gebhart/patrepeval huggingface dataset:
Phase I trial of a MART-1 peptide vaccine with incomplete Freund's adjuvant for resected high-risk melanoma. (1999)

Twenty-five patients with high-risk resected stages IIB, III, and IV melanoma were immunized with a vaccine consisting of the minimal epitope, immunodominant 9-amino acid peptide derived from the MART-1 tumor antigen (AAGIGILTV) complexed with incomplete Freund's adjuvant. The last three patients received the MART-1(27-35) peptide with incomplete Freund's adjuvant mixed with CRL 1005, a block copolymer adjuvant. Patients were immunized with increasing doses of the MART-1(27-35) peptide in a Phase I trial to evaluate the toxicity, tolerability, and immune responses to the vaccine. Immunizations were administered every 3 weeks for a total of four injections, preceded by leukapheresis to obtain peripheral blood mononuclear cells for immune analyses, followed by a post-vaccine leukapheresis 3 weeks after the fourth vaccination. Skin testing with peptide and standard delayed-type hypersensitivity skin test reagents was also performed before and after vaccinations. Local pain and granuloma formation were observed in the majority of patients, as were fevers or lethargy of grade 1 or 2. No vaccine-related grade III/IV toxicity was observed. The vaccine was felt to be well tolerated. Twelve of 25 patients were anergic to skin testing at the initiation of the trial, and 13 of 25 developed a positive skin test response to the MART-1(27-35) peptide. Immune responses were measured by release of IFN-gamma in an ELISA assay by effector cells after multiple restimulations of peripheral blood mononuclear cells in the presence of MART-1(27-35) peptide-pulsed antigen-presenting cells. An ELISPOT assay was also developed to measure more quantitatively the change in numbers of peptide-specific effector cells after vaccination. Ten of 22 patients demonstrated an immune response to peptide-pulsed targets or tumor cells by ELISA assay after vaccination, as did 12 of 20 patients by ELISPOT. Nine of 25 patients have relapsed with a median of 16 months of follow-up, and 3 patients in this high-risk group have died. Immune response by ELISA correlated with prolonged relapse-free survival. These data suggest a significant proportion of patients with resected melanoma mount an antigen-specific immune response against a peptide vaccine and support further development of peptide vaccines for melanoma.
Attribute Pivots for Guiding Relevance Feedback in Image Search (2013)

In interactive image search, a user iteratively refines his results by giving feedback on exemplar images. Active selection methods aim to elicit useful feedback, but traditional approaches suffer from expensive selection criteria and cannot predict in formativeness reliably due to the imprecision of relevance feedback. To address these drawbacks, we propose to actively select "pivot" exemplars for which feedback in the form of a visual comparison will most reduce the system's uncertainty. For example, the system might ask, "Is your target image more or less crowded than this image?" Our approach relies on a series of binary search trees in relative attribute space, together with a selection function that predicts the information gain were the user to compare his envisioned target to the next node deeper in a given attribute's tree. It makes interactive search more efficient than existing strategies-both in terms of the system's selection time as well as the user's feedback effort.
Bayesian Regularization and Pruning Using a Laplace Prior (1995)

Standard techniques for improved generalization from neural networks include weight decay and pruning. Weight decay has a Bayesian interpretation with the decay function corresponding to a prior over weights. The method of transformation groups and maximum entropy suggests a Laplace rather than a gaussian prior. After training, the weights then arrange themselves into two classes: (1) those with a common sensitivity to the data error and (2) those failing to achieve this sensitivity and that therefore vanish. Since the critical value is determined adaptively during training, pruning—in the sense of setting weights to exact zeros—becomes an automatic consequence of regularization alone. The count of free parameters is also reduced automatically as weights are pruned. A comparison is made with results of MacKay using the evidence framework and a gaussian regularizer.
Improved disk-drive failure warnings (2002)

