gebhart/patrepeval huggingface dataset:
Synthesis of Proteins Containing Modified Arginine Residues (2007)

Unnatural amino acid mutagenesis provides the wherewithal to study protein function in great detail. To extend the repertoire of functionalized amino acids available for study by this technique, seven structural analogues of arginine were prepared and used to activate a suppressor tRNACUA. These included Ngamma-methylarginine, Ngamma-nitroarginine, citrulline, homoarginine, and three conformationally constrained analogues based on proline. These misacylated tRNAs were shown to be capable of introducing the arginine analogues into dihydrofolate reductase (position 22) and Photinus pyralis luciferase (positions 218 and 437). Most of the modified luciferases containing arginine analogues at position 218 emitted light with less efficiency and at longer wavelength than the wild type. This is consistent with the postulated role of this residue as essential for maintaining the polarity and rigidity of the luciferin-binding site. Interestingly, the luciferase containing Ngamma-methylarginine at position 218 emitted light at the same wavelength as the wild type and was at least as efficient. Alteration of the arginine residue at position 437 had no effect on the wavelength of emitted light but afforded analogues, all of which emitted light less efficiently than the wild type. This is altogether consistent with the putative role of Arg437, which is an invariant residue within the superfamily of enzymes that includes P. pyralis luciferase. This amino acid is part of the linker between the two structural domains of luciferase that is believed to be essential for efficient enzyme function but not part of the substrate-binding site.
Covariance approximation for fast and accurate computation of channelized Hotelling observer statistics (2000)

Describes a method for computing linear observer statistics for maximum a posteriori (MAP) reconstructions of PET images. The method is based on a theoretical approximation for the mean and covariance of MAP reconstructions. In particular, the authors derive here a closed form for the channelized Hotelling observer (CHO) statistic applied to 2D MAP images. The theoretical analysis models both the Poission statistics of PET data and the inhomogeneity of tracer uptake. The authors show reasonably good correspondence between these theoretical results and Monte Carlo studies. The accuracy and low computational cost of the approximation allow the authors to analyze the observer performance over a wide range of operating conditions and parameter settings for the MAP reconstruction algorithm.
Refined Structure of an Intact IgG2a Monoclonal Antibody<sup>,</sup> (1997)

The structure of an intact, anti-canine lymphoma monoclonal antibody (Mab231) was determined by molecular replacement and refined in a triclinic cell to an R-value of 20.9%, using synchrotron diffraction data from 2.8 to 20 A resolution. All segments of the antibody, including the hinge region and carbohydrate component, are visible in electron density maps. There is no overall symmetry to the antibody, as the Fc is disposed in an entirely oblique manner with respect to the Fabs. The CH2 and CH3 domains do, however, possess a nearly exact, local 2-fold relationship. The Fab segments are related by a second, independent, local dyad axis, exact only with respect to constant domains. Variable domains exhibit no symmetry relationship as a consequence of the 16 degrees difference in Fab elbow angles. Variable domain pair associations VL:VH for the Fabs are virtually the same, and corresponding CDRs of the two Fabs also are nearly identical in structure. CDR-H3 displays the greatest difference. Hypervariable loops of both Fabs are involved in contacts with symmetry-related Fc segments at the CH2-CH3 switch junction, suggesting a "complex" structure. The hinge segment connecting Fabs with the Fc is quite extended and exhibits thermal factors indicative of a high degree of mobility. It consists of a well-defined upper hinge that partially maintains dyad symmetry and a fairly rigid core bounded above and below by fluid polypeptides that provide segmental flexibility. This structure represents the first visualization by X-ray analysis of a murine Fc segment, and its CH2 domains exhibit substantial rigid body conformational changes with respect to the human Fc used as an initial molecular replacement model. The oligosaccharides were found by difference Fourier syntheses to be very similar to those of the free human Fc fragment, although differences are present in the terminal residues. The detailed structure of the IgG presented here, and the distribution of effector binding sites, appears consistent with effector activation mechanisms involving translocation and/or aggregation of the Fc following antigen binding by the Fabs.
Subtle Structural Changes in Tetrahydroquinolines, A New Class of Nonsteroidal Selective Androgen Receptor Modulators, Induce Different Functions (2012)

Tetrahydroquinolines (THQs), a new class of nonsteroidal selective androgen receptor (AR) modulators, have two indispensable functional groups, that is, a hydroxyl group for AR binding and a nitro group for agonistic activity. Interestingly, switching the nitro to a cyano group, the compound acts as an antagonist. To understand this phenomenon, molecular dynamics simulations were applied for dihydrotestosterone (DHT) and representative THQs complexes with AR. Upon ligand binding, the hydroxyl group formed a tight hydrogen-bond (H-bond) with Asn705 on Helix 3 (H3). The immobilization of Asn705 on H3 is helpful in the formation of tight H-bonds with Asp890 on loop 11-12, and this immobilization consequently leads to a stabilization of H12. The difference in the DHT carbonyl isosteres affected the presence or absence of the H-bonds between the hydroxyl group of THQ and Thr877 and the distortion of H12, which is caused by the methyl group of THQ. Thus, the binding, agonist, and antagonist functions were controlled by subtle structural changes in THQ.
Cutting Edge: Nitric Oxide Inhibits the NLRP3 Inflammasome (2012)

