gebhart/patrepeval huggingface dataset:
Characterization and Kinetic Mechanism of Catalytic Domain of Human Vascular Endothelial Growth Factor Receptor-2 Tyrosine Kinase (VEGFR2 TK), a Key Enzyme in Angiogenesis (1998)

Vascular endothelial growth factor (VEGF) is a dimeric protein which induces formation of new blood vessels (angiogenesis) through binding to VEGF-receptor-2 tyrosine kinase (VEGFR2 TK) or KDR (kinase insert domain-containing receptor) on the surface of endothelial cells. Angiogenesis has been shown to be essential for malignancy of tumors; therefore, VEGFR2 TK is a potential therapeutic target for the treatment of cancer. Sequence homology studies indicate that VEGFR2 TK contains three domains: extracellular (ligand-binding domain), transmembrane, and intracellular (catalytic domain). In this work, the catalytic domain of VEGFR2 TK was cloned and expressed in a soluble active form using a baculovirus expression system. In the absence of ligand, the enzyme is shown to catalyze its autophosphorylation in a time-dependent and enzyme-concentration-dependent manner, consistent with a trans mechanism for this reaction. Mass spectrometry analysis revealed incorporation of 5.5 +/- 0.5 mol of phosphate/mole of enzyme (monomer). In addition, the enzyme was shown to catalyze phosphorylation of a synthetic peptide, poly(E4Y). Using poly(E4Y) as substrate, the kinetic constants of both native and phosphorylated enzyme were determined. Enzyme phosphorylation increased catalytic efficiency of the enzyme by at least an order of magnitude. Furthermore, the enzyme was shown to catalyze the reverse reaction using phospho-poly(E4Y) as substrate. Cd2+ was found to be an inhibitor of the enzyme. Kinetic studies revealed that inhibition by Cd2+ was competitive with respect to Mg2+ and noncompetitive with respect to MgATP. These results indicate that Cd2+ competes for a second metal-binding site. Therefore, the reaction catalyzed by this enzyme was treated as a terreactant system. The kinetic mechanism of VEGFR2 TK was elucidated through the use of steady-state kinetic studies. According to these studies, the enzyme binds Mg2+ and MgATP in a random fashion followed by ordered addition of the peptide substrate. The release of product is also ordered, with MgADP being released last. The order of substrate binding was confirmed by using AMP-PCP, a dead-end inhibitor.
Robust state-space realizations of discrete-time systems against finite word length errors (2009)

In this paper, a novel class of robust state-space realizations, called normal realizations, is derived for reducing roundoff noise and self-sustained oscillations which ultimately can not be avoided in real-time applications. It is shown that these realizations are free of limit cycles. Another interesting property of the normal realizations is that they yield a minimal error propagation gain. This class is characterized and the optimal realization problem, defined as to find those normal realizations that minimize roundoff noise gain, is solved analytically. A design example is presented to demonstrate the behavior of the optimal normal realizations and to compare them with several well-known digital filter realizations in terms of minimizing roundoff noise and error propagation.
Cross-coupling of N-heteroaryl halides with active methylene compounds in the presence of tetrakis(triphenylphosphine)palladium. (1988)

The cross-coupling of 3-iodo- and 3-bromopyridine with the carbanions derived from ethyl cyanoacetate and malononitrile in the presence of tetrakis(triphenylphosphine)palladium in 1, 2-dimethoxyethane gave ethyl α-cyanopyridine-3-acetate and 3-pyridinemalononitrile in moderate yields. This palladium-catalyzed cross-coupling proceeded smoothly with halopyrimidines, haloquinolines, haloisoquinolines, and also bromobenzene.
URETHRAL AFFERENT NERVE ACTIVITY AFFECTS THE MICTURITION REFLEX; IMPLICATION FOR THE RELATIONSHIP BETWEEN STRESS INCONTINENCE AND DETRUSOR INSTABILITY (1999)

