gebhart/patrepeval huggingface dataset:
Clinicopathologic analysis of non-muscle invasive urothelial bladder tumor in young and old patients (2013)

Objective To investigate the clinical feature,pathologic characteristics and prognosis of non-muscle invasive urothelial bladder tumor in young and old patients.Methods From January 2000 to March 2011,the clinicial data of 48 young patients (age ≤ 40 years) with non-muscle invasive urothelial bladder tumor and 50 patients randomly selected with non-muscle invasive urothelial tumor (age ≥ 60 years) were analyzed and compared retrospectively.There were 38 male and 10 female with a median age of 35.4 years (range,18 to 40).There were 34 male and 16 female with a median age of 68.5 years (range,68.5 to 87).All patients had postoperative intravesical instillation for one year.Young patients presented with gross hematuria mostly,which were similmar with old patients.Solitary tumor were 45 cases and 40 cases,and the multiple tumors were 3 cases and 10 cases in the young and old groups,respectively.Of the young group,40 patients were treated by transurethral resection of bladder tumor,and 8 patients by partial cystectomy.Of the old group,35 patients were treated by transurethral resection of bladder tumor,and 15 patients by partial cystectomy.Results According to 2004 WHO classification of papillary urothelial tumor,lower grade tumor were more frequentto occur in young group than in old group.There was significant difference in incidence of PUNLMP between young group and old group (16/48,33.3％ and 8/50,16.0％,P ＜ 0.05).There was significant difference in incidence of high grade bladder cancer between young group and old group (7/48,14.6％ and 17/50,34.0％,P ＜0.05).The incidence of PTa tumor was 70.8％ and 44.0％ in the young and old groups,respectively (P ＜ 0.05).Median follow up was 34 months (range,6 to 132) in young group and 35 months (range,6 to 130) in old group,respectively.Five-year recurrence rate was 36.7％ and 64.3％ respectively (P ＜ 0.05).Conclusions Non-muscle invasive urothelial bladder tumor in young patients had a better prognosis than those in the old group,with lower grade and stage at diagnosisand lower recurrence rate.

Key words: 
Non-muscle invasive urothelial tumor;  Bladder;  Prognosis
The Abl SH2‐kinase linker naturally adopts a conformation competent for SH3 domain binding (2007)

Abstract The core of the Abelson tyrosine kinase (c‐Abl) is structurally similar to Src‐family kinases where SH3 and SH2 domains pack against the backside of the kinase domain in the down‐regulated conformation. Both kinase families depend upon intramolecular association of SH3 with the linker joining the SH2 and kinase domains for suppression of kinase activity. Hydrogen deuterium exchange (HX) and mass spectrometry (MS) were used to probe intramolecular interaction of the c‐Abl SH3 domain with the linker in recombinant constructs lacking the kinase domain. Under physiological conditions, the c‐Abl SH3 domain undergoes partial unfolding, which is stabilized by ligand binding, providing a unique assay for SH3:linker interaction in solution. Using this approach, we observed dynamic association of the SH3 domain with the linker in the absence of the kinase domain. Truncation of the linker before W254 completely prevented cis ‐interaction with SH3, while constructs containing amino acids past this point showed SH3:linker interactions. The observation that the Abl linker sequence exhibits SH3‐binding activity in the absence of the kinase domain is unique to Abl and was not observed with Src‐family kinases. These results suggest that SH3:linker interactions may have a more prominent role in Abl regulation than in Src kinases, where the down‐regulated conformation is further stabilized by a second intramolecular interaction between the C‐terminal tail and the SH2 domain.
Coupling Capillary Electrophoresis and High-Field Asymmetric Waveform Ion Mobility Spectrometry Mass Spectrometry for the Analysis of Complex Lipopolysaccharides (2004)

