gebhart/patrepeval huggingface dataset:
Characterization of the gene celD and its encoded product 1,4-β-d-glucan glucohydrolase D from Pseudomonas fluorescens subsp. cellulosa (1992)

A genomic library of Pseudomonas fluorescens subsp. cellulosa DNA constructed in pUC18 and expressed in Escherichia coli was screened for recombinants expressing 4-methylumbelliferyl beta-D-glucoside hydrolysing activity (MUGase). A single MUGase-positive clone was isolated. The MUGase hydrolysed cellobiose, cellotriose, cellotetraose, cellopentaose and cellohexaose to glucose, by sequentially cleaving glucose residues from the non-reducing end of the cello-oligosaccharides. The Km values for cellobiose and cellohexaose hydrolysis were 1.2 mM and 28 microM respectively. The enzyme exhibited no activity against soluble or insoluble cellulose, xylan and xylobiose. Thus the MUGase is classified as a 1,4-beta-D-glucan glucohydrolase (EC 3.2.1.74) and is designated 1,4-beta-D-glucan glucohydrolase D (CELD). When expressed by E. coli, CELD was located in the cell-envelope fraction; a significant proportion of the native enzyme was also associated with the cell envelope when synthesized by its endogenous host. The nucleotide sequence of the gene, celD, which encodes CELD, revealed an open reading frame of 2607 bp, encoding a protein of M(r) 92,000. The deduced primary structure of CELD was confirmed by the M(r) of CELD (85,000) expressed by E. coli and P. fluorescens subsp. cellulosa, and by the experimentally determined N-terminus of the enzyme purified from E. coli, which showed identity with residues 52-67 of the celD translated sequence. The structure of the N-terminal region of full-length CELD was similar to the signal peptides of P. fluorescens subsp. cellulosa plant-cell-wall hydrolases. Deletion of the N-terminal 47 residues of CELD solubilized MUGase activity in E. coli. CELD exhibited sequence similarity with beta-glucosidase B of Clostridium thermocellum, particularly in the vicinity of the active-site aspartate residue, but did not display structural similarity with the mature forms of cellulases and xylanases expressed by P. fluorescens subsp. cellulosa.
Molecular cloning of the human casein kinase II .alpha. subunit (1989)

A human cDNA encoding the alpha subunit of casein kinase II and a partial cDNA encoding the rat homologue were isolated by using a Drosophila casein kinase II cDNA probe. The 2.2-kb human cDNA contains a 1.2-kb open reading frame, 150 nucleotides of 5' leader, and 850 nucleotides of 3' noncoding region. Except for the first 7 deduced amino acids that are missing in the rat cDNA, the 328 amino acids beginning with the amino terminus are identical between human and rat. The Drosophila enzyme sequence is 90% identical with the human casein kinase II sequence, and there is only a single amino acid difference between the published partial bovine sequence and the human sequence. In addition, the C-terminus of the human cDNA has an extra 53 amino acids not present in Drosophila. Northern analysis of rat and human RNA showed predominant bands of 5.5, 3.1, and 1.8 kb. In rat tissues, brain and spleen had the highest levels of casein kinase II alpha subunit specific RNA, while skeletal muscle showed the lowest. Southern analysis of human cultured cell and tissue genomic DNA using the full-length cDNA probe revealed two bands with restriction enzymes that have no recognition sites within the cDNA and three to six bands with enzymes having single internal sites. These results are consistent with the possibility that two genes encode the alpha subunits.
Applicability of FT-IR Techniques and Goniometry on Characterization of Carbon Fiber Surfaces (2016)

