gebhart/patrepeval huggingface dataset:
GeneAssist (1997)

DNA sequence data accumulate at a higher rate than our knowledge of protein functions and biology. Therefore, it becomes increasingly important to predict as accurately as possible the functions of encoded proteins based on the homology to previously described sequences.
Silencing expression of the catalytic subunit of DNA-dependent protein kinase by small interfering RNA sensitizes human cells for radiation-induced chromosome damage, cell killing, and mutation. (2002)

Targeted gene silencing in mammalian cells by RNA interference (RNAi) using small interfering RNAs (siRNAs) was recently described by Elbashir et al. (S. M. Elbashir et al., Nature (Lond.), 411: 494-498, 2001). We have used this methodology in several human cell strains to reduce expression of the Prkdc (DNA-PKcs) gene coding for the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) that is involved in the nonhomologous end joining of DNA double-strand breaks. We have also demonstrated a radiosensitization for several phenotypic endpoints of radiation damage. In low-passage normal human fibroblasts, siRNA knock-down of DNA-PKcs resulted in a reduced capacity for restitution of radiation-induced interphase chromosome breaks as measured by premature chromosome condensation, an increased yield of acentric chromosome fragments at the first postirradiation mitosis, and an increased radiosensitivity for cell killing. For three strains of related human lymphoblasts, DNA-PKcs-targeted siRNA transfection resulted in little or no increase in radiosensitivity with respect to cell killing, a 1.5-fold decrease in induced mutant yield in TK6- and p53-null NH32 cells, but about a 2-fold increase in induced mutant yield in p53-mutant WTK1 cells at both the hypoxanthine quanine phosphoribosyl transferase (hprt) and the thymidine kinase loci.
Effect of self-organization in polymer/fullerene bulk heterojunctions on solar cell performance (2006)

The authors investigate the effect of self-organization by controlling the growth rate on the performance of polymer/fullerene bulk-heterojunction solar cells. The effect of growth rate on the morphology of the active layer is studied by atomic force microscopy technique. The electrical characterization by dark current and photocurrent measurements is performed. The hole mobility in the polymer increases by about two orders in magnitude and the carrier transport becomes highly balanced. Increased exciton generation rate, more efficient electron-hole pair dissociation, higher carrier mobility, and balanced carrier transport in the active layer explain the enhancement in the short-circuit current and fill factor.
New display-type analyzer for the energy and the angular distribution of charged particles (1988)

A new principle for analyzing the kinetic energy as well as the angular distribution of charged particles has been discovered. A new display type analyzer was constructed according to theory. It consists of an inner hemispherical grid and an outer hemispherical electrode which has a radius two times larger than that of the inner grid. Charged particles with the same kinetic energy radiate from one point to all directions inside the inner grid, are repelled by the electric field between the two spheres, and converge at the point which is symmetric to the center of the hemispheres. When an aperture is put at the point, the angular distribution of the charged particles can be observed using a two-dimensional detector which is positioned out of the aperture. The characteristics of the analyzer are (1) the acceptance cone is ultimately wide, for instance, 2π sr for the charged particles emitted from a flat surface, (2) the pattern obtained is not distorted, and (3) the two electrodes are very simple and easy to construct.
Broadband Population Inversion (1983)

A theory is presented for construction of sequences of phase-shifted radiation pulses for coherently inverting populations over a broad band of transition frequencies. Such sequences have applications in nuclear magnetic resonance and coherent optics. Examples of sequences are derived, together with computer simulations of their inversion properties.
Iterative decoding of compound codes by probability propagation in graphical models (1998)

We present a unified graphical model framework for describing compound codes and deriving iterative decoding algorithms. After reviewing a variety of graphical models (Markov random fields, Tanner graphs, and Bayesian networks), we derive a general distributed marginalization algorithm for functions described by factor graphs. From this general algorithm, Pearl's (1986) belief propagation algorithm is easily derived as a special case. We point out that iterative decoding algorithms for various codes, including "turbo decoding" of parallel-concatenated convolutional codes, may be viewed as probability propagation in a graphical model of the code. We focus on Bayesian network descriptions of codes, which give a natural input/state/output/channel description of a code and channel, and we indicate how iterative decoders can be developed for parallel-and serially concatenated coding systems, product codes, and low-density parity-check codes.
A Collagen Peptide‐Based Physical Hydrogel for Cell Encapsulation (2011)