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is a new technology for atmospheric pressure, room temperature separation of gas-phase ions. The FAIMS system acts as an ion filter that can continuously transmit one type of ion, independent of mass-to-charge ratio (m/z). Capillary electrophoresis-electrospray mass spectrometry (CE-MS) has been extensively used for the analysis of complex bacterial lipopolysaccharides (LPS). The coupling of FAIMS to CE-MS provides a sensitive technique for the characterization of these complex glycolipids, permitting the separation of trace-level LPS oligosaccharide glycoforms for subsequent structural characterization using tandem mass spectrometry. This was demonstrated for LPS from nontypeable Haemophilus influenzae strain 375 following O-deacylation with anhydrous hydrazine. This strain of H. influenzae can express a triheptosyl-containing glycoform to which four hexose residues are linked forming the outer-core region of the molecule. This has been referred to as the Hex4 glycoform. Glycoforms have been identified which differ in the number of phosphoethanolamine substituents in the inner-core. With the use of CE-FAIMS, isomeric Hex4 glycoforms containing two PEtn groups were separated and characterized by MS/MS. FAIMS provided a significant reduction in mass spectral noise, leading to improved detection limits ( approximately 70 amol of the major glycoform). The extracted mass spectrum showed that the apparent noise was virtually eliminated. In addition to the reduction of chemical background, the ion current was increased by as much as 7.5 times as a result of the atmospheric pressure ion-focusing effect provided by the FAIMS system. The linearity of response of the CE-FAIMS-MS system was also studied. The calibration curve is linear for approximately 3 orders of magnitude, over a range of 40 pg/microL to 10 ng/microL.
Capability Maturity Model . . . (1993)

(maximum 200 words) 14. SUBJECT TERMS 15. NUMBER OF PAGES 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT UNCLASSIFIED 18. SECURITY CLASSIFICATION OF THIS PAGE UNCLASSIFIED 19. SECURITY CLASSIFICATION OF ABSTRACT UNCLASSIFIED 20. LIMITATION OF ABSTRACT UL NSN 7540-01-280-5500 Standard Form 298 (Rev. 2-89) Prescribed by ANSI Std. Z39-18 298-102 Capability Maturity Model SM for Software, Version 1.1 Mark C. Paulk, Bill Curtis, Mary Beth Chrissis, Charles V. Weber In November 1986, the Software Engineering Institute (SEI), with assistance from the Mitre Corporation, began developing a process maturity framework that would help organizations improve their software process. This effort was initiated in response to a request to provide the federal government with a method for assessing the capability of its software contractors. In September 1987, the SEI released a brief description of the process maturity framework [Humphrey 87a] and a maturity questionnaire [Humphrey87b]....
Squaryl Group as a New Mimic of Phosphate Group in Modified Oligodeoxynucleotides:  Synthesis and Properties of New Oligodeoxynucleotide Analogues Containing an Internucleotidic Squaryldiamide Linkage (2002)

This paper describes the synthesis and properties of a new type of modified oligodeoxynucleotide containing a neutral but highly polarized squaryl group as a novel mimic of the phosphate group. A modified thymidine dimer derivative (TsqT) having a squaryldiamide linkage was synthesized in almost quantitative yield by a two-step substitution of diethyl squarate with 3'-amino-5'-O-(4,4'-dimethoxytrityl)-3'-deoxythymidine and 5'-amino-5'-deoxythymidine. The CD and UV studies of TsqT suggest that this dimer has basically a structure similar to that of TpT. The NMR studies of TsqT show a unique property, namely, that the squaryl group of TsqT is influenced by Mg2+ concentration. The ab initio calculations of TsqT showed a highly polarized structure resembling that of a phosphate group. This dimer structural motif was finally incorporated into oligodeoxynucleotides by use of the phosphoramidite approach. The hybridization affinity of these modified oligodeoxynucleotides for the complementary and mismatched oligodeoxynucleotides was studied in detail by using Tm experiments. Consequently, it turned out that in a matched duplex of 5'-d(CGCATsqTAGCC)-3'/5'-d(GGCTAATGCG)-3' the A-T base pairs at the modified site can be preserved, but instead thermal destabilization of the overall structure was observed. To estimate the structure of the duplex, two kinds of fluorescein chromophores (fluorescein (FL) and cyanine 3 (Cy3)) were introduced into the 5'-terminal site of 5'-d(GACGCATsqTAGCCGAT)-3' and 5'-d(ATCGGCTAATGCGTC)-3', respectively. The fluorescence resonance energy transfer experiments using these functionalized oligodeoxynucleotides suggest that the matched duplexes have a bent structure at the modified site. This conclusion was also strongly supported by computational MM and MD simulations.
A framework for caching relevant data items for checking integrity constraints of mobile database (2008)

