gebhart/patrepeval huggingface dataset:
Processive proofreading is intrinsic to T4 DNA polymerase. (1992)

DNA replication occurs in vivo with very high processivity, meaning that the replication complex assembles at the origin(s) of replication and then performs template-directed synthesis of DNA over virtually the entire genome without dissociation. Such processivity also characterizes reconstituted replication holoenzyme complexes in vitro. However, the isolated DNA polymerases are much less processive, especially under physiological conditions. In this paper we monitor the degree of processivity displayed by the bacteriophage T4-coded DNA polymerase while in its proofreading mode by asking whether an isolated polymerase can "edit-out" the 3'-terminal nucleotide from the primer (using the 3'----5'-exonuclease activity of the polymerase) and then switch into the synthesis mode without dissociating from the DNA template. This "switch experiment" is accomplished by using mismatched primer/template substrates as an experimental tool to mimic the situation that T4 DNA polymerase encounters after a misincorporation event has occurred. By performing experiments under single-turnover conditions (obtained using a heparin trap), we demonstrate that T4 DNA polymerase, upon encountering a misincorporated base, neither synthesizes the next base nor dissociates into solution. Instead, with a greater than 80% probability, it removes the misincorporated base and then continues synthesis in a fully processive manner. We also show that the removal of a doubly mispaired sequence from the 3'-terminus of the primer, followed by synthesis, is comparably processive. In contrast, the apparent processivity of removing a triply mispaired terminus is much reduced. Taken together, these observations are consistent with the notion that the "editing active site" of the T4 enzyme optimally accommodates only two unpaired nucleotide residues. Our results do not support the idea that the exonuclease activity of T4 DNA polymerase is highly selective for mismatched termini; they suggest instead that the dwell time at a misincorporated base determines overall editing efficiency. The integrated results of this study provide additional insight into the structure of the T4 DNA polymerase, as well as into the interactions between the polymerase and the polymerase accessory proteins that are required to provide the holoenzyme complex with full processivity.
[A gene probe test for serum RNA proteolipid in neoplasia]. (1989)

We describe for the first time the specific determination of a tumor associated nucleic acid found in 50 of 57 sera from cancer patients. The novel tumor marker "RNA-proteolipid" described by us contains an mRNA of about 10 kilobases. We have established a test to determine this RNA by hybridization. A cDNA was obtained by reversed transcription from RNA using serum from a patient with Hodgkin's lymphoma. The cDNA was then ligated into a M13 phage and cloned in Escherichia coli. The phage DNA was sulfonated chemically and hybridized to RNA from neoplastic sera which was immobilized on nylon. The bound DNA was detected by an immunoassay.
Plant-based culture media: Efficiently support culturing rhizobacteria and correctly mirror their in-situ diversity (2015)

Our previous publications and the data presented here provide evidences on the ability of plant-based culture media to optimize the cultivability of rhizobacteria and to support their recovery from plant-soil environments. Compared to the tested chemically-synthetic culture media (e.g. nutrient agar and N-deficient combined-carbon sources media), slurry homogenates, crude saps, juices and powders of cactus (Opuntia ficus-indica) and succulent plants (Aloe vera and Aloe arborescens) were rich enough to support growth of rhizobacteria. Representative isolates of Enterobacter spp., Klebsiella spp., Bacillus spp. and Azospirillum spp. exhibited good growth on agar plates of such plant-based culture media. Cell growth and biomass production in liquid batch cultures were comparable to those reported with the synthetic culture media. In addition, the tested plant-based culture media efficiently recovered populations of rhizobacteria associated to plant roots. Culturable populations of >10(6)-10(8) cfu g(-1) were recovered from the ecto- and endo-rhizospheres of tested host plants. More than 100 endophytic culture-dependent isolates were secured and subjected to morphophysiological identification. Factor and cluster analyses indicated the unique community structure, on species, genera, class and phyla levels, of the culturable population recovered with plant-based culture media, being distinct from that obtained with the chemically-synthetic culture media. Proteobacteria were the dominant (78.8%) on plant-based agar culture medium compared to only 31% on nutrient agar, while Firmicutes prevailed on nutrient agar (69%) compared to the plant-based agar culture media (18.2%). Bacteroidetes, represented by Chryseobacterium indologenes, was only reported (3%) among the culturable rhizobacteria community of the plant-based agar culture medium.
Tumor-infiltrating human CD4 + regulatory T cells display a distinct TCR repertoire and exhibit tumor and neoantigen reactivity (2019)

