gebhart/patrepeval huggingface dataset:
MicroRNA—implications for cancer (2007)

MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression post-transcriptionally. After the discovery of the first miRNA in the roundworm Caenorhabditis elegans, these short regulatory RNAs have been found to be an abundant class of RNAs in plants, animals, and DNA viruses. About 3% of human genes encode for miRNAs, and up to 30% of human protein coding genes may be regulated by miRNAs. MicroRNAs play a key role in diverse biological processes, including development, cell proliferation, differentiation, and apoptosis. Accordingly, altered miRNA expression is likely to contribute to human disease, including cancer. This review will summarize the emerging knowledge of the connections between human miRNA biology and different aspects of carcinogenesis. Various techniques available to investigate miRNAs will also be discussed.
High-Resolution Raman Spectra with Femtosecond Pulses: An Example of Combined Time- and Frequency-Domain Spectroscopy (2006)

Frequency-domain spectroscopy requires long pulses, whereas time-domain spectroscopy requires short pulses. This Letter demonstrates both theoretically and experimentally that simultaneous detection in frequency and time generates well-resolved spectra using intermediate-length pulses. In the case of coherent Raman spectroscopy, typical femtosecond pulses lie between the time and frequency domains. To demonstrate this method, a high-resolution Raman spectrum of nitrobenzene is obtained from 60 fs pulses. Phase control, pulse shaping, or pulses of widely differing duration are not required.
Serum Protein Profiles to Identify Head and Neck Cancer (2004)

We propose that this technique has potential for the development of a screening test for the detection of HNSCC.
Loss of p16 protein expression associated with methylation of the p16INK4A gene is a frequent finding in Hodgkin's disease. (1999)

p16 protein binds and inactivates cyclin D-CDK4/6 complexes, stopping the cell cycle at the G1/S boundary. Loss of p16 expression is found frequently in human cancer tissues, often resulting from allelic loss or promoter region hypermethylation in non-Hodgkin's lymphomas. Hodgkin's disease has been shown to be a monoclonal neoplasm of B-cells in which a majority of cells are cycling. In the attempt to identify hypothetical CDK inhibitor inactivation that could explain the accumulation of proliferating cells, we decided to focus on the p16INK4A gene. To determine whether inactivation of this gene is implicated in the development of Hodgkin's disease, we immunostained 40 cases with a monoclonal antibody for the p16 protein. At the same time, we used a methylation-specific PCR technique to determine the methylation status of exon 1 of the p16INK4A gene in 23 cases in this series. Loss of p16 expression was found in 30 of 37 cases (absence of expression in most Hodgkin's/Reed-Sternberg cells, with a normal scattered pattern of p16 expression in the reactive background). Only seven samples showed nuclear p16 expression in a significant proportion of large tumoral cells. In agreement with this finding, hypermethylation of p16INK4A gene was found in 14 of 23 cases by PCR. All the p16 cases found positive by immunohistochemistry also showed unmethylated DNA. These results show that loss of p16 protein expression is usually observed in Hodgkin's/Reed-Sternberg cells in Hodgkin's disease, frequently associated with p16INK4A gene hypermethylation. The high frequency of abnormal methylation found in this study suggests that this genetic event may play an important role in the pathogenesis of the disease.
Chemical characterisation and dilute-acid hydrolysis of rice hulls from an artisan mill (2010)

The chemical composition of rice hulls produced in an artisan mill and its conversion to fermentable sugars was investigated. The carbohydrate fraction represented 59.2% (w/w) of the dry hulls. Cellulose, with 36.6%, was the main component, followed by xylan with 13.9%. An important contribution of starch (8.7%) was also detected. The content of ash (19.6%) and lignin (15.5%) was comparable with that of rice hulls obtained in industrial mills. Dilute-sulphuric acid hydrolysis at different temperatures, from 160 to 210, was evaluated for production of fermentable sugars. Due to starch hydrolysis, the concentration of glucose in the hydrolysates produced at 160°C was higher than the values that have previously been reported for industrial sorts of rice hulls under comparable conditions. The xylan-to-xylose conversion increased steadily with increase of the temperature and reached a maximum (67.7%) at 190°C. Further increases of the hydrolysis temperature decreased the yield of sugars due to their dehydration to furfural and HMF.
Dietary lipids containing gangliosides reduceGiardia murisinfectionin vivoand survival ofGiardia lambliatrophozoitesin vitro (2004)

