gebhart/patrepeval huggingface dataset:
Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia (2020)

Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies.
Porphyrin−Oligothiophene−Fullerene Triads as an Efficient Intramolecular Electron-Transfer System (2002)

A series of porphyrin-oligothiophene-fullerene triads containing quaterthiophene, octithiophene, and dodecithiophene spacers has been synthesized. The fluorescence of the porphyrin chromophore in benzonitrile is efficiently quenched by electron transfer to the fullerene moiety. This process shows a weak distance dependence of the oligothiophene spacer with an attenuation factor beta= 0.11 A(-1).
Synthesis of peptide gels for the investigation of oligopeptide–oligonucleotide interactions (1986)

Abstract Peptide gels usable as protein model systems have been synthesized by a cross‐linking copolymerization of acryloyl substituted peptides with 1,4‐tetramethylene dimethacrylate. A specially adapted approach to peptide synthesis allows the removal of the amino terminal Cbo group at the end of the peptide synthesis, followed by the introduction of an acryloyl group. The polymerizable peptide monomers obtained can be transferred into insoluble peptide gels by radical copoylmerization with cross‐linking agents. After cleavage of the protecting groups of the side chains, these peptide gels can be used both as protein model systems for investigating peptide–oligonucleotide interaction and as sorbents for affinity chromatography. The preparation and characterization of the peptide gels Ala‐Lys‐Glu‐Lys‐Ala‐OMe (I), Ala‐Arg‐Glu‐Arg‐Ala‐OMe (II), Ala‐Arg‐Glu‐Lys‐Ala‐OMe (III), and Ala‐Arg‐Ala‐Lys‐Ala‐OMe (IV) as well as the conditions for the removal of the protecting groups is presented. Gel III contains the natural peptide sequence Arg‐Glu‐Lys while the other gels are analogs of this sequence.
Application of Complex Event Processing Paradigm in Situation Awareness and Management (2011)

This paper describes a novel approach to situation awareness and management in critical infrastructures using an emerging Complex Event Processing paradigm in combination with ECA (Event Condition Action) rules. Every modern infrastructural facility, especially critical ones, would want to catch or predict exceptions and threats at the earliest possible moment. The crucial prerequisite for this is a holistic and accurate situation assessment. To be able to assess the situation, evaluate the risk and provide decision support to the emergency managers, we need to define event chains that identify what is normal, compliant and expected, and what is exceptional and/or dangerous. These problems introduce a novel genre of applications - event-driven applications that make automated decisions based on a complex event or pattern of events, their detection, correlation and aggregation. In cases where an automated reaction is not possible, a recommendation is given to a human operator who remains in the control loop.
Glycoprotein IIb/IIIa Blockade Inhibits Platelet-mediated Force Development and Reduces Gel Elastic Modulus (1995)

The effects of GPIIb/IIIa blockade on clot retraction were studied utilizing an instrument which directly measures force produced by platelets. GPIIb/IIIa disruption by calcium chelation, and GPIIb/IIIa blockade by peptides and anti-GPIIb/IIIa antibodies were investigated. One mM EDTA suppressed ADP-induced platelet aggregation by 72% and reduced force developed at 1200 s by 33%. At 234 microM, the tetrapeptide Arg-Gly-Asp-Ser (RGDS) suppressed platelet aggregation by 74%, reduced force at 1200 s by 45% and reduced gel elastic modulus by 19%. At 10 microM, the peptide D-Arg-Gly-L-Asp-L-Try (D-RGDW) completely suppressed platelet aggregation, reduced force development by 38% and reduced gel elastic modulus by 29%. At 0.133 microM, monoclonal anti-GPIIIa antibody (AP-3) reduced force development by 74% and reduced gel modulus by 60%. Murine antiGPIIb/IIIa antibodies 10E5 and 7E3 markedly suppressed force development. At 0.133 microM, 10E5 reduced force by 89% and reduced gel modulus by 67%. At 0.053 microM, 7E3 completely stopped force development and reduced gel modulus by 46%. Platelet aggregation was blocked by 0.027 microM 7E3. Selective GPIIb blockade by antibodies did not affect force development. None of the agents studied altered fibrin structure as monitored by effects of fibrin mass/length ratios. Suppression of platelet aggregation occurred at inhibitor concentrations substantially lower than those required to suppress force development. Complete suppression of platelet aggregation did not assure inhibition of clot retraction probably due to profound platelet activation by thrombin.(ABSTRACT TRUNCATED AT 250 WORDS)
Reliability of Multi-Terminal Copper Dual-Damascene Interconnect Trees (2003)

