gebhart/patrepeval huggingface dataset:
The Non-catalytic Chitin-binding Protein CBP21 from Serratia marcescens Is Essential for Chitin Degradation (2005)

The Gram-negative soil bacterium Serratia marcescens uses three different family 18 chitinases to degrade chitin, an abundant insoluble carbohydrate polymer composed of beta(1,4)-linked units of N-acetylglucosamine. We show that efficient chitin degradation additionally depends on the action of a small non-catalytic protein, CBP21, which binds to the insoluble crystalline substrate, leading to structural changes in the substrate and increased substrate accessibility. CBP21 strongly promoted hydrolysis of crystalline beta-chitin by chitinases A and C, while it was essential for full degradation by chitinase B. CBP21 variants with single mutations on the largely polar binding surface lost their ability to promote chitin degradation, while retaining considerable affinity for the polymer. Thus, binding alone is not sufficient for CBP21 functionality, which seems to depend on specific, mostly polar interactions between the protein and crystalline chitin. This is the first time a secreted binding protein is shown to assist in the enzymatic degradation of an insoluble carbohydrate via non-hydrolytic disruption of the substrate. Interestingly, homologues of CBP21 occur in most chitin-degrading microorganisms, suggesting a general mechanism by which chitin-binding proteins enhance chitinolytic activity. Homologues also occur in chitinase-containing insect viruses, whose infectiousness is known to depend on chitinase efficiency.
Apple Peels as a Value-Added Food Ingredient (2003)

There is some evidence that chronic diseases, such as cancer and cardiovascular disease, may occur as a result of oxidative stress. Apple peels have high concentrations of phenolic compounds and may assist in the prevention of chronic diseases. Millions of pounds of waste apple peels are generated in the production of applesauce and canned apples in New York State each year. We proposed that a valuable food ingredient could be made using the peels of these apples if they could be dried and ground to a powder without large losses of phytochemicals. Rome Beauty apple peels were treated with citric acid dips, ascorbic acid dips, and blanches before being oven-dried at 60 degrees C. Only blanching treatments greatly preserved the phenolic compounds, and peels blanched for 10 s had the highest total phenolic content. Rome Beauty apple peels were then blanched for 10 s and dried under various conditions (oven-dried at 40, 60, or 80 degrees C, air-dried, or freeze-dried). The air-dried and freeze-dried apple peels had the highest total phenolic, flavonoid, and anthocyanin contents. On a fresh weight basis, the total phenolic and flavonoid contents of these samples were similar to those of the fresh apple peels. Freeze-dried peels had a lower water activity than air-dried peels on a fresh weight basis. The optimal processing conditions for the ingredient were blanching for 10s and freeze-drying. The process was scaled up, and the apple peel powder ingredient was characterized. The total phenolic content was 3342 +/- 12 mg gallic acid equivalents/100 g dried peels, the flavonoid content was 2299 +/- 52 mg catechin equivalents/100 g dried peels, and the anthocyanin content was 169.7 +/- 1.6 mg cyanidin 3-glucoside equivalents/100 g dried peels. These phytochemical contents were a significantly higher than those of the fresh apple peels if calculated on a fresh weight basis (p < 0.05). The apple peel powder had a total antioxidant activity of 1251 +/- 56 micromol vitamin C equivalents/g, similar to fresh Rome Beauty peels on a fresh weight basis (p > 0.05). One gram of powder had an antioxidant activity equivalent to 220 mg of vitamin C. The freeze-dried apple peels also had a strong antiproliferative effect on HepG(2) liver cancer cells with a median effective dose (EC(50)) of 1.88 +/- 0.01 mg/mL. This was lower than the EC(50) exhibited by the fresh apple peels (p < 0.05). Apple peel powder may be used in a various food products to add phytochemicals and promote good health.
Tetrahydrobiopterin‐responsive phenylalanine hydroxylase deficiency in Dutch neonates (2001)

