. All rights reserved. Most deep reinforcement learning algorithms are data inefficient in complex and rich environments, limiting their applicability to many scenarios. One direction for improving data efficiency is multitask learning with shared neural network parameters, where efficiency may be improved through transfer across related tasks. In practice, however, this is not usually observed, because gradients from different tasks can interfere negatively, making learning unstable and sometimes even less data efficient. Another issue is the different reward schemes between tasks, which can easily lead to one task dominating the learning of a shared model. We propose a new approach for joint training of multiple tasks, which we refer to as Distral (distill &amp; transfer learning). Instead of sharing parameters between the different workers, we propose to share a "distilled" policy that captures common behaviour across tasks. Each worker is trained to solve its own task while constrained to stay close to the shared policy, while the shared policy is trained by distillation to be the centroid of all task policies. Both aspects of the learning process are derived by optimizing a joint objective function. We show that our approach supports efficient transfer on complex 3D environments, outperforming several related methods. Moreover, the proposed learning process is more robust to hyperparameter settings and more stable - attributes that are critical in deep reinforcement learning.
New six degree of freedom position sensor greatly improves flexible manufacturing -- but will manufacturers adapt? (1998)

The manufacturing industry needs better multi-dimensional position sensors to keep pace with increased speed and capabilities of automated equipment and robots. The market for laser and vision sensors is growing at a rapid speed; however, most of the robot- mounted sensors are one or two dimensional, three dimensional at most, while the robotics industry has progressed to 6-axis machines, leaving a gross mismatch in its capability to perform and sense the required task. A new laser sensor provides information. on up to six degrees of position, enabling robots to sense as well as it can physically manipulate, and opening the door to vast improvements in flexible manufacturing. To expedite these improvements, the manufacturing industry should take a lead and not let an outdated norm hinder implementation.
Purification, Cloning, and Bacterial Expression of Retinol Dehydratase from (1996)

Anhydroretinol and 14-hydroxy-4,14-retro-retinol, retro-retinoids endogenous to both mammals and insects, act as agonist and antagonist, respectively, in controlling proliferation in lymphoblasts and other retinol-dependent cells. We describe here the identification, purification, cloning, and bacterial expression of the enzyme retinol dehydratase, which converts retinol to anhydroretinol in Spodoptera frugiperda. Retinol dehydratase has nanomolar affinity for its substrate and is, therefore, the first enzyme characterized able to utilize free retinol at physiological intracellular concentrations. The enzyme shows sequence homology to the sulfotransferases and requires 3'-phosphoadenosine 5'-phosphosulfate for activity.
Tin-117m-labeled stannic (Sn/sup 4 +/) chelate of diethylenetriamine pentaacetic acid (DTPA) for application in diagnosis and therapy (1983)

The radiopharmaceutical reagents of this invention and the class of Tin-117m radiopharmaceuticals are therapeutic and diagnostic agents that incorporate gamma-emitting nuclides that localize in bone after intravenous injection in mammals (mice, rats, dogs, and rabbits). Images reflecting bone structure or function can then be obtained by a scintillation camera that detects the distribution of ionizing radiation emitted by the radioactive agent. Tin-117m-labeled chelates of stannic tin localize almost exclusively in cortical bone. Upon intravenous injection of the reagent, the preferred chelates are phosphonate compounds, preferable, PYP, MDP, EHDP, and DTPA. This class of reagents is therapeutically and diagnostically useful in skeletal scintigraphy and for the radiotherapy of bone tumors and other disorders.
Autonomous receivers for complex format identification and demodulation (2014)

We demonstrate a new universal DSP receiver architecture for ground-based optical communications that autonomously identifies and decode TDHMFs in addition to conventional formats. The combination of a flexible and modular architecture with proper statistical tools has enabled successful validation of autonomous identification and demodulation, suggesting that these methods are extensible to any format including those not yet examined. Similar architectural concepts can be generalized to wireless communications, thus spanning the whole communication range of the avionics ecosystem.
Circulating tumor cells monitored over time in lung cancer patients (2009)

11025 Background: Circulating tumor cell (CTC) detection and enumeration is a valuable tool for monitoring cancer patient status and outcome. While many current techniques employ immunomagnetic-enrichment based protocols focused on the importance of a particular CTC number as the indicator of patient status or outcome, we employ a cytometric, enrichment free approach using an immunofluorescent protocol to monitor CTC counts in patients with non-small cell lung cancer (NSCLC) over the course of treatment. Methods: Eligible patients had progressive stage IV NSCLC. The histological subtypes in the 42 cases for which the data was available included adenocarcinoma (22/42), squamous cell carcinoma (6/42), large cell undifferentiated carcinoma (3/42), and non-small cell lung carcinoma not further described, poorly differentiated, or with a mixed pattern (11/42). Blood samples were collected 3 wks, 3 mo, 6 mo, 9 mo, and 1 yr after the initial sample. CTCs were identified via immunofluorescence and cytometric analysis. Patient response to therapy was determined by RECIST every 3 months between time 0 and time 12 mo. Results: 80 of 109 patient samples have CTCs (73%) and all of the 52 patients tested have CTCs. 13 of 52 patients have CTC data for time 0 and 3 wks. Only 4 of these patients (30.8%) show a correlation linking CTC count change between time 0 and 3 wks and clinical assessment. 13 patients have CTC data for time 0 and 3 mo, 10 of whom show a correlation linking CTC count change between time 0 and 3 mo and clinical assessment. 7 of the 8 patients (87.5%) showing stable or partial response at 3 mo show a decrease in CTC count between time 0 and 3 mo. Five of the 6 patients (83.3%) clinically showing progressive disease at the 3 mo time point show an increase in CTC count between time 0 and 3 mo. The patients that do not show a correlation linking CTC count change between time 0 and 3 mo and clinical assessment at 3 mo show a correlation at the 6 mo time point. Conclusions: CTCs can be effectively enumerated in metastatic NSCLC patients, with the majority demonstrating CTCs in the setting of progressive disease. The change in CTC count at 3 mo, but not at 3 wks, correlates with radiographic response to chemotherapy. Further follow-up will determine the predictive value of CTC enumeration on survival. No significant financial relationships to disclose.
Microwave nondestructive detection of chloride in cement based materials (1999)