Improved methods are proposed for disk-drive failure prediction. The SMART (self monitoring and reporting technology) failure prediction system is currently implemented in disk-drives. Its purpose is to predict the near-term failure of an individual hard disk-drive, and issue a backup warning to prevent data loss. Two experimental tests of SMART show only moderate accuracy at low false-alarm rates. (A rate of 0.2% of total drives per year implies that 20% of drive returns would be good drives, relative to /spl ap/1% annual failure rate of drives). This requirement for very low false-alarm rates is well known in medical diagnostic tests for rare diseases, and methodology used there suggests ways to improve SMART. Two improved SMART algorithms are proposed. They use the SMART internal drive attribute measurements in present drives. The present warning-algorithm based on maximum error thresholds is replaced by distribution-free statistical hypothesis tests. These improved algorithms are computationally simple enough to be implemented in drive microprocessor firmware code. They require only integer sort operations to put several hundred attribute values in rank order. Some tens of these ranks are added up and the SMART warning is issued if the sum exceeds a prestored limit. These new algorithms were tested on 3744 drives of 2 models. They gave 3-4 times higher correct prediction accuracy than error thresholds on will-fail drives, at 0.2% false-alarm rate. The highest accuracies achievable are modest (40%-60%). Care was taken to test will-fail drive prediction accuracy on data independent of the algorithm design data. Additional work is needed to verify and apply these algorithms in actual drive design. They can also be useful in drive failure analysis engineering. It might be possible to screen drives in manufacturing using SMART attributes. Marginal drives might be detected before substantial final test time is invested in them, thereby decreasing manufacturing cost, and possibly decreasing overall field failure rates.
Radiation damage and radioprotectants: new concepts in the era of molecular medicine (2012)

Exposure to ionising radiation results in mutagenesis and cell death, and the clinical manifestations depend on the dose and the involved body area. Reducing carcinogenesis in patients treated with radiotherapy, exposed to diagnostic radiation or who are in certain professional groups is mandatory. The prevention or treatment of early and late radiotherapy effects would improve quality of life and increase cancer curability by intensifying therapies. Experimental and clinical data have given rise to new concepts and a large pool of chemical and molecular agents that could be effective in the protection and treatment of radiation damage. To date, amifostine is the only drug recommended as an effective radioprotectant. This review identifies five distinct types of radiation damage (I, cellular depletion; II, reactive gene activation; III, tissue disorganisation; IV, stochastic effects; V, bystander effects) and classifies the radioprotective agents into five relevant categories (A, protectants against all types of radiation effects; B, death pathway modulators; C, blockers of inflammation, chemotaxis and autocrine/paracrine pathways; D, antimutagenic keepers of genomic integrity; E, agents that block bystander effects). The necessity of establishing and funding central committees that guide systematic clinical research into evaluating the novel agents revealed in the era of molecular medicine is stressed.
Avirulence gene diversity of Xanthomonas axonopodis pv. glycines isolated in Korea. (2008)

The hybridization patterns with the avrBs3 gene that is known to determine the recognition of host specificity were used to study the diversity of Xanthomonas axonopodis pv. glycines causing bacterial leaf pustule in soybean. A total of 155 strains were isolated from diverse tissues of soybean cultivars collected in Korea and were classified into six different type strains of OcsF, SL1017, SL1018, SL1045, SL1157, and SL2098 according to the patterns of avrBs3-homologous bands. When these type strains were inoculated on various cultivars, most of the Korean strains mildly induced disease symptoms on the resistant CNS1 cultivars. Unlike other type strains, strain SL2098, which appeared not to contain any avrBs3 homolog, induced only a few pustules on even highly susceptible cultivars. When a plasmid carrying the 3.7-kb avrBs3-homologous gene from strain SL1045 was introduced into SL2098, the transformant could not recover the pathogenicity in susceptible host plants. However, when avrBs3-homologous genes of strain SL1018 were mutated by transposon mutagenesis, one of the mutants in which a 5.2-kb chromosomal band homologous to avrBs3 was disrupted could not induce the hypersensitive response on resistant cultivars such as William82 or CNS2. Our results suggest that the avrBs3 homologs may play important roles in the pathogenicity of Xanthomonas axonopodis pv. glycines and the recognition of soybean cultivars.
Elevated Akt activation and its impact on clinicopathological features of renal cell carcinoma. (2003)