These results indicate that in the anesthetized rat activation of urethral afferents by urethral perfusion can modulate the micturition reflex. Thus in patients with stress urinary incontinence, leakage of urine into the proximal urethra may stimulate urethral afferents and facilitate voiding reflexes. This implies that stress incontinence can induce and/or increase detrusor instability. These findings have significant implications for the treatment of patients with mixed urge and stress incontinence. Correction of stress incontinence by surgery or pelvic floor exercise in patients with mixed incontinence may resolve the detrusor instability.
X-ray Crystal Structure of the Human Galectin-3 Carbohydrate Recognition Domain at 2.1-Å Resolution (1998)

Galectins are a family of lectins which share similar carbohydrate recognition domains (CRDs) and affinity for small beta-galactosides, but which show significant differences in binding specificity for more complex glycoconjugates. We report here the x-ray crystal structure of the human galectin-3 CRD, in complex with lactose and N-acetyllactosamine, at 2.1-A resolution. This structure represents the first example of a CRD determined from a galectin which does not show the canonical 2-fold symmetric dimer organization. Comparison with the published structures of galectins-1 and -2 provides an explanation for the differences in carbohydrate-binding specificity shown by galectin-3, and for the fact that it fails to form dimers by analogous CRD-CRD interactions.
Observation of extremely large quadratic susceptibility at 9.6–10.8μm in electric-field-biased AlGaAs quantum wells (1989)

We have observed an extremely large second-order susceptibility for second-harmonic generation of 9.6--10.8 \ensuremath{\mu}m radiation due to intersubband transitions in electric-field-biased GaAs quantum wells. For 92-A\r{} GaAs wells with 309-A\r{} ${\mathrm{Al}}_{0.48}$${\mathrm{Ga}}_{0.52}$As barriers under a bias of 36 kV/cm, the peak value of the susceptibility was 28 nm/V, 73 times larger than bulk GaAs. The magnitude and sign of the susceptibility depend on the bias field, and are in accord with theoretical predictions.
Distribution of frequencies of a single precessing spin detected by scanning tunneling microscope (2008)

We have measured high frequency signals in the tunneling current of scanning tunneling microscopy for a submonolayer oxide thin film on the Si(111)-7×7 surface. We demonstrate that the signal is related to the Larmor precession of the electron spin associated with a dangling bond. The detected precession frequency possesses a broad distribution (linewidth is comparable to that observed by conventional electron spin resonance) and a split near the maxima, both of which are attributed to the inhomogeneity of the g factor of a single spin.
Service-Oriented Architecture for VIEW: A Visual Scientific Workflow Management System (2008)

Scientific workflows have recently emerged as a new paradigm for scientists to formalize and structure complex and distributed scientific processes to enable and accelerate many scientific discoveries. In contrast to business workflows, which are typically control flow oriented, scientific workflows tend to be dataflow oriented, introducing a new set of requirements for system development. These requirements demand a new architectural design for scientific workflow management systems (SWFMSs). Although several SWFMSs have been developed that provide much experience for future research and development, a study from an architectural perspective is still missing. The main contributions of this paper are: (i) based on a comprehensive survey of the literature and identification of key requirements for SWFMSs, we propose the first reference architecture for SWFMSs, (ii) in compliance with the reference architecture, we further propose a service-oriented architecture for VIEW (a VIsual sciEntificWorkflow management system), (iii) we implement VIEW to validate the feasibility of the proposed architectures, and (iv) we present two case studies to showcase the applications of our VIEW system.
Macrocyclic and Lantern Complexes of Palladium(II) with Bis(amidopyridine) Ligands:  Synthesis, Structure, and Host−Guest Chemistry (2004)