ABSTRACT Carbon fibers have been widely used as structural reinforcement in aeronautical composites, because of their exceptional mechanical properties. However, carbon fibers present few polar groups on their surfaces inducing a weak interaction with some thermosetting and thermoplastic matrices. Surface treatments, such as thermal and electrochemical oxidation, are generally followed by sizing in order to improve interfacial adhesion between carbon fibers and some matrices. The precise surface characterization, by means of its chemical groups and radical identification, has been pointed out as an effective tool of carbon fibers finishing assessment process. Goniometry and Fourier transforminfrared spectroscopy are widely used to characterize some materials applied in industry, but not for carbon fibers, mainly because of their filamentary shape and the high concentration of carbon even in their near surface. In this paper, unsized and sized Torayca T300 carbon fibers were characterized by goniometry tests to evaluate hydrophilic or hydrophobic character. Qualitatively, it was noticed the effect of sizing on carbon fibers by their hydrophilic behavior, which has not been observed in unsized samples. Chemical analysis was performed by Fourier transform-infrared spectroscopy using different setups: photoacoustic, attenuated total reflectance and universal attenuated total reflectance. The Fourier transform-infrared spectroscopy/attenuated total reflectance/Germanium was shown to be the most promising technique to analyze carbon fibers surface, despite the low level of relative intensities of some bands. By this technique, it was possible to observe differences between unsized and sized carbon fibers spectra.
A rail-to-rail CMOS op amp (1988)

A CMOS op amp (operational amplifier) is reported which has a rail-to-rail voltage range at its input as well as its output. An area-efficient output stage has been used. While the entire op amp occupies only 600 mil/sup 2/, when used as a unity-gain buffer and with +or-5-V supplies, the op amp can drive a 9-V/sub pp//1-kHz sine wave across a 300- Omega load with -64 dB of harmonic distortion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Uncovering Hierarchical and Overlapping Communities with a Local-First Approach (2014)

Community discovery in complex networks is the task of organizing a network’s structure by grouping together nodes related to each other. Traditional approaches are based on the assumption that there is a global-level organization in the network. However, in many scenarios, each node is the bearer of complex information and cannot be classified in disjoint clusters. The top-down global view of the partition approach is not designed for this. Here, we represent this complex information as multiple latent labels, and we postulate that edges in the networks are created among nodes carrying similar labels. The latent labels are the communities a node belongs to and we discover them with a simple local-first approach to community discovery. This is achieved by democratically letting each node vote for the communities it sees surrounding it in its limited view of the global system, its ego neighborhood, using a label propagation algorithm, assuming that each node is aware of the label it shares with each of its connections. The local communities are merged hierarchically, unveiling the modular organization of the network at the global level and identifying overlapping groups and groups of groups. We tested this intuition against the state-of-the-art overlapping community discovery and found that our new method advances in the chosen scenarios in the quality of the obtained communities. We perform a test on benchmark and on real-world networks, evaluating the quality of the community coverage by using the extracted communities to predict the metadata attached to the nodes, which we consider external information about the latent labels. We also provide an explanation about why real-world networks contain overlapping communities and how our logic is able to capture them. Finally, we show how our method is deterministic, is incremental, and has a limited time complexity, so that it can be used on real-world scale networks.
Towards Automatically Classifying Case Law Citation Treatment Using Neural Networks (2019)

In common law legal systems, judges decide issues between parties (legal decision or case law) by reference to previous decisions that consider similar factual situations. Accordingly, these decisions typically feature rich citation networks, i.e., a new decision frequently cites previous relevant decisions (citation). These citations may, in varying degrees, express that a cited decision is applicable, not-applicable, or no longer current law. Such treatment label is important to a lawyer's process of determining whether a case is proper law. These labels serve as a matter of convenience in citation indices enabling lawyers to prioritise decisions to examine to understand the current state of the law. They also prove useful in other areas such as prioritisation for manual summarisation of cases, where not all cases can be summarised, and automatic summarisation, or, potentially, as a ranking feature in case law retrieval. While a lawyer can determine the treatment of a cited case by reading a decision, this is time consuming and can increase legal costs. Currently, not all newly decided cases feature these treatment labels. Further, older cases typically do not. Given the large amount of new legal decisions decided each year, manual annotation of such treatment is not feasible. In this paper, we explore the effectiveness of neural network architectures for identifying case law citation treatment and importance (whether a case is important to a lawyer's reasoning process). We find that these tasks are very difficult and various methods for text classification perform poorly. We address more comprehensively the task of citation importance for this reason while limiting our examination of the task of citation treatment to the modelling of the problem and the highlight of the intrinsic difficulty of the task. We make a test dataset available at github.com/ielab/caselaw-citations to stimulate further research that tackles this challenging problem. We also contribute a range of word embeddings learned over a large amount of processed case law text.
A CAM- and starch-deficient mutant of the facultative CAM species Mesembryanthemum crystallinum reconciles sink demands by repartitioning carbon during acclimation to salinity (2012)