We examined whether a ganglioside supplemented diet affected the course of Giardia muris infection in mice and survival of Giardia lamblia trophozoites in vitro. Female CD-1 mice were fed 1 of 5 experimental diets: standard lab chow as a control diet; semi-synthetic diets containing 20% (w/w) triglyceride based on the fat composition of a conventional infant formula; triglyceride diet; triglyceride diet containing a low level of ganglioside (0.1% w/w); and triglyceride diet containing a high level of ganglioside (1.0% w/w of diet). After 2 weeks of feeding, mice were inoculated with G. muris by gastric intubation and fed the experimental diets during the course of the infection. Cysts released in the faeces and trophozoites present in the small intestine were enumerated at various times post-infection. The average cyst output and the number of trophozoites during the course of the infection in mice fed ganglioside-containing diet were found to be significantly lower (3-log10 reduction) compared to animals fed control diets. The results of in vitro growth studies indicated that gangliosides may be directly toxic to the parasites. Thus, gangliosides have a protective effect against G. muris infection in vivo and affect the survival of G. lamblia trophozoites in vitro.
Modifying Human Thymidylate Kinase to Potentiate Azidothymidine Activation (1999)

Based on the knowledge of the crystal structures of yeast and Escherichia coli thymidylate kinases (TmpKs) and the observation that TmpK from E. coli can phosphorylate azidothymidine monophosphate (AZT-MP) much more efficiently than either the yeast or the highly homologous human enzyme, we have engineered yeast and human TmpKs to obtain enzymes that have dramatically improved AZT-MP phosphorylation properties. These modified enzymes have properties that make them attractive candidates for gene therapeutic approaches to potentiating the action of AZT as an inhibitor of human immunodeficiency virus (HIV) replication. In particular, insertion of the lid domain of the bacterial TmpK into the human enzyme results in a pronounced change of the acceptance of AZT-MP such that it is now phosphorylated even faster than TMP.
ITPP Treatment of RG2 Glioblastoma in a Rat Model (2016)

ITPP had no favourable effect upon survival in our animal model with RG2 glioblastoma tumours in Fischer 344 rats.
Plasma Proteomic Analysis of Pancreatic Cancer by 2-Dimensional Gel Electrophoresis (2007)

Proteomic analysis can simultaneously detect changes of multiproteins in plasma of PC, but detected proteins are abundant and common plasma proteins and their diagnostic value may be limited.
Effects of apomorphine on the expression of learned helplessness behavior. (2007)

Dopaminergic system and its D1 as well as D2 receptors are involved in the modulation of emotional behavior. This experiment investigated the role of dopaminergic activity in the inescapable stress-induced learned helplessness, a widely used depression animal model, by using the pharmacological manipulation through the apomorphine (APO), an agonist for D1 and D2 receptors, and sulpiride (SUL), a selective D2 antagonist. Male Sprague Dawley rats were used and tested in a shuttle box. In the day-1 session, the rats received a 10-trial (1 min/trial) inescapable stressor: a 3 sec conditioned stimulus (CS; 75 db sound and 250 lux red light) followed by a 10 sec unconditioned stimulus (UCS; electrical foot shock, 0.5 mA). In the day-2 session, a 15-trial active avoidance test, 3 sec CS followed by UCS, was performed 30 min after the administration of APO (0, 0.05, 0.5, 1, and 5 mg/kg, i.p.). The number of failures was counted and the UCS was stopped when the rats did not escape after 15 sec UCS. The results showed that APO at the dosage of 0.5 mg/kg had a tendency to enhance the avoidance behavior. In contrast, the treatment of higher dose of APO, 1 and 5 mg/kg, reduced the number of escape but increased the number of failure. Pretreatment of SUL (5 mg/kg, i.p.), 10 min before 1 mg/kg of APO, significantly enhanced the failure behavior. The present data suggest that the activity of D2 receptor may be associated with the adaptive or protective role in the prevention of escape deficits after exposure to inescapable stress. However, the excessive stimulation of D1 receptor may participate in the failure of coping behavior leading to learned helplessness and therefore in the pathophysiological mechanisms underling the development of depression.
A HOLOGRAPHIC MODEL OF MEMORY, LEARNING AND EXPRESSION (1990)