Collagen peptide-based hydrogels are prepared and characterized for application in 3D cell growth. Physical hydrogels are formed by covalently linking a collagen-based peptide to an 8-arm poly(ethylene glycol) star polymer. The resulting viscoelastic hydrogels have the ability to melt into a liquid-like state near the melting temperature of the collagen triple helix and reform back into an elastic-state at room temperature, adding a thermoresponsive feature to the material. In addition, the hydrogels possess desirable stiffness, as well as a highly cross-linked network of pores where cells are found to reside, making the hydrogels promising scaffolds for the culture of hMSCs.
Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing (2009)

We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact's Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green's-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.
Accelerated EM reconstruction in total-body PET: potential for improving tumour detectability (1994)

Total-body positron emission tomography (PET) is a useful diagnostic tool for evaluating malignant disease. However, tumour detection is limited by image artefacts due to the lack of attenuation correction and noise. Attenuation correction may be possible using transmission data acquired after or simultaneously with emission data. Despite the elimination of attenuation artefacts, however, tumour detection is still hampered by noise, which is amplified during image reconstruction by filtered backprojection (FBP). We have investigated, as an alternative to FBP, an accelerated expectation maximization (EM) algorithm for its potential to improve tumour detectability in total-body PET. Signal to noise ratio (SNR), calculated for a tumour with respect to the surrounding background, is used as a figure of merit. A software tumour phantom, with conditions typical of those encountered in a total-body PET study using simultaneous acquisition, is used to optimize and compare various reconstruction approaches. Accelerated EM reconstruction followed by two-dimensional filtering is shown to yield significantly higher SNR than FBP for a range of tumour sizes, concentrations and counting statistics (deltaSNR = 6.3 +/- 3.9, p < 0.001). The methods developed are illustrated by examples derived from physical phantom and patient data.
Fusarium wilt ( <i>Fusarium oxysporum</i> f. sp. <i>vasinfectum</i> ) genes expressed during infection of cotton ( <i>Gossypium hirsutum</i> )† (2006)

SUMMARY We sought to identify Fusarium oxysporum f. sp. vasinfectum (Fov) genes that may be associated with pathogenicity. Initially we utilized microarray and Q-PCR technology to identify Fov genes expressed in root and hypocotyl tissues during a compatible infection of cotton. We identified 218 fungal clones representing 174 Fov non-redundant genes as expressed in planta. The majority of the expressed sequences were expressed in infected roots, with only six genes detected in hypocotyl tissue. The Fov genes identified were predominately of unknown function or associated with fungal growth and energy production. We then analysed the expression of the identified fungal genes in infected roots and in saprophytically grown mycelia and identified 11 genes preferentially expressed in plant tissue. A putative oxidoreductase gene (with homology to AtsC) was found to be highly preferentially expressed in planta. In Agrobacterium tumefaciens, AtsC is associated with virulence. Inoculation of a susceptible and a partially resistant cotton cultivar with either a pathogenic or a non-pathogenic isolate of Fov revealed that the expression of the Fov AtsC homologue was associated with pathogenicity and disease symptom formation.
Intent Mining from past conversations for Conversational Agent (2020)

Conversational systems are of primary interest in the AI community. Organizations are increasingly using chatbot to provide round-the-clock support and to increase customer engagement. Many commercial bot building frameworks follow a standard approach that requires one to build and train an intent model to recognize user input. These frameworks require a collection of user utterances and corresponding intent to train an intent model. Collecting a substantial coverage of training data is a bottleneck in the bot building process. In cases where past conversation data is available, the cost of labeling hundreds of utterances with intent labels is time-consuming and laborious. In this paper, we present an intent discovery framework that can mine a vast amount of conversational logs and to generate labeled data sets for training intent models. We have introduced an extension to the DBSCAN (Ester et al., 1996) algorithm and presented a density-based clustering algorithm ITER-DBSCAN for unbalanced data clustering. Empirical evaluation on one conversation dataset, six intent dataset, and one short text clustering dataset show the effectiveness of our hypothesis. We release the datasets and code for future evaluation at
Structural requirements for cellular uptake of α-helical amphipathic peptides (1999)