Although the NLRP3 inflammasome plays a pivotal role in host defense, its uncontrolled activation is associated with inflammatory disorders, suggesting that regulation of the inflammasome is important to prevent detrimental effects. Type I IFNs and long-term LPS stimulation were shown to negatively regulate NLRP3 activation. In this study, we found that endogenous NO is involved in the regulation of NLRP3 inflammasome activation by either IFN-β pretreatment or long-term LPS stimulation. Furthermore, S-nitroso-N-acetylpenicillamine (SNAP), an NO donor, markedly inhibited NLRP3 inflammasome activation, whereas the AIM2 and NLRC4 inflammasomes were only partially inhibited by SNAP. An increase in mitochondrial reactive oxygen species induced by ATP was only modestly affected by SNAP treatment. Interestingly, S-nitrosylation of NLRP3 was detected in macrophages treated with SNAP, and this modification may account for the NO-mediated mechanism controlling inflammasome activation. Taken together, these results revealed a novel role for NO in regulating the NLRP3 inflammasome.
Commutability of Design Pattern Instantiation and Integration (2007)

Design patterns capture expert design experience in generic design structure and behavior. A design pattern needs to be instantiated before using. It can be integrated with other patterns as well. The instantiation and integration operations are two important operations when a designer uses a design pattern in a particular application. In this paper, we investigate the commutability of these two operations based on our formal specification framework. We provide rigorous proofs on the conditions when the order of these two operations does not matter. Our results enable the software designers to choose their design processes with assurance of their equivalence.
High-Performance Routing With Multipathing and Path Diversity in Ethernet and HPC Networks (2020)

The recent line of research into topology design focuses on lowering network diameter. Many low-diameter topologies such as Slim Fly or Jellyfish that substantially reduce cost, power consumption, and latency have been proposed. A key challenge in realizing the benefits of these topologies is routing. On one hand, these networks provide shorter path lengths than established topologies such as Clos or torus, leading to performance improvements. On the other hand, the number of shortest paths between each pair of endpoints is much smaller than in Clos, but there is a large number of non-minimal paths between router pairs. This hampers or even makes it impossible to use established multipath routing schemes such as ECMP. In this article, to facilitate high-performance routing in modern networks, we analyze existing routing protocols and architectures, focusing on how well they exploit the diversity of minimal and non-minimal paths. We first develop a taxonomy of different forms of support for multipathing and overall path diversity. Then, we analyze how existing routing schemes support this diversity. Among others, we consider multipathing with both shortest and non-shortest paths, support for disjoint paths, or enabling adaptivity. To address the ongoing convergence of HPC and “Big Data” domains, we consider routing protocols developed for both HPC systems and for data centers as well as general clusters. Thus, we cover architectures and protocols based on Ethernet, InfiniBand, and other HPC networks such as Myrinet. Our review will foster developing future high-performance multipathing routing protocols in supercomputers and data centers.
The role of double‐strand break‐induced allelic homologous recombination in somatic plant cells (2002)

During meiosis, homologous recombination occurs between allelic sequences. To evaluate the biological significance of such a pathway in somatic cells, we used transgenic tobacco plants with a restriction site for the rare cutting endonuclease I-SceI within a negative selectable marker gene. These plants were crossed with two tobacco lines containing, in allelic position, either a deletion or an insertion within the marker gene that rendered both marker gene and restriction site inactive. After the double-strand break induction, we selected for repair events resulting in a loss of marker gene function. This loss was mostly due to deletions. We were also able to detect double strand break-induced allelic recombination in which the break was repaired by a faithful copying process from the homologue carrying the shortened transgene. The estimated frequency indicates that homologous recombination in somatic cells between allelic sites appears to occur at the same order of magnitude as between ectopic sites, and is thus far too infrequent to act as major repair pathway. As somatic changes can be transferred to the germ line, the prevalence of intrachromatid rearrangements over allelic recombination might be an indirect prerequisite for the enhanced genome plasticity postulated for plants.
Azcapotzalco : una historia por construir (1991)

A pesar de la diversidad historica que se puede percibir en el proceso de Azcapotzaco existen escasos estudios sobre los diferentes aspectos de la region. De aqui el itneres de sistematizar algunas notas de investigacion que pueden contribuir a la construccion de la historia de esta delegacion.
Data Preprocessing Techniques for Pre-Fetching and Caching of Web Data through Proxy Server (2011)