Presented is a new paradigm for artificial neural system (ANS) design. The theoretical basis employs a novel concept whereby information is represented by phase angle orientations on a Riemann plane. Central to the theory of operation is the principle of information storage and expression in the form of stimulus-response patterns. The governing equations form a nonconnectionist approach in which a very large number of analog stimulus-response patterns or associations may be superimposed or enfolded onto a single neural element. The system indicates a mechanism by which the above associations may be both encoded and expressed on one noniterative transformation. A broad analogy may be made to digital holography 1 in the form of the constitutive equations and some general operating characteristics. Simulation results for the system indicate information storage capacities and effective rates of processing orders of magnitude beyond current ANS theory. Many observable characteristics are displayed by the system which suggest that the analytical method may provide insight into the information processing mechanism occurring within neurobiological systems.
Developing a Spectral and Colorimetric Database of Artist Paint Materials (2005)

As the project of the author's Master's thesis, the development of a spectral and colorimetric database of artist paint materials for acrylic paints was started. The goal of this research project was to: - provide the academic resource of colorant spectral characteristics - give scientifc explanations on various paint-particular phenomena (paint mixing, gloss effects and color gamut expansion by varnishing) These tasks were planned to satisfy possible interests on paint research from not only conservators in museums but also color educators in schools and color reproduction engineers in imaging companies.
Comparison of Acute Hemodynamic Effects of Aerosolized Iloprost and Inhaled Nitric Oxide in Adult Congenital Heart Disease with Severe Pulmonary Arterial Hypertension (2012)

Aerosolized iloprost can be effectively and safely used and might be an alternative to NO for testing pulmonary vascular reactivity and treating severe PAH in adult CHD patients.
Causes and Consequences of Increased Sympathetic Activity in Renal Disease (2004)

Much evidence indicates increased sympathetic nervous activity (SNA) in renal disease. Renal ischemia is probably a primary event leading to increased SNA. Increased SNA often occurs in association with hypertension. However, the deleterious effect of increased SNA on the diseased kidney is not only caused by hypertension. Another characteristic of renal disease is unbalanced nitric oxide (NO) and angiotensin (Ang) activity. Increased SNA in renal disease may be sustained because a state of NO-Ang II unbalance is also present in the hypothalamus. Very few studies have directly compared the efficacy of adrenergic blockade with other renoprotective measures. Third-generation beta-blockers seem to have more protective effects than traditional beta-blockers, possibly via stimulation of NO release. Although it has been extensively documented that muscle SNA is increased in chronic renal failure, data on renal SNA and cardiac SNA are not available for these patients before end-stage renal disease. It is also unknown whether additional treatment with third-generation beta-blockers can delay the progression of renal injury and prevent cardiac injury in chronic renal failure more efficiently than conventional treatment with angiotensin-converting enzyme inhibitors only.
The density of muscarinic M1 receptors is decreased in the caudate-putamen of subjects with schizophrenia. (1996)

Changes in cholinergic neurons have been implicated in the pathology of schizophrenia. Clozapine, an atypical anti-psychotic drug, has been shown to bind with high affinity to the muscarinic1 (M1) receptor suggesting this receptor could be involved in the therapeutic efficacy of the drug. Because of this we measured the density of M1 receptors in the caudate-putamen, obtained at autopsy, from 19 schizophrenic subjects and 19 non-schizophrenic subjects. The density of M1 receptors was decreased in the caudate-putamen from the schizophrenic subjects (181 +/- 20 vs 287 +/- 10 fmol mg-1 TE; mean +/- s.e.m.; P < 0.001). Furthermore, preliminary studies would not suggest that the change in the density of M1 receptors in the tissue from the schizophrenic subjects had resulted from drug treatment prior to death. These data raise the possibility that changes in muscarinic receptors may be involved in the pathology of schizophrenia.
Prolonged Storage of Red Cells: The Effect of pH, Adenine and Phosphate (1994)