The structure of the cell-permeable alpha-helical amphipathic model peptide FLUOS-KLALKLALKALKAALKLA-NH2 (I) was modified stepwise with respect to its helix parameters hydrophobicity, hydrophobic moment and hydrophilic face as well as molecular size and charge. Cellular uptake and membrane destabilizing activity of the resulting peptides were studied using aortic endothelial cells and HPLC combined with CLSM. With the exceptions that a reduction of molecule size below 16 amino acid residues and the introduction of a negative net charge abolished uptake, none of the investigated structural parameters proved to be essential for the passage of these peptides across the plasma membrane. Membrane toxicity also showed no correlation to any of the parameters investigated and could be detected only at concentrations higher than 2 microM. These results implicate helical amphipathicity as the only essential structural requirement for the entry of such peptides into the cell interior, in accord with earlier studies. The pivotal role of helical amphipathicity was confirmed by uptake results obtained with two further pairs of amphipathic/non-amphipathic 18-mer peptides with different primary structure, net charge and helix parameters from I. The amphipathic counterparts were internalized into the cells to a comparable extent as I, whereas no cellular uptake could be detected for the non-amphipathic analogues. The mode of uptake remains unclear and involves both temperature-sensitive and -insensitive processes, indicating non-endocytic contributions.
Clinical Use of Bone Densitometry (1991)

IF measurements of bone mass are to be clinically useful, they must be safe, precise, accurate, and of reasonable cost in relation to the information provided. Since when bone mass is low the clinical outcome of concern is fracture, there must be a demonstrated relation between the measurement and the subsequent risk of fracture. The information provided must be helpful to the clinician in making a decision to intervene or not; and if a therapeutic regimen is chosen, it must have a positive influence on health (e.g., a reduction in the incidence of fractures) without an unreasonable increase in other . . .
Translational Selection and Yeast Proteome Evolution (2003)

The primary structures of peptides may be adapted for efficient synthesis as well as proper function. Here, the Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation. Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates. Amino acid usage also shows striking relationships with expression levels. Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed proteins than among less abundant proteins support adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis. Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels. Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.
Acetylcysteine for Prevention of Acute Deterioration of Renal Function Following Elective Coronary Angiography and Intervention (2003)

Acetylcysteine protects patients with moderate chronic renal insufficiency from contrast-induced deterioration in renal function after coronary angiographic procedures, with minimal adverse effects and at a low cost.
Extrapulmonary Sarcoidosis (2007)

Sarcoidosis can affect any organ in the body. Frequently extrapulmonary manifestations of the disease are the major cause of morbidity. Treatment of extrapulmonary sarcoidosis often requires consideration of alternative immunosuppressive agents, topical therapy, or therapy that is not specifically directed against the granulomatous inflammation of the disease. This article reviews the clinical presentation and therapy of extrapulmonary sarcoidosis.
Test results: SEGS LS-2 solar collector (1994)

A SEGS LS-2 parabolic trough solar collector was tested to determine the collector efficiency and thermal losses with two types of receiver selective coatings, combined with three different receiver configurations: glass envelope with either vacuum or air in the receiver annulus, and glass envelope removed from the receiver. As expected, collector performance was significantly affected by each variation in receiver configuration. Performance decreased when the cermet selective coating was changed to a black chrome coating, and progressively degraded as air was introduced into the vacuum annulus, and again when the glass envelope was removed from the receiver. For each receiver configuration, performance equations were derived relating collector efficiency and thermal losses to the operating temperature. For the bare receiver (no glass envelope) efficiency and thermal losses are shown as a function of wind speed. An incident angle modifier equation was also developed for each receiver case. Finally, equations were derived showing collector performance as a function of input insolation value, incident angle, and operating temperature. Results from the experiments were compared with predictions from a one-dimensional analytical model of the solar receiver. Differences between the model and experiment were generally within the band of experimental uncertainty.
Histone H3K27ac separates active from poised enhancers and predicts developmental state (2010)

Developmental programs are controlled by transcription factors and chromatin regulators, which maintain specific gene expression programs through epigenetic modification of the genome. These regulatory events at enhancers contribute to the specific gene expression programs that determine cell state and the potential for differentiation into new cell types. Although enhancer elements are known to be associated with certain histone modifications and transcription factors, the relationship of these modifications to gene expression and developmental state has not been clearly defined. Here we interrogate the epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse. We find that histone H3K27ac distinguishes active enhancers from inactive/poised enhancer elements containing H3K4me1 alone. This indicates that the amount of actively used enhancers is lower than previously anticipated. Furthermore, poised enhancer networks provide clues to unrealized developmental programs. Finally, we show that enhancers are reset during nuclear reprogramming.
Hepatic encephalopathy (2001)