Four neonates with a positive phenylalanine screening test (Phe concentrations between 258 and 1250 micromol/L) were investigated further to differentiate between phenylalanine hydroxylase (PAH) deficiency and variant hyperphenylalaninaemia (HPA) forms. In patients 1 and 2 a tetrahydrobiopterin (BH4) load caused a significant decrease of the plasma Phe levels. A combined phenylalanine/BH4 loading test was performed in patients 2, 3 and 4. In the latter two patients, plasma Phe concentrations completely normalized within 8 h after the BH4 load (20 mg/kg). Basal urinary pterins were normal in all four patients. The activity of dihydropteridine reductase (DHPR) was normal in patients 1, 2 and 3 and 50% of control values in patient 4 (not in the range of DHPR-deficient patients). In patient 3 a subsequent phenylalanine loading test with concomitant analysis of plasma biopterins revealed a normal increase of biopterin, excluding a BH4 biosynthesis defect. Pterins and neurotransmitter metabolites in CSF of patients 1, 3 and 4 were normal. DNA mutations detected in the PAH gene of patients 1-4 were A313T, and L367fsinsC; V190A and R243X; A300S and A403V; R241C and A403V. The results are suggestive for mutant PAH enzymes with decreased affinity for the cofactor BH4.
Epoch-incremental reinforcement learning algorithms (2013)

Abstract In this article, a new class of the epoch-incremental reinforcement learning algorithm is proposed. In the incremental mode, the fundamental TD(0) or TD(λ) algorithm is performed and an environment model is created. In the epoch mode, on the basis of the environment model, the distances of past-active states to the terminal state are computed. These distances and the reinforcement terminal state signal are used to improve the agent policy.
The Nature and Significance of Platelet Products in Human Plasma (1967)

SUMMARY Fresh plasma freed of intact platelets can be shown to contain minute particulate material (platelet‐dust) which can be separated by ultracentrifugation. Much of this material is rich in phospholipid and shows coagulant properties resembling those of Platelet Factor 3. The supernatant plasma, freed of these particles, shows a corresponding deficiency in Platelet Factor 3 activity. Electron microscopic studies suggest that the lipid‐rich particles may originate from the osmophilic granules of platelets and that they are extruded on storage of platelets, even in the absence of coagulation. It is suggested that the liberation of this material is the basis of the process of ‘activation’ of platelets known to occur with storage. When clotting occurs, coagulant particulate material is released from platelets, considerably in excess of what is required for thrombin generation and it can be detected in serum. Its presence accounts for the platelet‐like activity of serum. The material can be distinguished from intact platelets, red cell stroma and chylomicra. It was observed that chylomicra, freed of platelet‐dust, were inactive in a thrombin generation test, which thus appeared responsive only to platelet type lipid. Both chylomicra and platelet‐dust were effective in a Stypven time test. Attention is drawn to possible errors of interpretation which may arise from the use of the latter test as an index of Platelet Factor 3 activity. Preliminary immunological investigation of platelets revealed the presence of fibrinogen and at least three other constitutents which appear to be primarily platelet components.
Regulatory T-cell adoptive immunotherapy: potential for treatment of autoimmunity (2011)

Tregs have shown considerable potential in treating preclinical models of autoimmunity. These studies have highlighted the importance of Treg antigen (Ag) specificity. Translation of these promising results to the clinic will require a robust method of generating large pure populations of Ag-specific Tregs. These include the recently described T-cell receptor gene transfer approach, which has proven to be a rapid and reliable method to generate large populations of Ag-specific Tregs. In this article, we will examine these various approaches and discuss their relative merits. Furthermore, we will discuss the obstacles that need to be surmounted to allow adoptive Treg therapy to progress to the clinic for the benefit of autoimmune patients.
The SDDS-PC: a diagnostic aid for multiple mental disorders in primary care. (1995)

The Symptom Driven Diagnostic System for Primary Care (SDDS-PC) is a new computerized clinical procedure to assist primary care physicians in diagnosing mental disorders during the course of routine practice. It has three components: (1) a 5-minute patient-administered 16-item screening questionnaire, (2) six 5-minute physician-administered diagnostic interview modules based on DSM-III-R criteria, and (3) a longitudinal tracking form. The SDDS-PC covers five disorders (major depression, panic disorder, alcohol abuse or dependence, generalized anxiety disorder, and obsessive compulsive disorder) as well as suicidal ideation. Patients who screen positive for a disorder receive the corresponding diagnostic interview module. Patients who meet mental disorder criteria on the diagnostic interview module are then followed with the longitudinal tracking form. Minor or subsyndromal conditions are also addressed at the physician's discretion. This article describes the development of SDDS-PC and summarizes results from two studies which involved comparisons between the SDDS-PC and independently administered full-length structured diagnostic interviews.
A Multiple Comparison Procedure for Comparing Several Treatments with a Control (1955)