The reactions of [PdCl2(NCPh)2] in a 1:1 ratio with the bis(amidopyridine) ligands LL=C6H3(5-R)(1,3-CONH-3-C5H4N)2 with R=H (1a) or R=t-Bu (1b) give the corresponding neutral dipalladium(II) macrocycles trans,trans-[Pd2Cl4(mu-LL)2], 2a and 2b, which crystallize from dimethylformamide with one or two solvent molecules as macrocycle guests. The reaction of [PdCl2(NCPh)2] with LL in a 1:2 ratio gave the cationic lantern complex [Pd2(mu-LL)4]Cl4, 3c (LL=1b), and the reaction in the presence of AgO2CCF3 gave the corresponding trifluoroacetate salts [Pd2(mu-LL)4](CF3CO2)4, 3a (LL=1a) and 3b (LL=1b). These lantern complexes exhibit a remarkable host-guest chemistry, as they can encapsulate cations, anions, and water molecules by interaction of the guest with either the electrophilic NH or the nucleophilic C=O substituents of the amide groups, which can be directed toward the center of the lantern through easy conformational change. The structures of several of these host-guest complexes were determined, and it was found that the cavity size and shape vary according to the ligand conformation, with Pd...Pd separations in the range from 9.45 to 11.95 A. Supramolecular ordering of the lanterns was observed in the solid state, through either hydrogen bonding or secondary bonding to the cationic palladium(II) centers. The selective inclusion by the lantern complexes of alkali metal ions in the sequence Na+ >> K+ >> Li+ was observed by ESI-MS.
Full dose vincristine (without 2-mg dose limit) in the treatment of lymphomas (1994)

Full dose vincristine in lymphoma protocols is feasible but is associated with increased toxicity. The therapeutic advantage of full dose vincristine has yet to be proven.
A semi-autonomous vision-based navigation system for a mobile robotic vehicle (2003)

Direct teleoperation of a mobile vehicle over a communications channel with delay on the order of one second is problematic for precise maneuvering and obstacle avoidance. To curb both operator vigilance and maneuvering mishaps during vehicle teleopera-tion, this thesis aims to develop a semi-autonomous vision-based navigation system for a small mobile robotic vehicle designed by Draper Laboratory. The system re-lies on monocular vision processing to employ an optical flow balance strategy for real-time obstacle avoidance. The system utilizes a multimedia processor for video processing and is implemented within a payload module built for a visual servoing task. The system design relies on a flexible communication protocol to integrate with
Efficient (stack) algorithms for analysis of write-back and sector memories (1989)

For the class of replacement algorithms known as stack algorithms, existing analysis techniques permit the computation of memory miss ratios for all memory sizes simultaneously in one pass over a memory reference string. We extend the class of computations possible by this methodology in two ways. First, we show how to compute the effects of copy-backs in write-back caches. The key observation here is that a given block is clean for all memory sizes less than or equal to C blocks and is dirty for all larger memory sizes. Our technique permits efficient computations for algorithms or systems using periodic write-back and/or block deletion. The second extension permits stack analysis simulation for sector (or subblock) caches in which a sector (associated with an address tag) consists of subsectors (or subblocks) that can be loaded independently. The key observation here is that a subsector is present only in caches of size C or greater. Load forward prefetching in a sector cache is shown to be a stack algorithm and is easily simulated using our technique. Running times for our methods are only slightly higher than for a simulation of a single memory size using nonstack techniques.
BACTERIA ISOLATION FROM WHOLE BLOOD FOR SEPSIS DIAGNOSTICS (2011)

Rapid and reliable detection of bloodstream infections would gain a lot from improved and straightforward isolation of highly purified bacteria from whole blood. Here, we report a microfluidics- based sample preparation strategy to continuously isolate microorganisms from whole blood for downstream analysis. The continuous-flow method takes advantage of the fact that bacteria cells have rigid cell wall enables selective and complete blood cell lysis while ~ 100% of bacteria are readily recovered. The method as a sample preparation unit offers opportunities to develop molecular based POC for sepsis diagnostics.
Amino acids content and electrophoretic profile of camel milk casein from different camel breeds in Saudi Arabia (2011)