In the halophytic species Mesembryanthemum crystallinum, the induction of crassulacean acid metabolism (CAM) by salinity requires a substantial investment of resources in storage carbohydrates to provide substrate for nocturnal CO(2) uptake. Acclimation to salinity also requires the synthesis and accumulation of cyclitols as compatible solutes, maintenance of root respiration, and nitrate assimilation. This study assessed the hierarchy and coordination of sinks for carbohydrate in leaves and roots during acclimation to salinity in M. crystallinum. By comparing wild type and a CAM-/starch-deficient mutant of this species, it was sought to determine if other metabolic sinks could compensate for a curtailment in CAM and enable acclimation to salinity. Under salinity, CAM deficiency reduced 24 h photosynthetic carbon gain by >50%. Cyclitols were accumulated to comparable levels in leaves and roots of both the wild type and mutant, but represented only 5% of 24 h carbon balance. Dark respiration of leaves and roots was a stronger sink for carbohydrate in the mutant compared with the wild type and implied higher maintenance costs for the metabolic processes underpinning acclimation to salinity when CAM was curtailed. CAM required the nocturnal mobilization of >70% of primary carbohydrate in the wild type and >85% of carbohydrate in the mutant. The substantial allocation of carbohydrate to CAM limited the export of sugars to roots, and the root:shoot ratio declined under salinity. The data suggest a key role for the vacuole in regulating the supply and demand for carbohydrate over the day/night cycle in the starch-/CAM-deficient mutant.
Bone Marrow Biopsy Involvement by Non-Hodgkin's Lymphoma (2005)

To evaluate the features of bone trephine biopsy involvement by non-Hodgkin lymphoma, 450 specimens were evaluated for percentage of marrow involvement, pattern of involvement, presence of germinal centers or follicular structures, and discordance with other involved sites. A subset of 197 cases was evaluated for evidence of concurrent peripheral blood involvement. Follicular grade 1 lymphoma (30.4%) was the most common type to involve the marrow, followed by diffuse large B-cell lymphoma (16.0%), mantle cell lymphoma (9.3%), low-grade B-cell lymphoma, not otherwise specified (8.7%), lymphoplasmacytic lymphoma (8.4%), follicular grade 2 lymphoma (7.1%), and mature T- and NK-cell lymphomas (6.4%). A mixed pattern of infiltration was most common, followed by paratrabecular, nodular, diffuse, and interstitial patterns. Greater than 90% of follicular lymphomas had at least a focal paratrabecular infiltration pattern, but this pattern was also seen with other lymphoma types. Interstitial disease infiltration tended to correlate with lymphoplasmacytic lymphoma but was also not specific. The presence of germinal centers or follicular structures was associated with follicular lymphoma in 88% of cases. Discordance between the bone marrow morphology and other tissue sites was observed in 24.9% of cases and was most often seen with follicular or diffuse large B-cell lymphoma. Peripheral blood involvement by lymphoma was observed in 29% of cases, found in all disease groups except for follicular grade 3 lymphoma. This study highlights the frequency of different lymphoma patterns in the marrow, limitations of primary lymphoma classification on biopsy material alone, and the relative frequency of marrow discordance and peripheral blood involvement by marrow lymphoma.
TiO2 nanocrystals grown on graphene as advanced photocatalytic hybrid materials (2010)

A graphene/TiO2 nanocrystals hybrid has been successfully prepared by directly growing TiO2 nanocrystals on graphene oxide (GO) sheets. The direct growth of the nanocrystals on GO sheets was achieved by a two-step method, in which TiO2 was first coated on GO sheets by hydrolysis and crystallized into anatase nanocrystals by hydrothermal treatment in the second step. Slow hydrolysis induced by the use of EtOH/H2O mixed solvent and addition of H2SO4 facilitates the selective growth of TiO2 on GO and suppresses growth of free TiO2 in solution. The method offers easy access to the GO/TiO2 nanocrystals hybrid with a uniform coating and strong interactions between TiO2 and the underlying GO sheets. The strong coupling gives advanced hybrid materials with various applications including photocatalysis. The prepared graphene/TiO2 nanocrystals hybrid has superior photocatalytic activity to other TiO2 materials in the degradation of rhodamine B, showing an impressive three-fold photocatalytic enhancement over P25. It is expected that the hybrid material could also be promising for various other applications including lithium ion batteries, where strong electrical coupling to TiO2 nanoparticles is essential.
Isolation and partial characterization of a cDNA encoding a rabbit liver carboxylesterase that activates the prodrug irinotecan (CPT-11). (1998)