In a mobile environment, due to the various constraints inherited from limitations of wireless communication and mobile devices, checking for integrity constraints to maintain the consistent state of mobile databases is an important issue that needs to be addressed. Hence, in this paper we propose a framework for caching relevant data items needed during the process of checking integrity constraints of mobile databases. This is achieved by analyzing the relationships among the integrity tests (simplified form of integrity constraints) to be evaluated for a given update operation. This improves the checking mechanism by preventing delays during the process of checking constraints and performing the update. Hence, our model speeds up the checking process.
Appearance and Accumulation of C<sub>4</sub> Carbon Pathway Enzymes in Developing Wheat Leaves (1986)

Soluble protein has been extracted from sections of wheat leaves, from base to tip, and the content of several key enzymes of photosynthetic carbon assimilation in each section has been determined by the protein blot method. In the first leaf, ribulose 1,5-bisphosphate carboxylase (RuBPC) (EC 4.1.1.39) in the basal 0 to 1 centimeter section is about 12% the level in the tip section, whereas phosphoenolpyruvate carboxylase (EC 4.1.1.31) is present in small amounts in the basal section and does not change much in the tip. Pyruvate orthophosphate dikinase (PPDK) (EC 2.7.9.1) first appears in the 4 to 6 centimeter section and increases gradually with development to 10-fold in the tip. Malic enzyme, NADP-dependent (EC 1.3.1.37) also appears in the 4 to 6 centimeter section but remains low to the tip.Fixation of (14)CO(2) by wheat leaf base sections resulted in 42% of total incorporation into malate and aspartate, indicating beta-carboxylation, whereas in the tip section these labeled compounds were only 8% of the total. Although the amount of PPDK in wheat leaves is only 1 to 3% of that in maize leaves, this C(3) PPDK may have a limited role in photosynthesis leading to formation of C(4) compounds. The possibility of a further role, similar to that in C(4) plants, but for intracellular carbon transport in wheat leaves is discussed. The presence of malic dehydrogenase, NADP-specific (EC 1.1.1.82) in wheat leaf chloroplasts was shown, a necessary though not sufficient condition for such a proposed role. Assuming each of the four enzymes associated with C(4) carbon transport were fully active in vivo during photosynthesis, PPDK would still be rate limiting, even in the leaf tip where its activity is maximal. Possible evolutionary and breeding implications are discussed.
The domain organization of<i>Nae</i>I endonuclease: Separation of binding and catalysis (1998)

NaeI is a remarkable type II restriction endonuclease. It must bind two recognition sequences to cleave DNA, forms a covalent protein-DNA intermediate, and is only 1 aa change away from topoisomerase and recombinase activity. The latter activities apparently derive from reactivation of a cryptic DNA ligase active site. Here, we demonstrate that NaeI has two protease-resistant domains, involving approximately the N-terminal and C-terminal halves of the protein, linked by a protease-accessible region of 30 aa. The domains were purified by cloning. The C-terminal domain was shown by gel mobility-shift assay to have approximately 8-fold lower DNA-binding ability than intact NaeI. Analytical ultracentrifugation showed this domain to be a monomer in solution. The N-terminal domain, which contains the catalytic region defined by random mutagenesis, did not bind DNA and was a mixture of different-sized complexes in solution implying that it mediates self-association. DNA greatly inhibited proteolysis of the linker region. The results identify the DNA-binding domain, imply that DNA cleavage and recognition are independent and separable, and lead us to speculate about a cleft-like structure for NaeI.
Toll-like receptor 4-dependent upregulation of cytokines in a transgenic mouse model of Alzheimer's disease (2008)

This is the first demonstration of TLR4-dependent upregulation of cytokines in an AD mouse model. Our results suggest that TLR4 signaling is involved in AD progression and that TLR4 signaling can be a new therapeutic target for AD.
Differences in vertebrate microRNA expression (2006)