Elevated Akt activation could be a common finding, especially in high grade tumor and metastatic disease. It could have an important role in the pathogenesis and progression of renal cell carcinoma.
Anthracycline Cardiotoxicity: Prevalence, Pathogenesis and Treatment (2012)

Anthracyclines, such as doxorubicin and idarubicin, remain an important class of chemotherapeutic agents. Unfortunately, their efficacy in treating cancer is limited by a cumulative dose-dependent cardiotoxicity, which can cause irreversible heart failure. In this review, we discuss the pathogenesis and incidence of anthracycline-induced cardiotoxicity as well as methods to detect, prevent and treat the condition.
Energy auctions and market power: an experimental examination (2003)

Testing auction mechanisms experimentally in a controlled environment provides an inexpensive means for evaluating their relative merits. The first part of this paper focuses on the comparison of three different auctions with regard to market efficiency and pricing, given scenarios with two, four, and six competitors. Though the uniform price last accepted offer auction was superior overall, the number of competitors proved to be a more significant factor in determining auction performance. Significant exploitation of market power was observed in the duopoly case. The second part of the paper focuses on a transmission network with six sellers in which network constraints give rise to market power opportunities. Experimental evidence based on tests with student and expert subjects show exploitation of this strategic advantage. Several other scenarios are described in which the transmission network creates market power.
Anticonvulsant Activities of 4–Bromobenzaldehyde Semicarbazone (1994)

Some of the properties of 4-bromobenzaldehyde semicarbazone (compound IV), a prototype molecule of a new class of anticonvulsants, aryl semicarbazones, are described. Compound IV demonstrated activity in the maximal electroshock (MES) and subcutaneous pentylenetetrazol (scPTZ) tests in mice, with low neurotoxicity. When given orally to rats, it displayed high potency in the MES test and very low neurotoxicity, resulting in a high protective index (PI). Compound IV displayed no proconvulsant properties, and development of rapid tolerance was not noted. When administered intraperitoneally (i.p.) at doses of 100, 300, or 600 mg/kg to peritoneally (i.p.) at doses of 100, 300, or 600 mg/kg to rats, compound IV had no effect on levels of gamma-aminobutyric acid (GABA) or on GABA-T activity in whole brain. When tested in vitro, compound IV had no effect on rat brain GABA-T at a drug concentration of 100 microM. Although the activities of certain drug-metabolizing enzymes were increased after oral administration of compound IV to rats, these effects were less prominent than those of phenytoin (PHT) and carbamazepine (CBZ). The principal mode of action of compound IV does not appear to be an interaction with the GABAA receptor complex, and other mechanisms, involving excitatory amino acid neurotransmission, will have to be considered in future investigations of the anticonvulsant activity of this compound.
SERUM MARKERS CASA, CEA, CYFRA-21-1, MSA, NSE, TPA AND TPS IN LUNG-CANCER (1994)

Serum CASA, CEA, CYFRA 21-1, NSE, MSA, TPA, and TPS were determined in patients with lung cancer (LC), benign lung disease (BL), and healthy control (HC) donors. Using predefined cutpoints, the cytokeratin-related markers TPA, TPS, and CYFRA showed the highest sensitivity in non-small cell lung cancer (TPA 69%, TPS 63%, CYFRA 54%), while NSE gave the highest sensitivity in small cell lung cancer (50%), indicating that these markers may be most appropriate in monitoring the course of disease and the patients response to therapy. Receiver-operator analysis was performed to compare assays at the same specificity. At high specificities (greater than or equal to 95%), CYFRA was significantly better than all assays except CASA in the LC vs. HC and LC vs. non-infectious BL comparisons (p<0.05), while CEA was the only assay which was not significantly different to CYFRA in the LC vs. BL comparison. CASA was of particular value when used in combination with these markers, as the sensitivity was increased. In addition, pretreatment CASA was the best indicator of patient survival (one year survival of 83% for patients with CASA <5 units/ml and 10% for patients with CASA greater than or equal to 5 units/ml).
Li+ Defects in a Solid-State Li Ion Battery: Theoretical Insights with a Li3OCl Electrolyte (2017)