We have isolated a cDNA encoding a rabbit carboxylesterase (CE; EC 3.1.1.1) that converts the camptothecin-derived prodrug irinotecan (CPT-11) to the potent topoisomerase I inhibitor 7-ethyl-10-hydroxycamptothecin. NH2-terminal amino acid sequencing of a purified rabbit CE allowed the design of redundant oligonucleotides to perform PCR from rabbit liver cDNA. DNA sequencing of the PCR product confirmed the identity of the clone, and after both 5' and 3' rapid amplification of cDNA ends, oligonucleotide primers were designed to amplify the entire cDNA. The 1698-bp open reading frame encoded a 565-amino acid protein containing the characteristic CE B-1 and B-2 motifs, a hydrophobic NH2-terminal leader sequence, and the COOH-terminal residues HIEL that are thought to be responsible for protein localization in the endoplasmic reticulum. Transient expression of the cDNA in COS-7 cells resulted in CE activity in cell extracts and increased the sensitivity of cells to CPT-11. Additionally, stable expression of the rabbit liver CE cDNA in the human glioma U-373 MG cell line resulted in a 56-fold decrease in the IC50 value for CPT-11, whereas the expression of a human alveolar macrophage cDNA encoding a highly homologous CE produced no change in drug sensitivity.
Correlation of serum metalloproteinase levels with lung cancer metastasis and response to therapy. (1992)

Cancer cells elaborate metalloproteinases which may play a role in invasion and metastasis. The serum level of the M(r) 72,000 type IV collagenase (MMP-2) was measured in 87 lung cancer patients. Stage IV cancer levels were significantly elevated (P less than 0.0001) compared to normal sera. A significant difference (P less than 0.01) was found between enzyme levels in the presence versus the absence of distant metastasis. For 29 patients treated with combination chemotherapy, a positive relationship was noted between response failure and elevated enzyme levels. Serum metalloproteinase levels may provide information relevant to prognosis as well as treatment decisions.
An analysis of vertebrate mRNA sequences: intimations of translational control. (1991)

Five structural features in mRNAs have been found to contribute to the fidelity and efficiency of initiation by eukaryotic ribosomes. Scrutiny of vertebrate cDNA sequences in light of these criteria reveals a set of transcripts--encoding oncoproteins, growth factors, transcription factors, and other regulatory proteins--that seem designed to be translated poorly. Thus, throttling at the level of translation may be a critical component of gene regulation in vertebrates. An alternative interpretation is that some (perhaps many) cDNAs with encumbered 5' noncoding sequences represent mRNA precursors, which would imply extensive regulation at a posttranscriptional step that precedes translation.
High-Performance Polyquinolines with Pendent High-Temperature Chromophores for Second-Order Nonlinear Optics (1998)

A series of high-temperature and chemically stable chromophores were covalently attached onto the polyquinoline backbones. These NLO side-chain polyquinolines possess high glass transition temperature (Tg > 200 °C), excellent processibility, thermal stability, and electrooptical properties. Poling results of these polymers demonstrate large electrooptic coefficient (r33) values (up to 17 pm/V measured at 0.83 μm) and good temporal alignment stability of polymer films (the r33 value retained more than 80% of the original value at 100 °C for more than 3000 hours).
Renal transplantation: Basic concepts and evolution of therapy (2003)