The rapid growth of the Web in terms of Web sites and their users during the last decade has put lots of pressure for Web site owners in reducing the latency of Web pages. Web caching and Web pre-fetching are two important techniques used to tackle these problems and reduce the noticeable response time perceived by users. These two techniques complement each other since the Web caching technique exploits the temporal locality, whereas Web pre-fetching technique utilizes the spatial locality of Web object. By integrating Web caching and Web pre-fetching techniques, the latency time and search space get reduced. Due to this dramatic changes, a huge amount of data related to the user’s interactions with the Web sites are recorded in the Web access log. Web access log plays an important role in predicting the user access pattern and pre-fetching and caching of Web data for better performance. Different data mining techniques can be applied on Web usage data to mine user access patterns and this knowledge can be used in a variety of applications such as system improvement, Web site modification, business intelligence etc. This paper discusses various data preprocessing techniques that are carried out at proxy server access log which generate Web access pattern and can also be used for further applications. Key words Web mining, proxy server, data mining, preprocessing, pre-
Role delegation in role-based access control (2000)

In distributed-computing environments, applications or users have to share resources and communicate with each other to perform their jobs more efficiently. For better performance, it is important to keep resources and the information integrity from the unexpected use by unauthorized user. Therefore, there is a strong demand for the authentication and the access control of distributed-shared resources. Nowadays, three kinds of access control, discretionary access control (DAC) mandatory access control (MAC) and role-based access control (RBAC) have been proposed. In RBAC, there are role hierarchies in which a senior role can perform the permission of a junior role. However, it is sometimes necessary for a junior role to perform a senior role's permission, which is not allowed basically by a junior role. In this paper, we will propose a role delegation method, consisting of a role delegation server, and a role delegation protocols. We divide the delegation into two by the triggered object: active delegation and passive delegation. Consequently, a junior role can gain a senior role's permissions.
Effect of growth temperature on the lipids, outer membrane proteins, and lipopolysaccharides of Pseudomonas aeruginosa PAO (1987)

Growth of Pseudomonas aeruginosa PAO1 at 15 to 45 degrees C in tryptic soy broth resulted in changes in the lipids, lipopolysaccharides (LPSs), and outer membrane proteins of the cells. Cells grown at 15 degrees C contained, relative to those cultivated at 45 degrees C, increased levels of the phospholipid fatty acids hexadecenoate and octadecenoate and reduced levels of the corresponding saturated fatty acids. Furthermore, the lipid A fatty acids also showed thermoadaptation with decreases in dodecanoic and hexadecanoic acids and increases in the level of 3-hydroxydecanoate and 2-hydroxdodecanoate as the growth temperature decreased. In addition, LPS extracted from cells cultivated at the lower temperatures contained a higher content of long-chain S-form molecules than that isolated from cells grown at higher temperatures. On the other hand, the percentage of LPS cores substituted with side-chain material decreased from 37.6 mol% at 45 degrees C to 19.3 mol% at 15 degrees C. The outer membrane protein profiles indicated that at low growth temperatures there was an increase in a polypeptide with an apparent molecular weight of 43,000 and decreases in the content of 21,000 (protein H1)- and 27,500-molecular-weight proteins.
Sender Policy Framework (SPF) Authentication Failure Reporting Using the Abuse Reporting Format (2012)

This memo presents extensions to the Abuse Reporting Format (ARF) and
Sender Policy Framework (SPF) specifications to allow for detailed
reporting of message authentication failures in an on-demand fashion.
This memo updates RFC 4408 by providing an IANA registry for SPF
modifiers. [STANDARDS-TRACK]
Visual Studies: A Skeptical Introduction (2003)

"Visual studies is a rapidly expanding intellectual field, growing throughout colleges and universities around the world. But is it asking the most interesting questions? And is it just too easy to do? In his latest book, James Elkins offers a road map through the field of visual studies, describing its major concerns and its principal theoretical sources. Then, with the skill and insight that have marked his successful books on art and visuality, Elkins takes the reader down a side road where visual studies can become a more interesting place. Why look only at the same handful of theorists? Why exclude from one's field of vision non-Western art or the wealth of scientific images? The centerpiece of Visual Studies is Elkins's proposal for ten ways in which visual studies could be made more difficult - theoretically, practically, and in terms of its interpretative and historical range. As Stories of Art offered an antidote to the authorized version of art history, Visual Studies: A Skeptical Introduction proposes a refreshingly open-minded introduction to a growing field. This handsome volume is illustrated throughout." http://www.loc.gov/catdir/enhancements/fy0651/2003013585-d.html.
Stereoselective Syntheses of 4-Oxa Diaminopimelic Acid and Its Protected Derivatives via Aziridine Ring Opening (2007)