In a solid-state Li ion battery, the solid-state electrolyte exists principally in regions of high externally applied potentials, and this varies rapidly at the interfaces with electrodes because of the formation of electrochemical double layers. We investigate the implications of these for a model solid-state Li ion Li|Li3OCl|C battery, where C is simply a metallic intercalation cathode. We use density functional theory to calculate the potential dependence of the formation energies of the Li+ charge carriers in superionic Li3OCl. We find that Li+ vacancies are the dominant species at the cathode while Li+ interstitials dominate at the anode. With typical Mg aliovalent doping of Li3OCl, Li+ vacancies dominate the bulk of the electrolyte, as well, with freely mobile vacancies that are only ∼10–4 of the Mg doping density at room temperature. We study the repulsive interaction between Li+ vacancies and find that this is extremely short-range, typically only one lattice constant because of local structural relaxation around the vacancy, and this is significantly shorter than pure electrostatic screening. We model a Li3OCl–cathode interface by treating the cathode as a nearly ideal metal using a polarizable continuum model with an εr of 1000. There is a large interface segregation free energy of approximately −1 eV per Li+ vacancy. Combined with the short range for repulsive interactions of the vacancies, this means that very large vacancy concentrations will build up in a single layer of Li3OCl at the cathode interface to form a compact double layer. The calculated potential drop across the interface is ∼3 V for a nearly full concentration of vacancies at the surface. This suggests that nearly all the cathode potential drop in Li3OCl occurs at the Helmholtz plane rather than in a diffuse space–charge region. We suggest that our conclusions can be generalized to other superionic conductors, as well.
Feature-map methods for extracting sound frequency modulation (2002)

The role of frequency modulation (FM) in the auditory system is investigated. Psychoacoustic evidence shows that FM is a cue for noncontextual auditory scene analysis, and neurophysiological evidence shows that it is detected by neurons in some animal auditory systems. Some filters for detecting FM in sound are presented. One method uses correlation of a kernel with a time-frequency representation of cochlear neural impulses of a sound to reveal its FM components. Another correlation method is based on detecting FM in channel-by-channel autocorrelation images, with some data reduction and sharpening applied. The filters are tuned for various spatiotemporal frequencies to extract information about sound with various FM characteristics, producing maps showing time-frequency points at which the features are present. These maps can allow another process to decide what sources are present or to use FM cues for pattern recognition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
[Irradiation of bone homografts. Their use following tumor resection. Apropos of 4 cases]. (1986)

Since 1978 gamma irradiation has been used for sterilization of bone allografts. The radiation source used was Co 60 (2.5 to 3 megarads). Which was applied at the Atomic Centre of Saclay. The technique of sterilization is absolutely reliable at relatively low cost. It allows pieces of bone from cadavers to be harvested several hours after death, without special aseptic precautions. It appears to diminish antigenicity of the graft very little and incorporation is perhaps slowed down. The grafts did not become radioactive. The graft is carefully packed and frozen as soon as it is taken from the cadaver. Freezing is continued during the irradiation process and the graft may then be stored for several months. This technique was used for reconstruction after tumor resection twice in the knee, once in the pelvis and once in the fibula. There was no postoperative infection. Scintigraphy showed satisfactory incorporation. In one case of replacement of the femoral condyle the cartilage of the graft was replaced by the intact articular cartilage of the patient. Later, this articular cartilage was shown to be necrotic and a total prosthesis was inserted. The fibular graft was secondarily complicated by a fracture. Sterilization using irradiation makes bone harvesting in cadavers easier and allows bone banks to be established. It should lead to more extensive use of allograft bone.
Selective Cyclooxygenase-2 (COX-2) Inhibitors Used for Preventing or Regressing Cancer (2009)