Within the last 5 years, dramatic changes in the area of renal transplantation have occurred. There have been shifts in the dominant types of rejection, and in the types and utilization of immunosuppressants. Hyperacute rejection is now rarely seen, and acute cellular rejection within the first 6 to 12 months has been reduced to about 10%. However, humoral/antibody-mediated rejection has become a more prevalent problem. In the area of immunosuppressants, the ability to reduce acute cellular rejection to about 10% has been achieved through more judicious use of calcineurin inhibitors (cyclosporine and tacrolimus), increased use of mycophenolate mofetil, and the recent introduction of sirolimus (rapamycin). The polyclonal antibody (antithymocyte globulin), as well as monoclonal antibodies directed against the alpha chain of CD25 (daclizumab and basilixamab), have added substantially to the improved success of renal allografts. Because of numerous serious toxicities from glucocorticoids and calcineurin inhibitors, particularly cyclosporine, new studies are utilizing calcineurin-free and/or glucocorticoid avoidance or rapid elimination protocols often in combination with a monoclonal antibody and sirolimus. New immunosuppressants such as FTY720 and Campath-1 are also under study. In addition to its use in treating patients with low-level donor-specific antibody before transplantation in order to avoid hyperacute rejection, apheresis is utilized in various combination protocols after transplantation in the management of humoral/antibody-mediated rejection, in the treatment of hemolytic uremia syndrome that sometimes occurs with calcineurin inhibitors and sirolimus, as well as in the treatment of focal segmental glomerulosclerosis that has a major risk of recurrence in renal transplants.
Transducing Bacteriophage for Bacillus cereus (1968)

A phage, designated CP-51, that carries out generalized transduction in Bacillus cereus 569 was isolated from soil. All auxotrophic mutants tested, those requiring tryptophan, histidine, leucine, isoleucine, methionine, or phenylalanine, were transduced to prototrophy. The phage was extremely unstable when stored at 2 to 4 C, but stability was enhanced by storage at higher temperatures. The optimal temperature of those tested for maintenance of plaque-forming units was 15 C.
[Hepatitis non-A, non-B-associated DNA--demonstration of DNA in proven infectious anti-D-immunoglobulin]. (1988)

An anti-D-immunoglobulin preparation implicated in a hepatitis non-A,non-B transmission was analyzed for the presence of a DNA, which was originally isolated, cloned and sequenced from feces of a patient with posttransfusion HNANB. The investigation was performed by a DNA polymerase chain reaction using synthetic oligoprimers. Commercially available immunoglobulin preparations served as controls. The demonstration of identical DNA sequences in the infectious material speaks in favour of this up to now unknown circular and partially double-stranded DNA to be a virus genome involved in hepatitis non-A,non-B.
Inhibition of matrix metalloproteinases by N-carboxyalkyl peptides (1993)

An extensive study of the requirements for effective binding of N-carboxyalkyl peptides to human stromelysin, collagenase, and to a lesser extent, gelatinase A has been investigated. These efforts afforded inhibitors generally in the 100-400 nM range for these matrix metalloproteinases. The most significant increase in potency was obtained with the introduction of a beta-phenylethyl group at the P1' position, suggesting a small hydrophobic channel into the S1' subsite of stromelysin. One particular compound, N-[1(R)-carboxyethyl]-alpha(S)-(2-phenylethyl)glycyl-L-leucine,N- phenylamide (79a), is relatively selective for rabbit stromelysin with a K(i) = 6.5 nM and may prove useful for elucidating the role of endogenously-produced stromelysin in lapine models of tissue degradation.
Rao-Blackwellized particle filtering for 6-DOF estimation of attitude and position via GPS and inertial sensors (2006)

The authors present an innovative method for the efficient joint estimation of attitude and position in six degrees of freedom via sensors such as GPS, inertial measurement units, and odometry. Traditional methods for attitude estimation via Kalman filtering are beset by many conceptual problems relating to the representation of orientations in linear spaces, leading to difficulties in implementation and the interpretation of uncertainty estimates, among other issues. These problems are compounded when it is necessary to jointly estimate position and attitude. We demonstrate how Rao-Blackwellized particle filtering provides a framework for approaching this estimation problem that is both conceptually appealing and practical. Results are shown that demonstrate the filter's robustness to sensor outages and its ability to perform well even in situations with noisy sensors and high initial uncertainty in all state dimensions; these situations are precisely those in which traditional Kalman filtering approaches are most likely to experience problems