MicroRNAs (miRNAs) attenuate gene expression by means of translational inhibition and mRNA degradation. They are abundant, highly conserved, and predicted to regulate a large number of transcripts. Several hundred miRNA classes are known, and many are associated with cell proliferation and differentiation. Many exhibit tissue-specific expression, which aids in evaluating their functions, and it has been assumed that their high level of sequence conservation implies a high level of expression conservation. A limited amount of data supports this, although discrepancies do exist. By comparing the expression of approximately 100 miRNAs in medaka and chicken with existing data for zebrafish and mouse, we conclude that the timing and location of miRNA expression is not strictly conserved. In some instances, differences in expression are associated with changes in miRNA copy number, genomic context, or both between species. Variation in miRNA expression is more pronounced the greater the differences in physiology, and it is enticing to speculate that changes in miRNA expression may play a role in shaping the physiological differences produced during animal development.
Structures of the thermophilic F <sub>1</sub> -ATPase ε subunit suggesting ATP-regulated arm motion of its C-terminal domain in F <sub>1</sub> (2007)

The epsilon subunit of bacterial and chloroplast F(o)F(1)-ATP synthases modulates their ATP hydrolysis activity. Here, we report the crystal structure of the ATP-bound epsilon subunit from a thermophilic Bacillus PS3 at 1.9-A resolution. The C-terminal two alpha-helices were folded into a hairpin, sitting on the beta sandwich structure, as reported for Escherichia coli. A previously undescribed ATP binding motif, I(L)DXXRA, recognizes ATP together with three arginine and one glutamate residues. The E. coli epsilon subunit binds ATP in a similar manner, as judged on NMR. We also determined solution structures of the C-terminal domain of the PS3 epsilon subunit and relaxation parameters of the whole molecule by NMR. The two helices fold into a hairpin in the presence of ATP but extend in the absence of ATP. The latter structure has more helical regions and is much more flexible than the former. These results suggest that the epsilon C-terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of F(o)F(1)-ATP synthase.
Chain-Link Confidentiality (2012)

Disclosing personal information online often feels like losing control over one’s data forever; but this loss is not inevitable. This essay proposes a “chain-link confidentiality” approach to protecting online privacy. One of the most difficult challenges to guarding privacy in the digital age is the protection of information once it is exposed to other people. A chain-link confidentiality regime would contractually link the disclosure of personal information to obligations to protect that information as the information moves downstream. The system would focus on the relationships not only between the discloser of information and the initial recipient, but also between the initial recipient and subsequent recipients. Through the use of contracts, this approach would link recipients of personal information as in a chain, with each recipient bound by the same obligation to protect the information. These chain contracts would contain at least three kinds of terms: 1) obligations and restrictions on the use of the disclosed information; 2) requirements to bind future recipients to the same obligations and restrictions; and 3) requirements to perpetuate the contractual chain. This approach would create a system for the permissible dissemination of personal information online. It would also protect Internet users by ensuring that a website’s obligation to safeguard personal information is extended to third parties.
Ultralong Sb<sub>2</sub>Se<sub>3</sub> Nanowire-Based Free-Standing Membrane Anode for Lithium/Sodium Ion Batteries (2016)

Metal chalcogenides have emerged as promising anode materials for lithium ion batteries (LIBs) and sodium ion batteries (SIBs). Herein, a free-standing membrane based on ultralong Sb<sub>2</sub>Se<sub>3</sub> nanowires has been successfully fabricated via a facile hydrothermal synthesis combined with a subsequent vacuum filtration treatment. The as-achieved free-standing membrane constructed by pure Sb<sub>2</sub>Se<sub>3</sub> nanowires exhibits good flexibility and integrity. Meanwhile, we investigate the lithium and sodium storage behavior of the Sb<sub>2</sub>Se<sub>3</sub> nanowire-based free-standing membrane. When applied as the anode for LIBs, it delivers a reversible capacity of 614 mA h g<sup>-1</sup> at 100 mA g<sup>-1</sup>, maintaining 584 mA h g<sup>-1</sup> after 50 cycles. When applied as the anode for SIBs, it delivers a reversible capacity of 360 mA h g<sup>-1</sup> at 100 mA g<sup>-1</sup>, retaining 289 mA h g<sup>-1</sup> after 50 cycles. Such difference in electrochemical performance can be attributed to the more complex sodiation process relative to the corresponding lithiation process. This work may provide insight on developing Sb<sub>2</sub>Se<sub>3</sub>-based anode materials for high-performance LIBs or SIBs.
Modeling curiosity for intelligent agents (2014)

Siyuan Liu and Yuan Liu, for their discussion and sharing of knowledge in the curious recommender agent problem. I want
New microassay for quantitation of endotoxin using Limulus amebocyte lysate combined with enzyme-linked immunosorbent assay (1988)