This study aimed to evaluate amino acids content and the electrophoretic profile of camel milk casein from different camel breeds. Milk from three different camel breeds (Majaheim, Wadah and Safrah) as well as cow milk were used in this study. Results showed that ash and moisture contents were significantly higher in camel milk casein of all breeds compared to that of cow milk. On the other hand, casein protein of cow milk was significantly higher compared to that of all camel milk breeds. Molecular weights of casein patterns of camel milk breeds were higher compared to that of cow milk. Essential (Phe, Lys and His) and non-essential amino acids content was significantly higher in cow milk casein compared to the casein of all camel milk breeds. However, there was no significant difference for the other essential amino acids between cow casein and the casein of Safrah breed and their quantities in cow and Safrah casein were significantly higher compared to the other two breeds. Non-essential amino acids except Arg and the essential amino acids (Met, Ile, Lue and Phe) were also significantly higher in cow milk α-casein compared to α-casein from all camel breeds. Moreover, essential amino acids (Val, Phe and His) and the non-essential amino acids (Gly and Ser) content was significantly higher in cow milk β-casein compared to the β-casein of all camel milk breeds and the opposite was true for Lys, Thr, Met and Ile. However, Met, Ile, Phe and His were significantly higher for β-casein of Majaheim compared to the other two milk breeds. The non-essential amino acids (Gly, Tyr, Ala and Asp) and the essential amino acids (Thr, Val and Ile) were significantly higher in cow milk κ-casein compared to that for all camel milk breeds. There was no significant difference among all camel milk breeds in their κ-casein content of most essential amino acids. Relative migration of casein bands of camel milk casein was not identical. The relative migration of αs-, β- and κ-casein of camel casein was slower than those of cow casein. The molecular weights of αs-, β- and κ-casein of camel caseins were 27.6, 23.8 and 22.4 KDa, respectively. More studies are needed to elucidate the structure of camel milk.
Predicting the long-term risk of prostate cancer-specific mortality after radical prostatectomy (2009)

5007 Background: Nomograms that predict prostate-specific antigen (PSA) defined biochemical recurrence (BCR) of prostate cancer after radical prostatectomy are the most widely used prediction tools in oncology for treatment decision making and counseling. While BCR universally antedates prostate cancer-specific mortality (PCSM), it is a limited surrogate endpoint due to its variable natural history. Nomograms that accurately predict the risk of PCSM are needed. Methods: Using Fine and Gray competing risk regression analysis, the clinical data and follow-up information of 11,521 patients treated with radical prostatectomy at four academic centers from 1987 to 2005 were modeled to predict PCSM. The model was externally validated on 12,893 patients treated at a separate institution during the same period. Results: The 15-year PCSM and all-cause mortality was 7% and 33%, respectively. The 15-year PCSM for patients with final pathological Gleason score 2–6, 3+4, 4+3, and 8–10 was 1%, 7%, 8%, and 49%, respectively. By pathologic stage, the risks were 2%, 7%, 29%, and 23% for organ-confined, extraprostatic extension, seminal vesicle invasion, and lymph node-positive prostate cancer. Of 3756 patients with organ-confined and Gleason 2–6 cancer, only 1 (0.03%) died from prostate cancer. Primary and secondary Gleason grade (p &lt; 0.001 for both), seminal vesicle invasion (p &lt; 0.001), and year of surgery (p = 0.002) were significant predictors of PCSM. A nomogram predicting 15-year PCSM based on pathologic parameters was accurate and discriminating with an externally-validated concordance index of 0.92. Conclusions: A nomogram has been constructed that predicts the long-term risk of PCSM after radical prostatectomy based on the pathologic grade and stage of the cancer. The presence of poorly differentiated cancer and seminal vesicle invasion are the prime determinants of PCSM. Our study suggests that biomarkers may have limited empiric prognostic utility as PCSM can be accurately predicted once the pathologic features of prostate cancer are known. No significant financial relationships to disclose.
Significance of Sentinel Lymph Node Micrometastases in Human Breast Cancer (2007)