Regio- and stereoselective aziridine ring opening with oxygen nucleophiles derived from serine and threonine provides a route to stereochemically pure 4-oxa-2,6-diaminopimelic acid (oxa-DAP) and its methyl-substituted derivatives. Oxa-DAP is a substrate of DAP epimerase, a key enzyme for biosynthesis of l-lysine and formation of peptidoglycan precursors. Orthogonally protected analogues of lanthionine and beta-methyllanthionine wherein oxygen replaces sulfur were prepared that could be used for solid-supported peptide synthesis to make oxa derivatives of lantibiotics.
A graphic tool for tracking variance & comorbidities in cardiac surgery case management. (1993)

Nursing case management has been documented as one solution to the balance of cost and quality issues in healthcare. A current focus in healthcare is continuous quality improvement (CQI). CQI methods are focused on outcome measurements. Outcome research is a recent development in case management. Tracking variance, evaluating cost reduction and patient effectiveness, and determining types of patients at risk for negative variance are current case management research demands. Tracking patient comorbidities would allow for additional subset "tailoring" of existing critical pathways for specific comorbidities. Little research has been done on these issues. Few systems exist that track both variance and comorbidities. This article presents a graphic, simple, multidisciplinary tracking system that includes comorbidities and allows for individual and group patient variance analysis.
An examination of the data and concepts germane to the oxygenation of cultured animal cells. (1983)

With the increasing demand for high productivity cultures (including unit process monolayer cultures) oxygenation has now become a problem much sooner in the scaling-up process. There are no problems with measuring the dissolved oxygen concentration, but maintaining a desired concentration is one of the major challenges in Animal Cell Technology. It is of key importance, because the oxygen level has critical effects on cell metabolism (13, 5, 9, 22, 40, 36) which not only affect cell growth but also the products that can be expressed by the cell. As the oxygen level for these two functions is often different (e.g. the production of Ig from lymphocytes (27) more attention must be paid to defining the optimal oxygen levels and methods whereby such levels can be maintained in the least destructive manner.
Osteochondral Allograft Transplantation (2003)

Articular cartilage injuries are known to be associated with an increased incidence of degenerative arthritis. As a result, numerous ways have been explored as a method to treat articular cartilage defects. Unfortunately, no one technique has been found to be superior in all situations. Osteochondral allografts are appealing in that they prove a normal articular cartilage matrix and are not limited by the size or configuration of the defect. Their success in treating osteochondral defects (OCD) and post-traumatic lesions has been impressive even in long-term follow-up. Although rare, disease transmission and immune reject are justifiable concerns with their use. With all factors considered osteochondral allografts are an excellent option when treating lesions of 2 cm2 or greater.
Elevated Levels of Cytokeratin 19 in the Bronchoalveolar Lavage Fluid of Patients With Chronic Airway Inflammatory Diseases--A Specific Marker for Bronchial Epithelial Injury (1997)

Cytokeratin 19 (CK19) is a specific cytoskeletal structure of simple epithelia, including bronchial epithelial cells (BEC). Since CK19 is released from injured bronchial epithelium, we investigated the levels of CK19 fragments in the bronchoalveolar lavage fluid (BALF) of eight patients with chronic airway inflammatory diseases (CAID) using an enzyme-linked immunosorbent assay (ELISA). Included in our test group were four cases of chronic bronchitis, three cases of bronchiectasis, and one case of diffuse panbronchiolitis. There were also 15 control subjects (five asymptomatic smokers and 10 nonsmokers). BALF from the nonsmokers as well as from the asymptomatic smokers contained few CK19 fragments (0.2 +/- 0.2 and 1.9 +/- 0.8 pg/ml, respectively). In contrast, significantly high levels of CK19 were present in the BALF of patients with CAID (21.7 +/- 5.7 pg/ml; p < 0.01 versus nonsmoking controls). In addition, CK19 fragment concentrations in BALF correlated significantly with the number of neutrophils (r = 0.722, p < 0.01) but not with the numbers of macrophages or lymphocytes in BALF. BALF from patients with CAID contained high levels of neutrophil elastase (NE) activity, suggesting that NE might be an important stimulus for the release of CK19 from BEC. To prove this, we incubated BET-1A cells, a human immortalized bronchial epithelial cell line, both in the absence and the presence of inflammatory mediators (including NE, tumor necrosis factor-alpha [TNF-alpha], and hydrogen peroxide). We then measured the concentration of CK19 fragments in the culture supernatants with ELISA. BET-1A cells released CK19 fragments into their culture supernatants after treatment with NE but not after treatment with TNF or hydrogen peroxide. Further, we demonstrated that CK19 cleaved by NE could not be detected by ELISA. Our results suggest that CK19 measurement in BALF is useful for assessing the presence of bronchial epithelial injuries.