gebhart/patrepeval huggingface dataset:
Phosphatidylinositol 3-kinase p85 SH2 domain specificity defined by direct phosphopeptide/SH2 domain binding (1993)

We have developed a competition binding assay to quantify relative affinities of isolated Src-homology 2 (SH2) domains for phosphopeptide sequences. Eleven synthetic 11-12-amino acid phosphopeptides containing YMXM or YVXM recognition motifs bound to a PI 3-kinase p85 SH2 domain with highest affinities, including sequences surrounding phosphorylated tyrosines of the PDGF, CSF-1/c-Fms, and kit-encoded receptors, IRS-1, and polyoma middle T antigens; matched, unphosphorylated sequences did not bind. A scrambled YMXM phosphopeptide or sequences corresponding to the GAP or PLC-gamma SH2 domain binding motifs of the PDGF, FGF, and EGF receptors bound to the p85 SH2 domain with 30-100-fold reduced affinity, indicating that this affinity range confers specificity. Binding specificity was appropriately reversed with an SH2 domain from PLC-gamma: a phosphopeptide corresponding to the site surrounding PDGF receptor Tyr1021 binds with approximately 40-fold higher affinity than a YMXM-phosphopeptide. We conclude that essential features of specific phosphoprotein/SH2 domain interactions can be reconstituted using truncated versions of both the phosphoprotein (a phosphopeptide) and cognate SH2 domain-containing protein (the SH2 domain). SH2 domain binding specificity results from differences in affinity conferred by the linear sequence surrounding phosphotyrosine.
Pose view stability analysis for camera look angles computation (1996)

The main purpose of this paper is not to present a new camera calibration algorithm or a new pose estimation method, but just to analyse the stability of the camera pose estimation using the Haralick observation which is based on the fact that there is sufficient information on the 2D perspective projection of a rectangle of unknown size in 3D space to determine the three camera look angles. A brief description of the camera look angles computation is presented and a model for the expected stability of the camera look angles computation front noisy image data is described. A stability analysis as a function of the pose of the camera is also described, and the influence of the camera pose is confirmed with simulated data. As a result, camera pose view strategies for accurate camera orientation computation can be extracted from this pose view stability analysis.
Formal Total Synthesis of Ovalcin by Carbohydrate Approach (2007)

A formal total synthesis of ovalcin is described herein starting from readily available sugar ribose with selective zinc-mediated ring-opening reaction and Grubbs olefin metathesis as the key steps.
A phase I dose-escalation study of the Hsp90 inhibitor ganetespib (STA-9090) administered twice weekly in patients with solid tumors: Updated report. (2011)

3051 Background: Ganetespib is a potent, next-generation Hsp90 inhibitor that is structurally unrelated to the first-generation ansamycin class of Hsp90 inhibitors and has shown superior activity to these agents in preclinical studies. It has been well tolerated and shown promising antitumor activity in early trials in multiple cancers. Preclinical data indicate that different client proteins show disparate expression kinetics upon Hsp90 inhibition. Therefore, twice-weekly dosing may be needed in some tumor types. Methods: Patients (pts) with solid tumors who have exhausted standard treatment options received ganetespib as a 1 hr infusion twice weekly for 3 weeks (wks) of a 28 day cycle until disease progression. Serial PK and pharmacodynamic samples were obtained during cycle 1. Safety assessments included frequency and grade of AEs, laboratory parameters and ECG changes. Results: Data are presented for 49 pts (22 M, 27 F; median age 55 yrs, range 32-81; ECOG status range 0-2) treated at doses from 2-144 mg/m2. Pts received a median of 2 (range 1-12) cycles of ganetespib. AEs reported in ≥20% of pts treated at doses from 2-120 mg/m2 are fatigue, diarrhea, nausea, anemia, abdominal pain, constipation, anorexia, vomiting, and headache; the majority of events were mild to moderate in severity with absence of severe liver, ocular, cardiac and renal toxicity. Two DLTs (elevated transaminases) have been reported in the 10 and 144 mg/m2 cohorts; expansion of the latter cohort is ongoing. Ganetespib shows linear PK, rapid distribution, a mean terminal half-life of 10-14 hours, a volume of distribution greater than total body water and no accumulation in plasma. HSP70 plasma protein levels will be presented. A confirmed durable PR by RECIST has been seen in a pt with metastatic melanoma. Additionally, 2 NSCLC pts who received 6 months of treatment had durable SD, with tumor shrinkage. Conclusions: Ganetespib has been well tolerated at dose levels up to 120 mg/m2 administered twice weekly. Preliminary safety profile, activity signals and differences in client protein kinetics warrant continued evaluation of ganetespib using a twice-weekly dosing regimen. Dose escalation continues.
From transforming growth factor-β signaling to androgen action: Identification of Smad3 as an androgen receptor coregulator in prostate cancer cells (2001)