Prolonged storage of red blood cells (RBCs) at 4 degrees C results in decreased intracellular ATP levels with diminished posttransfusion survival. Meryman described a preservative medium, exceptional in its capacity to increase these intracellular levels during the first weeks of storage and later in maintaining adequate levels, for extended storage periods. We modified this medium, investigated its constituents, and found that its ATP-preserving effect was unrelated to its tonicity or to the presence of mannitol. Throughout storage, RBC potassium leakage and lactate production were moderate. No evidence of osmotic swelling was detected. In spite of high ATP levels, the cells became echinocytes, thus discounting a direct correlation between shape and metabolic status. The most striking finding in this study was that the prestorage pH of the blood unit (pH 7.0), has a crucial contribution in elevating nucleotide levels in a medium containing high levels of phosphate (18-40 mM) and adenine. We suggest that a combined effect of optimal pH, adenine, glucose and phosphate in the medium contributes to the ability of the RBCs to synthesize the necessary purine nucleotides by the 'salvage pathway'.
Bidirectional transmission at 622 Mb/s utilizing erbium-doped fiber amplifiers (1992)

Amplification of two bidirectional 622-Mb/s optical signals was demonstrated using a single erbium-doped fiber amplifier (EDFA). Bidirectional amplification was examined with the EDFA operating as a midspan repeater and as a pre/post amplifier at one terminal end of a 95-km fiber span. Without using any isolators in the EDFA, bidirectional optical amplification through a single EDFA was achieved while simultaneously improving system gain relative to a unidirectional link without an EDFA. The system gain improvement was 9.5 and 7 dB in the pre/post configuration, and 25.5 and 20.3 dB in the midspan configuration, when the signal wavelengths were 1537 and 1545 nm, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structurally inherent antigenic sites. Localization of the antigenic sites of the α-chain of human haemoglobin in three host species by a comprehensive synthetic approach (1982)

The antigenic structure of the alpha-chain of human haemoglobin was studied by a synthetic approach consisting of the synthesis of a series of consecutive overlapping peptides that together systematically represent the entire primary structure of the protein. This approach enabled the identification of a full profile of immunochemically active alpha-chain peptides and the localization of its major 'continuous' antigenic sites. Antibodies to haemoglobin raised in each of three different species (goat, rabbit and mouse) recognize similar sites on the alpha-chain. Further, the molecular locations of these sites coincide with alpha-chain regions extrapolated from antigenic sites of the conformationally similar myoglobin molecule. These findings support our earlier proposed concept of 'structurally inherent antigenic sites', namely that antigenicity is conferred on certain surface regions of proteins by virtue of their three-dimensional locations. Thus the antigenic sites of conformationally related proteins are likely to have similar molecular locations.
Egg traps monitor navel orangeworm (1977)

Increasing losses to the navel orange-worm, Paramyelois transitella (Walker), have led to a multi-disciplinary research program to find better methods of controlling this primary pest of almonds in California. One result of this research was the development of a new method for monitoring navel orangeworm (NOW) moth activity. The device used-an “egg trap”—enables growers, field men, and researchers to monitor female moth flights and egg-laying (oviposition) activity directly, rather than monitoring the flight of male moths, as when using sex pheromone traps.
Stem Cells and Their Niches (2006)

A constellation of intrinsic and extrinsic cellular mechanisms regulates the balance of self-renewal and differentiation in all stem cells. Stem cells, their progeny, and elements of their microenvironment make up an anatomical structure that coordinates normal homeostatic production of functional mature cells. Here we discuss the stem cell niche concept, highlight recent progress, and identify important unanswered questions. We focus on three mammalian stem cell systems where large numbers of mature cells must be continuously produced throughout adult life: intestinal epithelium, epidermal structures, and bone marrow.
Ultrasonic contrast agent shell rupture detected by inertial cavitation and rebound signals (2006)