CD4<sup>+</sup> regulatory T (T<sub>reg</sub>) cells have an essential function in maintaining self-tolerance; however, they may also play a detrimental role in antitumor immune responses. The presence of elevated frequencies of T<sub>reg</sub> cells in tumors correlates with disease progression and poor survival in patients with cancer. The antigen specificity of T<sub>reg</sub> cells that have expanded in the tumor microenvironment is poorly understood; answering this question may provide important insights for immunotherapeutic approaches. To address this, we used a novel combinatorial approach to characterizing the T cell receptor (TCR) profiles of intratumoral T<sub>reg</sub> cells from patients with metastatic melanoma, gastrointestinal, and ovarian cancers and elucidated their antigen specificities. The TCR repertoires of tumor-resident T<sub>reg</sub> cells were diverse yet displayed significant overlap with circulating T<sub>reg</sub> cells but not with conventional T cells in tumor or blood. TCRs isolated from T<sub>reg</sub> cells displayed specific reactivity against autologous tumors and mutated neoantigens, suggesting that intratumoral T<sub>reg</sub> cells act in a tumor antigen-selective manner leading to their activation and clonal expansion in the tumor microenvironment. Tumor antigen-specific T<sub>reg</sub>-derived TCRs resided in the tumor and in the circulation, suggesting that both T<sub>reg</sub> cell compartments may serve as a source for tumor-specific TCRs. These findings provide insights into the TCR specificity of tumor-infiltrating human T<sub>reg</sub> cells that may have potential implications for cancer immunotherapy.
A nuclear protein complex containing high mobility group proteins B1 and B2, heat shock cognate protein 70, ERp60, and glyceraldehyde-3-phosphate dehydrogenase is involved in the cytotoxic response to DNA modified by incorporation of anticancer nucleoside analogues. (2003)

Thiopurine treatment of human leukemia cells deficient in components of the mismatch repair system (Nalm6) initiated apoptosis after incorporation into DNA, as revealed by caspase activation and terminal deoxynucleotidyl transferase-mediated nick end labeling assay. To elucidate the cellular sensor(s) responsible for recognition of DNA damage in cells with an inactive mismatch repair system, we isolated a multiprotein nuclear complex that preferentially binds DNA with thioguanine incorporated. The components of this nuclear multiprotein complex, as identified by protein mass spectroscopy, included high mobility group proteins 1 and 2 (HMGB1, HMGB2), heat shock protein HSC70, protein disulfide isomerase ERp60, and glyceraldehyde 3-phosphate dehydrogenase. The same complex was also shown to bind synthetic oligodeoxyribonucleotide duplexes containing the nonnatural nucleosides 1-beta-D-arabinofuranosylcytosine or 5-fluoro-2'-deoxyuridine. Fibroblast cell line derived from Hmgb1(-/-) murine embryos had decreased sensitivity to thiopurines, with an IC(50) 10-fold greater than Hmgb1-proficient cells (P < 0.0001) and exhibited comparable sensitivity to vincristine, a cytotoxic drug that is not incorporated into DNA. These findings indicate that the HMGB1-HMGB2-HSC70-ERp60-glyceraldehyde 3-phosphate dehydrogenase complex detects changes in DNA structure caused by incorporation of nonnatural nucleosides and is a determinant of cell sensitivity to such DNA modifying chemotherapy.
<title>Industrial applications of shearography for inspection of aircraft components</title> (2005)

Shearography has been validated as fast and reliable inspection technique for aerospace components. Following several years phase of evaluation of the technique, meanwhile, shearography has entered the industrial production inspection. The applications basically range from serial inspection in the production line to field inspection in assembly and to applications in the maintenance and repair area. In all applications, the main advantages of shearography, as very fast and full field insection and high sensitivity even on very complex on composite materials have led to the decision for laser shearography as inspection tool. In this paper, we present some highlights of industrial shearography inspection. One of the first industrial installations of laser shearography in Europe was a fully automatic inspection system for helicopter rotorblades. Complete rotor blades are inspected within 10 minutes on delaminations and debondingg in the composite structure. In case of more complex components, robotic manipulation of the shearography camera has proven to be the optimal solution. An industry 6-axis robot give utmost flexibility to position the camera in any angle and distance. Automatic defect marking systems have also been introduced to indicate the exact position of the defect directly on the inspected component. Other applications are shearography inspection systems for abradable seals in jet engines and portable shearography inspection systems for maintenance and repair inspection in the field. In this paper, recent installations of automatice inspection systems in aerospace industries are presented.
RET protein expression has no prognostic impact on the long-term outcome of papillary thyroid carcinoma (2001)

In conclusion, our analysis indicates that RET expression is frequently found in PTC, and has no influence on tumor outcome.
A stretchable electrode array for non-invasive, skin-mounted measurement of electrocardiography (ECG), electromyography (EMG) and electroencephalography (EEG) (2010)