Although transforming growth factor-beta (TGF-beta) has been identified to mainly inhibit cell growth, the correlation of elevated TGF-beta with increasing serum prostate-specific antigen (PSA) levels in metastatic stages of prostate cancer has also been well documented. The molecular mechanism for these two contrasting effects of TGF-beta, however, remains unclear. Here we report that Smad3, a downstream mediator of the TGF-beta signaling pathway, functions as a coregulator to enhance androgen receptor (AR)-mediated transactivation. Compared with the wild-type AR, Smad3 acts as a strong coregulator in the presence of 1 nM 5alpha-dihydrotestosterone, 10 nM 17beta-estradiol, or 1 microM hydroxyflutamide for the LNCaP mutant AR (mtAR T877A), found in many prostate tumor patients. We further showed that endogenous PSA expression in LNCaP cells can be induced by 5alpha-dihydrotestosterone, and the addition of the Smad3 further induces PSA expression. Together, our findings establish Smad3 as an important coregulator for the androgen-signaling pathway and provide a possible explanation for the positive role of TGF-beta in androgen-promoted prostate cancer growth.
Substrate Recognition by β-Ketoacyl-ACP Synthases (2011)

β-Ketoacyl-ACP synthase (KAS) enzymes catalyze Claisen condensation reactions in the fatty acid biosynthesis pathway. These reactions follow a ping-pong mechanism in which a donor substrate acylates the active site cysteine residue after which the acyl group is condensed with the malonyl-ACP acceptor substrate to form a β-ketoacyl-ACP. In the priming KASIII enzymes the donor substrate is an acyl-CoA while in the elongating KASI and KASII enzymes the donor is an acyl-ACP. Although the KASIII enzyme in Escherichia coli (ecFabH) is essential, the corresponding enzyme in Mycobacterium tuberculosis (mtFabH) is not, suggesting that the KASI or II enzyme in M. tuberculosis (KasA or KasB, respectively) must be able to accept a CoA donor substrate. Since KasA is essential, the substrate specificity of this KASI enzyme has been explored using substrates based on phosphopantetheine, CoA, ACP, and AcpM peptide mimics. This analysis has been extended to the KASI and KASII enzymes from E. coli (ecFabB and ecFabF) where we show that a 14-residue malonyl-phosphopantetheine peptide can efficiently replace malonyl-ecACP as the acceptor substrate in the ecFabF reaction. While ecFabF is able to catalyze the condensation reaction when CoA is the carrier for both substrates, the KASI enzymes ecFabB and KasA have an absolute requirement for an ACP substrate as the acyl donor. Provided that this requirement is met, variation in the acceptor carrier substrate has little impact on the k(cat)/K(m) for the KASI reaction. For the KASI enzymes we propose that the binding of ecACP (AcpM) results in a conformational change that leads to an open form of the enzyme to which the malonyl acceptor substrate binds. Finally, the substrate inhibition observed when palmitoyl-CoA is the donor substrate for the KasA reaction has implications for the importance of mtFabH in the mycobacterial FASII pathway.
Inhibitory effects of a new bisphosphonate, minodronate, on proliferation and invasion of a variety of malignant bone tumor cells (2006)