(1955). A Multiple Comparison Procedure for Comparing Several Treatments with a Control. Journal of the American Statistical Association: Vol. 50, No. 272, pp. 1096-1121.
Expression of a retinoid-inducible tumor suppressor, Tazarotene-inducible gene-3, is decreased in psoriasis and skin cancer. (2000)

Tazarotene-induced gene-3 (TIG-3), isolated from human keratinocytes treated with the retinoic acid receptor-selective retinoid Tazarotene, is homologous to H-rev, a class II tumor suppressor. TIG-3 gene localized to chromosome 11q23, a site of loss of heterozygosity in several malignancies. Retinoids influence epidermal differentiation and are used to treat and prevent skin cancer. Therefore, we studied TIG-3 mRNA expression in psoriasis and in basal and SCCs by in situ hybridization and a quantitative QT-RT-PCR assay. Psoriasis lesions had significantly lower staining (median, 3) than paired normal control skin (median, 4; P = 0.012). TIG-3 mRNA was significantly higher in normal control skin (P = 0.001), in paired adjacent skin (median, 3; P = 0.007), and in overlying epidermis (median, 3.0; P = 0.0001) than in 21 SCC specimens as a group (median, 1.5).
Virulence characteristics of clinical and environmental isolates of Vibrio vulnificus (1992)

Twenty-four randomly selected clinical and environmental Vibrio vulnificus isolates were tested for virulence in iron-overloaded mice (250 mg of iron dextran per kg of body weight). The log10 50% lethal doses of 17 isolates were lower by greater than or equal to 3.5 log10 units in iron-overloaded mice than in control mice. These isolates were classified as virulent. The 50% lethal doses of these virulent isolates were also lower in mice that were immunosuppressed by treatment with cyclophosphamide (150 mg/kg). Four of the seven isolates initially classified as avirulent were virulent in mice that were simultaneously iron overloaded and immunosuppressed. These isolates were classified as moderately virulent. The remaining three isolates were avirulent under all conditions. The incidence of virulent strains among clinical and environmental isolates did not differ. The virulent isolates produced high titers of hemolysin, were resistant to inactivation by serum complement, produced phenolate siderophore, and utilized transferrin-bound iron. The moderately virulent isolates differed from the virulent isolates only in their increased sensitivity to inactivation by serum complement. The avirulent isolates differed from those of the other two classes in their inability to either produce significant amounts of phenolate siderophore or utilize transferrin-bound iron. A modified agar plate diffusion method for transferrin-bound iron utilization was developed to differentiate the two classes of virulent isolates from the avirulent isolates in vitro.
NF-kappaB and reperfusion injury (2004)

This review discusses the current understanding of mechanisms that mediate activation of the transcription factor nuclear factor-kappaB (NF-kappaB) and how such activation could in turn mediate reperfusion injury. NF-kappaB regulates the expression of several genes involved in inflammation, the immune response, apoptosis, cell survival and proliferation. Many of these same genes are activated during reperfusion injury. The rationale for considering inhibiting NF-kappaB activation as a promising molecular target for ameliorating reperfusion injury in the brain during stroke, the heart during myocardial infarction and the intestines following prolonged ischemia is discussed on the basis of a new understanding of the mechanisms by which NF-kappaB is activated. A complete anthology of the reperfusion injury literature is beyond the scope of this article and the authors apologize to any investigator not cited for their contributions.
Defect energies of graphite: Density-functional calculations (2005)