This paper reports a class of stretchable electrode array capable of intimate, conformal integration onto the curvilinear surfaces of skin on the human body. The designs employ conventional metallic conductors but in optimized mechanical layouts, on soft, thin elastomeric substrates. These devices exhibit an ability to record spontaneous EEG activity even without conductive electrolyte gels, with recorded alpha rhythm responses that are 40% stronger than those collected using conventional tin electrodes and gels under otherwise similar conditions. The same type of device can also measure high quality ECG and EMG signals. The results suggest broad utility for skin-mounted measurements of electrical activity in the body, with advantages in signal levels, wearability and modes of integration compared to alternatives.
The role of planning in Grid computing (2003)

Grid computing gives users access to widely distributed networks of computing resources to solve large-scale tasks such as scientific computation. These tasks are defined as standalone components that can be combined to process the data in various ways. We have implemented a planning system to generate task workflows for the Grid automatically, allowing the user to specify simply the desired data products. The planner uses heuristic control rules and searches a number of alternative complete plans in order to find a high-quality solution. We describe an implemented test case in gravitational wave interferometry and show how the planner is integrated in the Grid environment. We discuss promising future directions in this work. We believe AI planning will play a crucial role in developing complex application workflows for the Grid.
Stereocontrolled synthesis of sialyl Lex, the oligosaccharide binding ligand to ELAM-1 (sialyl =N-acetylneuramin) (1991)

Sialyl Lex1 the oligosaccharide binding ligand to ELAM-1 is synthesized from building blocks 2–5via a short route featuring the principle of a neighbouring PhS group as an auxiliary to facilitate and stereochemically control the formation of the desired glycoside bond in the target molecule.
Statistical methods in diagnosis (1992)

Motivations are presented for exploring formal statistical methods for use in medical diagnosis and the advantages and disadvantages are discussed. A brief review is presented of classical linear discriminant analysis, quadratic discriminant analysis, logistic regression, nearest neighbour and kernel methods, recursive partitioning methods, the independence model, regularized discriminant analysis, structured conditional probability distributions, methods for categorical data, and other methods. Criteria on which a choice might be made are presented and methods for assessing diagnostic performance are outlined. Particular applications of screening and chromosome analysis are used as illustrations and available software is described.
Bacillus amylolyticus sp. nov., nom. rev., Bacillus lautus sp. nov., nom. rev., Bacillus pabuli sp. nov., nom. rev., and Bacillus validus sp. nov., nom. rev. (1984)

The names “Bacillus amylolyticus” Choukévitch 1911, “Bacillus lautus” Batchelor 1919, “Bacillus pabuli” Schieblich 1923, and “Bacillus validus” Bredemann and Heigener 1935 were not included on the Approved Lists of Bacterial Names. The names Bacillus amylolyticus, Bacillus lautus, Bacillus pabuli, and Bacillus validus are here revived; all of these names except Bacillus amylolyticus are used for the same taxa to which they were originally applied. The name Bacillus amylolyticus is applied to the taxon described by Kellerman and McBeth. The type strains of B. amylolyticus, B. lautus, B. pabuli, and B. validus are strains NRRL NRS-290, NRRL NRS-666, NRRL NRS-924, and NRRL NRS-1000, respectively.
Synthesis and stereochemical studies of 2‐substituted thiazolidine‐4‐carboxamide derivatives (2000)

Abstract A series of new 2‐substituted thiazolidine‐4‐carboxamide derivatives which have potentially useful immunological properties, have been synthesized in a stereoselective manner by coupling 2‐subsituted thiazolidine‐4‐carboxylic acids with amines or amino esters. The structure of these compounds was established by combination of NMR methods and by X‐ray analysis.
Defense Against Adversarial Images Using Web-Scale Nearest-Neighbor Search (2019)

A plethora of recent work has shown that convolutional networks are not robust to adversarial images: images that are created by perturbing a sample from the data distribution as to maximize the loss on the perturbed example. In this work, we hypothesize that adversarial perturbations move the image away from the image manifold in the sense that there exists no physical process that could have produced the adversarial image. This hypothesis suggests that a successful defense mechanism against adversarial images should aim to project the images back onto the image manifold. We study such defense mechanisms, which approximate the projection onto the unknown image manifold by a nearest-neighbor search against a web-scale image database containing tens of billions of images. Empirical evaluations of this defense strategy on ImageNet suggest that it very effective in attack settings in which the adversary does not have access to the image database. We also propose two novel attack methods to break nearest-neighbor defense settings and show conditions under which nearest-neighbor defense fails. We perform a series of ablation experiments, which suggest that there is a trade-off between robustness and accuracy between as we use features from deeper in the network, that a large index size (hundreds of millions) is crucial to get good performance, and that careful construction of database is crucial for robustness against nearest-neighbor attacks.
Rotator cuff tears: why do we repair them? (2004)

Rotator cuff tears are among the most common conditions affecting the shoulder. Despite their ubiquity, however, there is substantial debate concerning their management. Partial and complete rotator cuff tears are known to occur with increasing frequency with increasing age in asymptomatic people1-3. The clinical results of rotator cuff repair in symptomatic patients who have been followed for as long as ten years are good to excellent in a high percentage of cases, even though rerupture of the cuff is known to occur 20% to 65% of the time4-7. Moreover, the presence of a massive, irreparable rotator cuff tear is not incompatible with good overhead function8. These observations have traditionally made clinical decision-making in the treatment of symptomatic rotator cuff tears difficult. Historically, treatment recommendations have included rehabilitation, surgical repair, subacromial decompression without repair, tendon transfers, and tendon substitution techniques6,8-21.