Little is known about the biological effects of bisphosphonates on primary malignant bone tumors. The purpose of this study was to investigate the antitumor effects of newly developed minodronate (MIN) on a variety of human malignant bone tumors. We examined the effects of MIN and clinically relevant incadronate (INC) on the proliferation, apoptosis, and cell cycle of two osteosarcoma (Saos-2, MG-63), two chondrosarcoma (SW1353, OUMS27), and two Ewing's sarcoma (RD-ES, SK-ES-1) cell lines. Furthermore, we investigated the anti-invasion effects of MIN on sarcoma cells and the effects of MIN on tumor growth in nude mice. MIN inhibited the viability of all six cell lines in a dose-dependent manner with IC50 values of 2.7 to 5.0 microM, which were significantly lower than those of INC. Importantly, both bisphosphonates affected the viability of normal bone marrow stromal cells much less than sarcoma cells. Both bisphosphonates induced cell cycle perturbation in all sarcoma cells tested and apoptosis in Saos-2 and SW1353 cells, although they failed to induce apoptosis in RD-ES and SK-ES-1 cells. MIN significantly suppressed invasion, even at a low concentration of 1 microM (p < 0.01). Daily injection of 5 microg of MIN inhibited the growth of SK-ES-1 xenograft sarcoma in nude mice without loss of body weight. These findings suggest that MIN may have a beneficial adjuvant role in the treatment of patients with malignant bone tumors.
SmartDrawer (2009)

Radio Frequency Identification (RFID) is an emerging technology, being used in monitoring including healthcare. We apply different types of RFID tags to monitor drug taking and its impact in an assistive environment. Compared to other active Wireless Sensor Networks (WSNs), RFID tags do not need a battery, recharging, and so have no battery power loss problems. RFID tags are tiny in volume, and can be embedded into different objects. This paper talks about an RFID-based application in an assistive environment called "Smart Drawer", which tracks medicine taking for the elderly. We investigate the hardware involved to build such an application and we develop the software infrastructure to create a functional system to assist patients and caregivers with the medication procedures and also collect data for future use.
Peptide nucleic acid-anthraquinone conjugates: strand invasion and photoinduced cleavage of duplex DNA (1997)

A bis-peptide nucleic acid (PNA)-anthraquinone imide (AQI) conjugate has been synthesized and shown to form strand invasion complexes with a duplex DNA target. The two arms of the bis-PNA each consist of five consecutive thymine residues and are linked by a flexible, hydrophilic spacer. Probing with potassium permanganate reveals that the bis-PNA complexes to duplex DNA at A5.T5sites with local displacement of the T5DNA strand. The 5 bp sequence targeted by the PNA is the shortest strand invasion complex reported to date. Irradiation of the strand invasion complex results in asymmetric cleavage of the displaced strand, with more efficient cleavage at the 3'-end of the loop. This result indicates that the bis-PNA binds to the DNA such that the C-terminal T5sequence forms the strand invasion complex, leaving the N-terminal T5sequence to bind by triplex formation, thereby placing the AQI closer to the 3'-end of the displaced strand, consistent with the observed photocleavage pattern. The ability of the PNA to directly report its binding site by photoinduced cleavage could have significant utility in mapping the secondary and tertiary structure of nucleic acids.
Eosinophilic Esophagitis: Rapidly Advancing Insights (2011)

Eosinophilic esophagitis (EoE) now represents a commonly recognized disorder among both pediatric and adult patients presenting to allergy and gastroenterology clinics throughout the world. The consequences of this localized and eosinophil-predominant inflammation of the esophagus can have an outsized and profound systemic and emotional impact for patients and their families. Unlike gastroesophageal reflux disease (GERD), whose symptoms closely overlap with those of EoE, EoE represents a primarily antigen-driven disorder whose symptoms and pathology are therapeutically mitigated with either long-term dietary control or chronic steroid therapies, rather than the acid-suppressive medications that are the mainstay of GERD treatment. Beyond the dissimilarities in their responses to treatment, these disorders are distinct in their gene expression profiles, heredity, genetic underpinning, and linkage with atopy. The antigen-driven nature of EoE has been reinforced by the remarkable impact of therapies utilizing elemental formulas to control the disease as well as a number of reports linking aeroallergens to seasonal worsening of disease.
Thin Film Transistors (1999)

Abstract The sections in this article are Amorphous Silicon Thin Film Transistors Polycrystalline Silicon Thin Film Transistors
Design, synthesis, and evaluation of heparan sulfate mimicking glycopolymers for inhibiting heparanase activity (2017)