The energies of point defects in graphite have been calculated from first principles. The various interplane interstitial configurations are found to have a wider range of energies than in some earlier calculations, implying a larger interstitial migration energy than previously expected $(&gt;1.5\phantom{\rule{0.3em}{0ex}}\mathrm{eV})$. Interplane interstitials are found to be stabilized by a shear of one graphite plane with respect to its neighbors, as this allows the interstitial to bond to three or four atoms in two planes in the ylid and spiro configurations. The minimum interstitial formation energy in sheared graphite is only $5.3\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ compared to $6.3\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ in perfect graphite. Such interstitials form a strongly bound vacancy-interstitial pair with a formation energy of only $10.2\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. The formation energy of a single vacancy is $7.6\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. The formation energy and the activation barrier of the Stone-Wales defect in a single layer of graphite were also calculated.
No-Reference Image Quality Assessment in the Spatial Domain (2012)

We propose a natural scene statistic-based distortion-generic blind/no-reference (NR) image quality assessment (IQA) model that operates in the spatial domain. The new model, dubbed blind/referenceless image spatial quality evaluator (BRISQUE) does not compute distortion-specific features, such as ringing, blur, or blocking, but instead uses scene statistics of locally normalized luminance coefficients to quantify possible losses of "naturalness" in the image due to the presence of distortions, thereby leading to a holistic measure of quality. The underlying features used derive from the empirical distribution of locally normalized luminances and products of locally normalized luminances under a spatial natural scene statistic model. No transformation to another coordinate frame (DCT, wavelet, etc.) is required, distinguishing it from prior NR IQA approaches. Despite its simplicity, we are able to show that BRISQUE is statistically better than the full-reference peak signal-to-noise ratio and the structural similarity index, and is highly competitive with respect to all present-day distortion-generic NR IQA algorithms. BRISQUE has very low computational complexity, making it well suited for real time applications. BRISQUE features may be used for distortion-identification as well. To illustrate a new practical application of BRISQUE, we describe how a nonblind image denoising algorithm can be augmented with BRISQUE in order to perform blind image denoising. Results show that BRISQUE augmentation leads to performance improvements over state-of-the-art methods. A software release of BRISQUE is available online: http://live.ece.utexas.edu/research/quality/BRISQUE_release.zip for public use and evaluation.
Formation and secretion of fragments of parathormone. Identification of cleavage sites. (1986)

Monolayer cultures of bovine parathyroid cells or fresh gland slices were incubated with radioactive amino acids in order to study the formation and metabolism of parathormone (PTH). PTH, secretory protein I, and COOH-terminal fragments of PTH were all released into media within 30 min, most strongly in the first hour after synthesis. Peptides in tissue, cells, and media were separated using reverse-phase high performance liquid chromatography. In eluates of media, six radioactive peaks were prominent. The first four and the sixth were immunoreactive in a COOH-terminal specific PTH radioimmunoassay, but only the sixth was reactive in an NH2-terminal specific assay. Under conditions where recovery of PTH(1-34) was quantitative, gel filtration of media was used to show that no NH2-terminal fragments of PTH were secreted. Sequence analyses of secreted COOH-terminal peptides indicated that the NH2 termini of the first three peaks corresponded to residues 43, 37, and 34 of PTH. The fourth peak contained a mixture of two peptides with NH2 termini at residues 24 and 28 of PTH. The fifth could not be identified; the sixth was PTH. Cleavages at the 23-24 bond of PTH occurred within minutes of the formation of PTH itself, and the other peptides were formed more slowly. Mandatory cleavage of PTH at the 23-24 peptide bond would destroy the biological activity of the hormone on kidney and bone, a situation consistent with the possibility that intracellular PTH metabolism participates in secretory regulation. The results showed that different peptides were generated in parathyroid cells than were previously shown to be produced by cathepsin B or D. The results suggest that the proteolytic pathway which results in the secretion of PTH fragments is nonlysosomal in nature.
Drug therapy of hypertensive crises. (1988)