1. Acute Encephalopathy in Cirrhosis A. GENERAL MEASURES. Tracheal intubation in patients with deep encephalopathy should be considered. A nasogastric tube is placed for patients in deep encephalopathy. Avoid sedatives whenever possible. Correction of the precipitating factor is the most important measure. B. SPECIFIC MEASURES i. Nutrition. In case of deep encephalopathy, oral intake is withheld for 24-48 h and i.v. glucose is provided until improvement. Enteral nutrition can be started if the patient appears unable to eat after this period. Protein intake begins at a dose of 0.5 g/kg/day, with progressive increase to 1-1.5 g/kg/day. ii. Lactulose is administered via enema or nasogastric tube in deep encephalopathy. The oral route is optimized by dosing every hour until stool evacuation appears. Lactulose can be replaced by oral neomycin. iii. Flumazenil may be used in selected cases of suspected benzodiazepine use. 2. Chronic Encephalopathy in Cirrhosis i. Avoidance and prevention of precipitating factors, including the institution of prophylactic measures. ii. Nutrition. Improve protein intake by feeding dairy products and vegetable-based diets. Oral branched-chain amino acids can be considered for individuals intolerant of all protein. iii. Lactulose. Dosing aims at two to three soft bowel movements per day. Antibiotics are reserved for patients who respond poorly to disaccharides or who do not exhibit diarrhea or acidification of the stool. Chronic antibiotic use (neomycin, metronidazole) requires careful renal, neurological, and/or otological monitoring. iv. Refer for liver transplantation in appropriate candidates. For problematic encephalopathy (nonresponsive to therapy), consider imaging of splanchnic vessels to identify large spontaneous portal-systemic shunts potentially amenable to radiological occlusion. In addition, consider the combination of lactulose and neomycin, addition of oral zinc, and invasive approaches, such as occlusion of TIPS or surgical shunts, if present. Minimal or Subclinical Encephalopathy Treatment can be instituted in selected cases. The most characteristic neuropsychological deficits in patients with cirrhosis are in motor and attentional skills (60). Although these may impact the ability to perform daily activities, many subjects can compensate for these defects. Recent studies suggest a small but significant impact of these abnormalities on patients' quality of life (61), including difficulties with sleep (62). In patients with significant deficits or complaints, a therapeutic program based on dietary manipulations and/or nonabsorbable disaccharides may be tried. Benzodiazepines should not be used for patients with sleep difficulties.
A West Nile Virus Recombinant Protein Vaccine That Coactivates Innate and Adaptive Immunity (2007)

A chimeric protein West Nile virus (WNV) vaccine capable of delivering both innate and adaptive immune signals was designed by fusing a modified version of bacterial flagellin (STF2 Delta ) to the EIII domain of the WNV envelope protein. This fusion protein stimulated interleukin-8 production in a Toll-like receptor (TLR)-5-dependent fashion, confirming appropriate in vitro TLR5 bioactivity, and also retained critical WNV-E-specific conformation-dependent neutralizing epitopes as measured by enzyme-linked immunosorbent assay. When administered without adjuvant to C3H/HeN mice, the fusion protein elicited a strong WNV-E-specific immunoglobulin G antibody response that neutralized viral infectivity and conferred protection against a lethal WNV challenge. This potent EIII-specific immune response requires a direct linkage of EIII to STF2 Delta , given that a simple mixture of the 2 components failed to induce an antibody response or to provide protection against virus challenge. The presence of a functional TLR5 gene in vivo is also required--TLR5-deficient mice elicited only a minimal antigen-specific response. These results confirm that vaccines designed to coordinately regulate the innate and adaptive immune responses can induce protective immune responses without the need for potentially toxic adjuvants. They also support the further development of an effective WNV vaccine and novel monovalent and multivalent vaccines for related flaviviruses.
ChemInform Abstract: Synthesis and Antimicrobial Activity of 4‐Isogramines, 4‐ Arylthiomethyl‐ and 3‐Aminoacetyl Derivatives of 2‐Methylindoles. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.