The current use of antineoplastic drugs in human therapy causes a substancial number of toxic or side effects which consequently lead to a reduction of the amount of drug to be administered, and in some cases to discontinuation of the therapy. A reduction of the amount of drug to be administered or discontinuation of the therapy causes an increase in primary tumour growth and/or the occurrence of tumour metastases. For this reason, the development of new anti-cancer drugs with lower side effects is necessary. This review gives a general idea about the origins of cancer and the importance of cyclooxygenase-2 (COX-2) in oncogenesis. Evidence from clinical and preclinical studies indicates that COX-2-derived prostaglandins participate in carcinogenesis, inflammation, immune response suppression, apoptosis inhibition, angiogenesis, and tumour cell invasion and metastasis. The recent anti-tumour drugs are based on tests of known selective COX-2 inhibitors and on the drawing and synthesis of new potent derivatives. Maybe, this can be the way to obtain new anti-tumour drugs with very low collateral effects. Selective COX-2 inhibitors are being mixtured with new anti-cancer drugs in order to obtain better results in the regression of cancers. Some natural products are selective COX-2 inhibitors and have anti-inflammatory and anti-cancer properties. The relevant patents are discussed.
Transient responses of hybridoma cells to nutrient additions in continuous culture: I. Glucose pulse and step changes (1989)

Glucose and glutamine are the main nutrients used by mammalian cells in culture. Each provides unique biosynthetic precursors but are complementary for production of other metabolites and energy. The transient and steady-state responses of hybridoma growth and metabolism to glucose pulse and step changes have been examined. Metabolic quotients are reported for oxygen, glucose, lactate, ammonia, glutamine, alanine, and other amino acids. The glucose consumption rate increased by 100-200% immediately after glucose was added to the reactor, and the increased glycolytic ATP production appears to be responsible for the concurrent rapid decrease in the oxygen consumption rate. The effects on glutamine consumption were delayed, probably due to buffering by the TCA cycle and interrelated pathways. A period of increased biosynthetic activity, as evidenced by an increase in the estimated specific ATP production rate and lower by-product yields from glutamine, preceded the increase in cell concentration after the glucose step change. The biosynthetic yield of cells from ATP was calculated, and it was estimated that maintenance accounted for about 60% of the energy used by the cells at a specific growth rate of 0.66 day(-1). The estimated 22% ATP production due to glycoysis was twice as great as that before the step change.
Hlx homeo box gene is essential for an inductive tissue interaction that drives expansion of embryonic liver and gut. (1996)

The divergent murine homeo box gene Hlx is expressed in restricted hematopoietic cell types and, during embryogenesis, prominently in visceral mesenchyme of the developing liver, gall bladder, and gut. Targeted disruption of the gene has now established that it plays a key role in visceral organogenesis. Embryos homozygous for the mutation died around embryonic day 15 with anemia and severe hypoplasia of the liver and gut. Liver ontogeny commenced normally with formation of the liver diverticulum and differentiation of hepatocytes, but the organ failed to expand and reached only 3% of normal size. The apparent liver hypoplasia was not associated with a notable increase in apoptotic cells. Gut development also began normally, but the intestines failed to undergo extensive elongation and looping and reached only a quarter of normal length. The anemia resulted from a deficiency in the fetal form of hematopoiesis, which occurs in the liver, but no intrinsic defect in Hlx-/- hematopoietic cells was observed in vitro, and liver-derived Hlx-/- hematopoietic stem cells that were transplanted to irradiated normal mice could fully reconstitute hematopoiesis. The impaired fetal hematopoiesis therefore reflects insufficient support function provided by the minute liver. Hlx is normally expressed in visceral mesenchyme lying adjacent to the developing liver and gut epithelia affected by the mutation, but not in the epithelia themselves. Hence, Hlx regulates a mesenchymal-epithelial interaction that drives a vital growth phase in visceral organogenesis. Moreover, because mutation of Hlx blocked liver growth but not its specification, early morphogenesis, or differentiation, development of this organ appears to occur by step-wise inductive interactions under separate genetic control.
Pseudomembranous Tracheobronchitis Caused by Aspergillus (1991)

Four immunosuppressed patients with a rapidly evolving, febrile, respiratory distress syndrome were found at autopsy to have Aspergillus pseudomembranes of their lower tracheobronchial tree. Steroids, neutropenia, broad spectrum antibiotic use, and alcoholism appear to be predisposing risk factors. Bronchoscopy may reveal the pathology but antemortem diagnosis is difficult because of the low yield of sputum cultures and fulminant nature of the disease.