Heparanase is an enzyme which cleaves heparan sulfate (HS) polysaccharides of the extracellular matrix. It is a regulator of tumor behavior, plays a key role in kidney related diseases and autoimmune diabetes. We report herein the use of computational studies to extract the natural HS-heparanase interactions as a template for the design of HS mimicking glycopolymers. Upon evaluation, a glycopolymer with 12 repeating units was determined to be the most potent inhibitor and to have tight-binding characteristics. This glycopolymer also lacks anticoagulant activity.
End-to-end available bandwidth: Measurement methodology, dynamics, and relation with TCP throughput (2003)

The available bandwidth (avail-bw) in a network path is of major importance in congestion control, streaming applications, quality-of-service verification, server selection, and overlay networks. We describe an end-to-end methodology, called self-loading periodic streams (SLoPS), for measuring avail-bw. The basic idea in SLoPS is that the one-way delays of a periodic packet stream show an increasing trend when the stream's rate is higher than the avail-bw. We have implemented SLoPS in a tool called pathload. The accuracy of the tool has been evaluated with both simulations and experiments over real-world Internet paths. Pathload is nonintrusive, meaning that it does not cause significant increases in the network utilization, delays, or losses. We used pathload to evaluate the variability ("dynamics") of the avail-bw in Internet paths. The avail-bw becomes significantly more variable in heavily utilized paths, as well as in paths with limited capacity (probably due to a lower degree of statistical multiplexing). We finally examine the relation between avail-bw and TCP throughput. A persistent TCP connection can be used to measure roughly the avail-bw in a path, but TCP saturates the path and increases significantly the path delays and jitter.
Development of Castration Resistant Prostate Cancer can be Predicted by a DNA Hypermethylation Profile (2015)

Epigenetic silencing of the mentioned genes could be novel molecular markers for the prognosis of advanced prostate cancer. It might predict castrate resistance during hormone deprivation and, thus, disease specific mortality. Gene hypermethylation is associated with disease progression in patients who receive hormone therapy. It could serve as a marker of the treatment response.
<title>Laser Scanning For The Graphic Arts</title> (1977)

Some general principles are presented for determining likely applications for laser scanning in the printing industry. The special requirements of imagery in this field are discussed. Stress is laid on cost/ effectiveness and the systems approach. The implications of these ideas for scanner design are developed. Three examples are given of production systems which follow these principles.
Potential for Hepatitis C Virus Resistance to Nitazoxanide or Tizoxanide (2008)

Nitazoxanide and its primary metabolite, tizoxanide, inhibit hepatitis C virus (HCV) replication in HCV replicon systems. To study the potential for resistance, we subjected Huh7 cells harboring HCV replicons to serial passage in 250 muM G418 and increasing concentrations of nitazoxanide or tizoxanide. Passage of the replicon-containing cell lines in either compound resulted in increases in the 50% effective concentrations (EC(50)s) (7- to 13-fold), EC(90)s (14- to 36-fold), and 50% cytotoxic concentrations (2- to 4-fold) of both compounds. Serial passage in either compound did not alter the susceptibility of HCV replicons to ribavirin or 2'-C-methylcytidine. Interestingly, serial passage in nitazoxanide or tizoxanide resulted in increased sensitivity to alpha interferon 2b: EC(50)s and EC(90)s were reduced three- and eightfold, respectively. Replicons isolated from these cell lines had no greater ability to confer tizoxanide resistance, or increased susceptibility to alpha interferon, than replicons isolated from the parental cell line that had not previously been exposed to nitazoxanide or tizoxanide. These findings are indicative of a cell-mediated activity differing from that of other anti-HCV drugs but complementary with interferon and are consistent with the enhanced response rates observed clinically when nitazoxanide is combined with pegylated interferon therapy. Finally, unlike data for other compounds in advanced clinical development for HCV, these data are consistent with resistance in HCV replicon-containing cell lines conferred by changes in the host and not by mutations in the virus.
Viruses cause heavy melon losses in desert valleys (1985)

Three mosaic viruses decreased 1984 spring melon yields 40 to 50 percent in southern California.
Vision-Based Stop Sign Detection and Recognition System for Intelligent Vehicles (2001)