Detection of micrometastatic carcinoma (N1mi) in the SLNs of invasive breast cancer patients is a major indicator of poorer survival compared with N0(i-) patients. Although survival of patients with an N0(i+) SLN does not statistically differ from that of N0(i-) patients, 9.3% of these patients had additional axillary nodal disease on axillary dissection, and N0(i+) patients had a decreased survival when axillary dissection was omitted.
α-Methylene Butyrolactone from Erythronium americanum (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTα-Methylene Butyrolactone from Erythronium americanumChester J. Cavallito and Theodore H. HaskellCite this: J. Am. Chem. Soc. 1946, 68, 11, 2332–2334Publication Date (Print):November 1, 1946Publication History Published online1 May 2002Published inissue 1 November 1946https://doi.org/10.1021/ja01215a057RIGHTS & PERMISSIONSArticle Views220Altmetric-Citations47LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (388 KB) Get e-Alertsclose Get e-Alerts
Lambda‐Toxin of Clostridium perfringens Activates the Precursor of Epsilon‐Toxin by Releasing Its N‐ and C‐Terminal Peptides (1997)

The effect of lambda-toxin, a thermolysin-like metalloprotease of Clostridium perfringens, on the inactive epsilon-prototoxin produced by the same organism was examined. When the purified epsilon-prototoxin was incubated with the purified lambda-toxin at 37 C for 2 hr, the 32.5-kDa epsilon-prototoxin was processed into a 30.5-kDa polypeptide, as determined by SDS-polyacrylamide gel electrophoresis. A mouse lethality test showed that the treatment activated the prototoxin: the 50% lethal doses (LD50) of the prototoxin with and without lambda-toxin treatment were 110 and 70,000 ng/kg of body weight, respectively. The lethal activity of the prototoxin activated by lambda-toxin was comparable to that with trypsin plus chymotrypsin and higher than that with trypsin alone: LD50 of the prototoxin treated with trypsin and trypsin plus chymotrypsin were 320 and 65 ng/kg of body weight, respectively. The epsilon-toxin gene was cloned and sequenced. Determination of the N-terminal amino acid sequence of each activated epsilon-prototoxin revealed that lambda-toxin cleaved between the 10th and 11th amino acid residues from the N-terminus of the prototoxin, while trypsin and trypsin plus chymotrypsin cleaved between the 13th and 14th amino acid residues. The molecular weight of each activated epsilon-prototoxin was also determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The C-terminus deduced from the molecular weight is located at the 23rd or 30th amino acid residue from the C-terminus of the prototoxin, suggesting that removal of not only N-terminal but also C-terminal peptide is responsible for activation of the prototoxin.
Comparison of patient‐controlled analgesia versus continuous infusion of tramadol in post‐cesarean section pain management (2013)

While tramadol administration by either of the methods used may ensure efficient early postoperative anesthesia in cesarean section patients, i.v. PCA may be preferred because of the lower drug consumption and higher patient satisfaction associated with it.
Mouse Polycomb Proteins Bind Differentially to Methylated Histone H3 and RNA and Are Enriched in Facultative Heterochromatin (2006)

The chromodomain (CD) of the Drosophila Polycomb protein exhibits preferential binding affinity for histone H3 when trimethylated at lysine 27. Here we have investigated the five mouse Polycomb homologs known as Cbx2, Cbx4, Cbx6, Cbx7, and Cbx8. Despite a high degree of conservation, the Cbx chromodomains display significant differences in binding preferences. Not all CDs bind preferentially to K27me3; rather, some display affinity towards both histone H3 trimethylated at K9 and H3K27me3, and one CD prefers K9me3. Cbx7, in particular, displays strong affinity for both H3K9me3 and H3K27me3 and is developmentally regulated in its association with chromatin. Cbx7 associates with facultative heterochromatin and, more specifically, is enriched on the inactive X chromosome. Finally, we find that, in vitro, the chromodomain of Cbx7 can bind RNA and that, in vivo, the interaction of Cbx7 with chromatin, and the inactive X chromosome in particular, depends partly on its association with RNA. We propose that the capacity of this mouse Polycomb homolog to associate with the inactive X chromosome, or any other region of chromatin, depends not only on its chromodomain but also on the combination of histone modifications and RNA molecules present at its target sites.