Determining the rupture pressure threshold of ultrasound contrast agent microbubbles has significant applications for contrast imaging, development of therapeutic agents, and evaluation of potential bioeffects. Using a passive cavitation detector, this work evaluates rupture based on acoustic emissions from single, encapsulated, gas-filled microbubbles. Sinusoidal ultrasound pulses were transmitted into weak solutions of Optison at different center frequencies (0.9, 2.8, and 4.6 MHz), pulse durations (three, five, and seven cycles of the center frequencies), and peak rarefactional pressures (0.07 to 5.39 MPa). Pulse repetition frequency was 10 Hz. Signals detected with a 13-MHz, center-frequency transducer revealed postexcitation acoustic emissions (between 1 and 5 micros after excitation) with broadband spectral content. The observed acoustic emissions were consistent with the acoustic signature that would be anticipated from inertial collapse followed by "rebounds" when a microbubble ruptures and thus generates daughter/free bubbles that grow and collapse. The peak rarefactional pressure threshold for detection of these emissions increased with frequency (e.g., 0.53, 0.87, and 0.99 MPa for 0.9, 2.8, and 4.6 MHz, respectively; five-cycle pulse duration) and decreased with pulse duration. The emissions identified in this work were separated from the excitation in time and spectral content, and provide a novel determination of microbubble shell rupture.
A Rapid Screen of Active Site Mutants in Glycinamide Ribonucleotide Transformylase (1996)

Specific and saturation site-directed mutageneses have been used to alter each polar residue within 6 A of the catalytic center of glycinamide ribonucleotide transformylase (EC 2.1.2.2). These mutants were rapidly screened for catalytic activity using functional complementation of auxotrophic cells. This screen allows a rapid qualitative estimate of enzyme activity for each of these mutants. These results have shown that none of the polar residues close to the catalytic center of the enzyme are irreplaceable, although several are important for full catalytic activity, namely, Asn106, His108, Ser135, and Asp144. A mechanism is proposed in which a fixed water molecule mediates the required proton transfers between substrate and cofactor, while the formyl group is transferred from 10-formyltetrahydrofolate by direct nucleophilic attack by the amine of glycinamide ribonucleotide. The active site polar residues may act to alter the pKa values of the attacking and leaving amino groups within a putative tetrahedral intermediate in order to facilitate the transfer of the formyl group.
Diagrammatic scale for assessment of soybean rust severity (2006)

A diagrammatic scale to assess soybean (Glycine max) rust severity, caused by the fungus Phakopsora pachyrhizi, was developed in this study. Leaflets showing different severity levels were collected for determination of the minimum and maximum severity limits; intermediate levels were determined according to "Weber-Fechner's stimulus-response law". The proposed scale showed the levels of 0.6; 2; 7; 18; 42, and 78.5%. Scale validation was performed by eight raters (four inexperienced and four experienced), who estimated the severity of 44 soybean leaflets showing rust symptoms, with and without the use of the scale. Except for rater number eight, all showed a tendency to overestimate severity without the aid of the diagrammatic scale. With the scale, the raters obtained better accuracy and precision levels, although the tendency to overestimate was maintained. Experienced raters were more accurate and precise than inexperienced raters, and assessment improvements with the use of the scale were more significant for inexperienced raters.
Thyroid Gland Tumor Diagnosis at US Elastography (2005)

Elastography is a promising imaging technique that can assist in the differential diagnosis of thyroid cancer.
The pharmacokinetics of an albumin-binding Fab (AB.Fab) can be modulated as a function of affinity for albumin (2006)

An AB.Fab (albumin-binding Fab) consists of a Fab and a phage-derived albumin-binding peptide. This molecule is capable of binding both antigen and albumin simultaneously. Using a Fab derived from Herceptin we generated a panel of AB.Fab variants with wide-ranging affinities for albumin. An assay that measured AB.Fab binding to albumin in solution was developed to most accurately reflect the binding affinity for albumin in vivo. Affinity varied depending upon the species of albumin tested. For rat and rabbit albumin, affinities ranged from 0.04 to 2.5 microM. Reduced affinity for albumin correlated with a reduced half-life and higher clearance rates in both species; the beta half-life ranged 6-fold while clearance ranged over 50-fold in rats and 20-fold in rabbits. To estimate the pharmacokinetic properties of an AB.Fab in humans, AB.Fab variants with similar affinities for rat and rabbit albumin were selected. Using their pharmacokinetic parameters and the principles of allometric scaling for albumin, we estimate an approximate beta half-life for an AB.Fab with 0.5 microM affinity for albumin of up to 4 days in humans with a clearance of 76 ml/h. These variants demonstrate the ability to modulate the clearance of a Fab fragment in vivo and help to establish guidelines for pharmacokinetic engineering of molecules through albumin binding.