The traffic sign detection and recognition system is an essential module of the driver warning and assistance system. A vision-based stop sign detection and recognition system is presented here. This system has two main modules: detection and recognition. In the detection module, the color thresholding in hue, saturation, and value color space is used to segment the image. The features of the traffic sign are investigated and used to detect potential objects. For the recognition module, one neural network is trained to perform the classification and another one is trained to perform the validation. Joint use of classification and validation networks can reduce the rate of false positives. The reliability demonstrated by the proposed algorithm suggests that this system could be a part of an integrated driver warning and assistance system based on computer vision technologies.
Minimum average correlation energy filters (1987)

The synthesis of a new category of spatial filters that produces sharp output correlation peaks with controlled peak values is considered. The sharp nature of the correlation peak is the major feature emphasized, since it facilitates target detection. Since these filters minimize the average correlation plane energy as the first step in filter synthesis, we refer to them as minimum average correlation energy filters. Experimental laboratory results from optical implementation of the filters are also presented and discussed.
Myotonic Dystrophy Type 2 Caused by a CCTG Expansion in Intron 1 of ZNF9 (2001)

Myotonic dystrophy (DM), the most common form of muscular dystrophy in adults, can be caused by a mutation on either chromosome 19q13 (DM1) or 3q21 (DM2/PROMM). DM1 is caused by a CTG expansion in the 3' untranslated region of the dystrophia myotonica-protein kinase gene (DMPK). Several mechanisms have been invoked to explain how this mutation, which does not alter the protein-coding portion of a gene, causes the specific constellation of clinical features characteristic of DM. We now report that DM2 is caused by a CCTG expansion (mean approximately 5000 repeats) located in intron 1 of the zinc finger protein 9 (ZNF9) gene. Parallels between these mutations indicate that microsatellite expansions in RNA can be pathogenic and cause the multisystemic features of DM1 and DM2.
Accelerated repetitive transcranial magnetic stimulation for treatment-resistant depression (2010)

Accelerated TMS demonstrated an excellent safety profile with efficacy comparable to that achieved in daily rTMS in other trials. Limitations primarily include open-label treatment and a small sample size.
Rapid Melt Growth of Germanium Crystals with Self-Aligned Microcrucibles on Si Substrates (2005)

A rapid melt growth method was developed to produce Ge crystals including Ge pillars, nanowires, and Ge-on-insulator. Amorphous Ge was deposited and patterned, then crystallized by melting and solidifying using Si substrates for seeding. Self-aligned microcrucibles were used to contain the Ge liquid during the crystallization anneal. The misfit defects were terminated within small regions around the seeding windows by a necking mechanism. Crystallization calculations showed that very high epitaxial growth velocity can be achieved when the temperature of Ge liquid is lower than but close to its melting point, while the random unseeded nucleation rate is very low in the same temperature range. High-quality Ge nanowires and Ge-on-insulator structures are produced with a simple and robust process. The rapid melt growth technique works very well with a variety of film thickness, including that of nanometer ultrathin structures. The surface smoothness obtained by Ge deposition is retained during crystallization and the film thickness is also controlled by deposition.
Gene characterized for membrane desaturase that produces ( E )-11 isomers of mono- and diunsaturated fatty acids (2002)

Moth species have evolved integral membrane desaturases that exhibit a wide diversity in substrate specificity, as well as in regiospecificity and stereospecificity of the unsaturated products. We report here the cloning and expression of a single desaturase from the sex pheromone gland of the light brown apple moth, Epiphyas postvittana, that makes E11 isomers of monounsaturated (E11-16 and E11-14) fatty acids and a diunsaturated (E9,E11-14) fatty acid. In the pheromone gland, the monoene precursor is made available by beta oxidation of E11-16 acid with a subsequent two-carbon loss to E9-14 acid. A functional assay using a baculovirus expression system required addition of myristic acid and E9-14 acid precursors to demonstrate the unusual regiospecificity and stereospecificity of this desaturase. The amino acid sequence of this desaturase has approximately 61% identity to that of Z11-desaturases from two other insect species, and only approximately 48% identity to the metabolic Z9-desaturases in those species. A pheromone-gland Z9-desaturase gene also was found with the light brown apple moth that differed in its deduced amino acid sequence (66% identity) with the metabolic Z9-desaturase from fat body in this species.