The clinical features, pathogenesis, and pharmacologic management of hypertensive crises are reviewed, with emphasis on newer therapies. Hypertensive crises may be divided into hypertensive emergencies and hypertensive urgencies. Hypertensive emergencies, in which acute organ damage exists, require blood pressure reduction within one hour. In hypertensive urgencies no acute end-organ damage has yet occurred; however, blood pressure should be controlled within 24 hours. Factors that may precipitate a hypertensive crisis include renovascular hypertension, acute glomerulonephritis, head injuries, renin- or catecholamine-secreting tumors, antihypertensive-therapy withdrawal syndromes, eclampsia, and ingestion of tyramine by patients receiving monoamine oxidase inhibitors. The traditional drug of choice for therapy of hypertensive emergencies is sodium nitroprusside. Intravenous labetalol produces a prompt, controlled reduction in blood pressure and is a promising alternative. Other agents used are diazoxide, trimethaphan camsylate, hydralazine, nitroglycerin, and phentolamine. However, all these agents have disadvantages, including unpredictable antihypertensive effects, difficult blood pressure titration, and serious potential adverse effects such as profound hypotension, reduced renal blood flow, and increased myocardial workload. Most patients with hypertensive urgencies can be effectively treated with orally or sublingually administered agents. Older regimens of reserpine, methyldopa, or guanethidine, with their slow onsets and long durations of action, have been largely replaced by clonidine and nifedipine. Captopril and minoxidil have also been used with some success. Despite the lack of comparative trials with traditional agents, demonstrated efficacy and desirable pharmacologic characteristics have made several new agents acceptable for therapy of hypertensive crises.
Respiratory Syncytial Virus Infections in Pediatric Liver Transplant Recipients (1992)

Respiratory syncytial virus (RSV) is the most important cause of lower respiratory tract infection in infants and young children. The charts of 17 children found to have RSV among 493 children who underwent liver transplantation between February 1985 and February 1991 were reviewed. The median age at diagnosis was 20 months. Median time of diagnosis was 24 days after transplantation. Thirteen patients developed nosocomial infections while convalescing from their transplant. Common symptoms included tachypnea, cough, fever, and congestion. Acute radiographic changes were seen in 12 patients. Two deaths were associated with progressive pulmonary disease and occurred in children with infection early in the postoperative period who were intubated before the onset of symptoms. RSV in children after liver transplantation has a clinical spectrum similar to that in normal children. Early onset of infection (less than 20 days) after transplantation and preexisting lung disease may predict more severe disease.
Crystal Structure of 4-(Cytidine 5′-diphospho)-2-C-methyl-d-erythritol kinase, an Enzyme in the Non-mevalonate Pathway of Isoprenoid Synthesis (2003)

The crystal structure of the enzyme 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CDP-ME) kinase from the thermophilic bacterium Thermus thermophilus HB8 has been determined at 1.7-A resolution. This enzyme catalyzes phosphorylation of the 2-hydroxyl group of CDP-ME, the fourth step of the non-mevalonate pathway, which is essential for isoprenoid biosynthesis in several pathogenic microorganisms. Since this pathway is absent in humans, it is an important target for the development of novel antimicrobial compounds. The structure of the enzyme is similar to the structures of mevalonate kinase and homoserine kinase, members of the GHMP superfamily. Lys8 and Asp125 are active site residues in mevalonate kinase that also appear to play a catalytic role in CDP-ME kinase. Both the mevalonate and the non-mevalonate pathways therefore involve closely related kinases with similar mechanisms. Assaying the enzyme showed that CDP-ME kinase will phosphorylate CDP-ME but not 4-(uridine 5'-diphospho)-2-C-methyl-D-erythritol, indicating the substrate pyrimidine moiety is involved in important interactions with the enzyme.
Reducing Image Noise in Computed Tomography (CT) Colonography (2014)

Computed tomography colonography images acquired using the IC detector had significantly lower noise than images acquired using the conventional detector. This noise reduction can permit further radiation dose reduction in CTC.
Exposure maps: removing reliance on attribution during scan detection (2006)

Current scanning detection algorithms are based on an underlying assumption that scanning activity can be attributed to a meaningful specific source (i.e. the root cause or scan controller). Sophisticated scanning activity including the use of botnets, idle scanning, and throwaway systems violates this assumption. We propose a class of scanning detection algorithms that focus on what is being scanned for instead of who is performing the scanning. We pursue this idea, introduce the concept of exposuremaps, and report on a preliminary proof-of-concept that allows one to: (1) estimate the information or exposures revealed to an adversary as a result of scanning activity; (2) detect sophisticated or targeted scanning activity with a footprint as low as a single packet or event; and (3) discover real-time changes in network exposures that may be indicative of a successful attack.