Controversy regarding the management of patients with symptomatic, full-thickness rotator cuff tears is largely the result of the heterogeneity of the patient population and the dearth of well-controlled comparative data. Much progress toward a more unified understanding of the surgical indications and outcomes of rotator cuff repair has been made in recent years, although there is still considerable confusion. The purposes of this symposium are to review the history and current controversies of rotator cuff tears and their management, to outline the indications and outcomes of both nonoperative management and surgical repair of rotator cuff tears, and to summarize the surgical options and outcomes in patients with irreparable rotator cuff tears.

### Rotator Cuff Injury

Injuries of the rotator cuff have been known to occur since the earliest of medical writings. A description of a rotator cuff injury appeared in Edwin Smith's Surgical Papyrus, one of the oldest known …
Glucose, Advanced Glycation End Products, and Diabetes Complications: What Is New and What Works (2003)

Editor’s note: This is one in a series of articles from the various professional section councils of the American Diabetes Association. This installment is from the Council on Complications. 



The incidence of diabetes, particularly type 2 diabetes, is increasing at an alarming rate. Worldwide, about 124 million people had diabetes by1997; by 2010, this number is estimated to reach 221 million. Because of the large number of severe pathologies complicating the clinical course of diabetes, one can easily speculate on the huge economic and psychosocial impact of diabetes across age groups and geographical regions.

A large number of studies have focused on the factors involved in the pathogenesis of diabetic complications, most seeking effective therapies, but the exact cellular or molecular basis of these complications has not yet been fully elucidated. Hyperglycemia is still considered the principal cause of diabetes complications. Its deleterious effects are attributable, among other things, to the formation of sugar-derived substances called advanced glycation end products (AGEs). AGEs form at a constant but slow rate in the normal body, starting in early embryonic development, and accumulate with time. However, their formation is markedly accelerated in diabetes because of the increased availability of glucose.

AGEs are a heterogeneous group of molecules formed from the nonenzymatic reaction of reducing sugars with free amino groups of proteins, lipids, and nucleic acids. The initial product of this reaction is called a Schiff base, which spontaneously rearranges itself into an Amadori product, as is the case of the well-known hemoglobin A1c (A1C). These initial reactions are reversible depending on the concentration of the reactants. A lowered glucose concentration will unhook the sugars from the amino groups to which they are attached; conversely, high glucose …
Development of a National Genetic Evaluation for Cow Fertility (2004)

A national fertility evaluation was developed based on pregnancy rate, which measures the percentage of nonpregnant cows becoming pregnant within each 21-d opportunity period. Data for evaluation are days open, which are calculated as date pregnant minus previous calving date. Date pregnant is determined from last reported breeding or from subsequent calving minus expected gestation length. Success or failure of last breeding can be confirmed by veterinary diagnosis or a report that the cow was sold because of infertility. Data are adjusted for parity and calving season within geographic region and time period and evaluated. Fertility records are considered complete at 250 d in milk, and lower and upper limits of 50 and 250 d are applied to days open. For calculation of genetic evaluations, days open are converted to pregnancy rate by the linear formula pregnancy rate = 0.25 (233 - days open). Evaluations are expressed as predicted transmitting ability for daughter pregnancy rate, and calculation is done with an animal model. Genetic correlations among several fertility measures and other evaluated traits were estimated from 3 large data sets. Correlation with days open was less for nonreturn rate than for days to first breeding, probably because nonreturn rate had lower heritability. Cow fertility was negatively correlated with yield but is a major component of longevity. Thus, recent selection for longevity may have slowed the long-term decline in fertility. Direct selection for fertility could halt or reverse the decline.
Digital bit-rate reduction systems of HDTV (2002)

A study of digital coding of an HDTV picture appropriate for use with contribution links is described. Three coding methods, which are based on differential pulse-code modulation (DPCM), discrete transform cosine (DCT), and vector quantization (VQ) techniques, respectively, are proposed and evaluated with the aid of computer simulation. It has been found that all three methods provide good picture quality without perceptible degradation when used at a bit rate of twice the H4 rate. The vector-quantization-based method is the most hopeful candidate for transmission at a rate of H4.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>