A combined method of the Limulus amebocyte lysate (LAL) test and the enzyme-linked immunosorbent assay for quantitation of endotoxin was developed based on our observation that the antigenicity of coagulogen, a major protein in LAL, was lost when LAL reacted with endotoxin as shown by immunoblotting. Determination of the residual coagulogen by an enzyme-linked immunosorbent assay system with monoclonal antibody against coagulogen revealed that the loss of the antigenicity of coagulogen was proportional to the concentration of endotoxin. An inverse linear curve was established between the endotoxin concentration and absorbance. Standard curves of the LAL enzyme-linked immunosorbent assay with different detection limits (from 0.1 to 100 pg of the control standard endotoxin per ml) were obtained from one batch of commercial LAL by adjusting incubation time and dilution of LAL. The reaction curves of various endotoxins were parallel to one another, whereas the kinetics differed from that of (1-3)-beta-D-glucan. The LAL enzyme-linked immunosorbent assay is a highly reproducible microassay, using only 10 microliter of test sample and LAL reagent; because the color and turbidity of plasma samples do not interfere with the assay, it is well suited for quantitation of endotoxins in clinical specimens.
Leukocyte Esterase Activity and Nitrite Test as a Rapid Screen for Significant Bacteriuria (1985)

The results of a simple, inexpensive reagent strip test for the detection of leukocyte esterase and nitrite in 252 urine specimens were compared with semiquantitative urine cultures. Negative reagent strip results predicted correctly all urine culture results with less than 10(5) CFU/mL. Screening of urine specimens with the Chemstrip L/N could aid in reducing the cost of laboratory testing.
Advanced Coating Lining Systems for Challenging Chemical Environments (1997)

Abstract Advanced coatings and coating lining systems are being increasingly used by industry to protect process equipment in challenging chemical environments. This includes not only severe corrosive liquors encountered in many Chemical Process Industry streams, but also the high purity process liquors and rinse systems of the pharmaceutical and microelectronics industries. This paper will discuss the design options for optimizing the performance of fluoropolymer-based coating systems for industry-specific applications such as these. Design factors discussed will include surface pre-treatment options, chemical and mechanical bonding systems, field-proven and advanced polymer barrier coatings, homogenous and graded polymer barrier stacks, and imbedded permeation barriers. The processing techniques for applying engineered coatings will be discussed since processing also plays an important role in the design options available to individual coating applicators and ultimate performance of the coating system applied. Several case studies will be presented and discussed.
Optimization of Switching Transient Waveform to Reduce Harmonics in Selective Frequency Bands (2013)

High-performance power switching devices are used to realize high-performance power converters. These devices tend to generate high-speed switching harmonics that cause electromagnetic interference (EMI). There are several methods for reducing undesirable effects of EMI. An EMI filter or shielding is one of the most popular ways to reduce EMI; however, both EMI filter and shielding increase the cost, size, and weight of power modules. It is well known that the shape of the switching transient strongly affects the harmonics distribution. This paper proposes a new method for reducing high-frequency noise at specific frequency bands by modifying switching transient slopes. This paper describes the improvement in the method of transient wave calculation for obtaining more effective waveforms. In addition, it provides experimental verifications to show the feasibility of the proposed method.
Noninvasive measurement of hydrogen and potassium ion flux from single cells and epithelial structures (2001)

This review introduces new developments in a technique for measuring the movement of ions across the plasma membrane. With the use of a self-referencing ion-selective (Seris) probe, transport mechanisms can be studied on a variety of preparations ranging from tissues to single cells. In this paper we illustrate this versatility with examples from the vas deferens and inner ear epithelium to large and small single cells represented by mouse single-cell embryos and rat microglia. Potassium and hydrogen ion fluxes are studied and pharmacological manipulation of the signals are reported. The strengths of the self-referencing technique are reviewed with regard to biological applications, and the expansion of self-referencing probes to include electrochemical and enzyme-based sensors is discussed.
A Three Inductor Static Machine (1926)

The quantitative theory of a three inductor static machine of the Holtz type is given. It is shown that such a machine is essentially a three phase electrostatic alternator, and that it can be star or mesh connected. A method for demonstrating the action of the machine visually by means of the glow in discharge tubes is described.