Preliminary results pertaining to the near-field microwave nondestructive detection and evaluation of chloride in cement paste and mortar specimens are presented. The technique used for this purpose utilizes an open-ended rectangular waveguide at the aperture of which the reflection properties of the specimens are measured. It is shown that the magnitude of reflection coefficient is a useful parameter for detecting chloride in these specimens. Furthermore, the difference in the amount of chloride present in these various specimens, at the time of mixing, can also be determined. Reflection property measurements were conducted in S-band (2.6 GHz-3.95 GHz) and X-band (8.2–12.4 GHz) for two sets of four mortar specimens with 0.50 and 0.60 water-to-cement ratio and varying salt (NaCl) contents added to the mixing water used in producing these specimens. It is shown that the reflection properties of these materials vary considerably as a function of their chloride content. Also, by monitoring the daily variation in the reflection coefficient of each specimen during the curing period, the effect of chloride on curing can be nondestructively ascertained. Finally, it is shown that the detection and evaluation of chloride content in cement based materials can be performed using a simple comparative process with respect to a non-contaminated specimen.
Long-Wavelength Infrared Digital Focal Plane Arrays for Earth Remote Sensing Applications (2019)

In this presentation, we will report our recent efforts in achieving high performance in Antimonides type-II strained-layer superlattice (T2SLS) based infrared photodetectors using the barrier infrared detector (BIRD) device architecture. The recent emergence of barrier infrared detectors such as the nBn [1] and the XBn [2] have resulted in mid-wave infrared (MWIR) and long-wave infrared (LWIR) detectors with substantially higher operating temperatures than previously available in III-V semiconductor based MWIR and LWIR detectors. The initial nBn devices used either InAs absorber grown on InAs substrate, or lattice-matched InAsSb alloy grown on GaSb substrate, with cutoff wavelengths of ~3.2 μm and ~4 μm, respectively. While these detectors could operate at much higher temperatures than existing MWIR detectors based on InSb, their spectral responses do not cover the full (3 - 5.5 μm) MWIR atmospheric transmission window. There also have been nBn detectors based on the InAs/GaSb type-II superlattice absorber [3] .
Actuators: Buckling of Elastomeric Beams Enables Actuation of Soft Machines (Adv. Mater. 41/2015) (2015)

Soft, pneumatic actuators that buckle when interior pressure is less than exterior provide a new mechanism of actuation. Upon application of negative pneumatic pressure, elastic beam elements in these actuators undergo reversible, cooperative collapse, and generate a rotational motion. These actuators are inexpensive to fabricate, lightweight, easy to control, and safe to operate. They can be used in devices that manipulate objects, locomote, or interact cooperatively with humans, as described by G. M. Whitesides and co-workers on page 6323.
Treatment of Patients with Scoliosis Using a Unique Anterior Scoliosis Correction Technique (2021)

Treatment for adolescent idiopathic scoliosis (AIS) is dependent upon multiple factors, including curve type and magnitude, curve progression, skeletal maturity, and clinical trunk deformity. While fusion is effective at achieving curve correction, it is associated with disadvantages including prominent implants beneath the skin, back muscle scarring and atrophy, decreased spine range of motion, and decreased functional spinal mobility. Additional concerns include the potential for longer term development of premature adjacent level disc and facet joint degeneration above and below the fusion. Due to these issues with spinal fusion, surgeons have explored alternative surgical approaches to correct spinal deformity and halt curve progression using either growth modulation or remodeling of the spine while preserving motion. This paper provides an overview of a non-fusion scoliosis correction technique called Anterior Scoliosis Correction (ASC).
Interactive Composing: An Overview. (1983)

Interactive composing is the name I have given to a method for using performable, real-time computer music systems in composing and performing music. The concept of interactive composing has grown in my work since 1967, at which time I proposed the design for a sequencer-programmable analog synthesis system, subsequently built by the R. A. Moog Co. and installed in the Electronic Music Studio at State University of New York at Albany in December 1969. That system's special capability in automating controls made possible the techniques that led to several compositions, in particular Ideas of Movement at Bolton Landing (1971) (Chadabe 1972), which involved the control of timbre and rhythm interactively with automated controls generated by sequencers, and Echoes (1972) (Chadabe 1975; 1977), in which the sounds performed by an instrumentalist are delayed for a few seconds, then transformed by a sound-processing system, then distributed to various loudspeakers. The transformed sounds appear as distant echoes to which the performer reacts in deciding how to play the next notes.