Electromigration tests on different Cu dual-damascene interconnect tree structures consisting of various numbers of straight via-to-via lines connected at the common middle terminal have been carried out. Like Al-based interconnects, the reliability of a segment in a Cu-based interconnect tree strongly depends on the stress conditions of connected segments. The analytic model based on a nodal analysis developed for Al trees gives a conservative estimate of the lifetime of Cu-based interconnect trees. However, there are important differences in the results obtained under similar test conditions for Al-based and Cu-based interconnect trees. These differences are attributed to the variations in the architectural schemes of the two metallization systems. The absence of a conducting electromigration-resistant overlayer in Cu technology and the low critical stress for void nucleation at the Cu/inter-level diffusion barrier (i.e. Si₃N₄) interface leads to different failure modes between Cu and Al interconnects. As a result, the most highly stressed segment in a Cu-based interconnect tree is not always the least reliable. Moreover, the possibility of liner rupture at stressed dual-damascene vias leads to significant differences in tree reliabilities in Cu compared to Al. While an interconnect tree can be treated as a fundamental unit whose reliability is independent of that of other units in Al-based interconnect architectures, interconnect trees can not be treated as fundamental units for circuit-level reliability analyses for Cu-based interconnects.
Neuromuscular Blocking Activity and Therapeutic Potential of Mixed-Tetrahydroisoquinolinium Halofumarates and Halosuccinates in Rhesus Monkeys (2003)

Structure-activity relationships in rhesus monkeys for a novel mixed-onium class of ultra-short-acting nondepolarizing tetrahydroisoquinolinium neuromuscular blockers (NMBs) are described. Bis-onium chlorofumarate 20a with (1R,2S)-benzyltetrahydroisoquinolinium groups was a potent lead compound (ED(95) = 0.079 mg/kg) with an ultra-short duration of NMB effect (7.1 min) and a selectivity index (SI: defined as a ratio of the cardiovascular threshold dose to the ED(95)) similar to that of mivacurium (3). The mean threshold dose for cardiovascular effects with 20a was ca. 20 times its ED(95) value (SI = 20). A novel mixed-onium analogue of 20a was prepared by replacing the benzyltetrahydroisoquinolinium group distal to the fumarate chlorine atom with a (1S,2R)-phenyltetrahydroisoquinolinium moiety. The resulting mixed-onium chlorofumarate 24a displayed good NMB potency (ED(95) = 0.063 mg/kg), ultra-short duration of action (5.6 min) and an improved selectivity index (SI = 57). Several other mixed-onium derivatives containing octanedioate (25a; ED(95) = 0.103 mg/kg), difluorosuccinate (27c; ED(95) = 0.056 mg/kg), and fluorofumarate (28a; ED(95) = 0.137 mg/kg) linkers were also potent, ultra-short-acting NMBs with good to excellent selectivity index values (SI = 37-96). Octanedioate 25a was longer acting at higher doses compared to difluorosuccinate 27c and chlorofumarate 24a. Durations of NMB effect following a 0.4 mg/kg bolus dose (100% block) of 25a, 27c, and 24a were 16.9, 13.0, and 10.0 min, respectively. Recovery time for mixed-onium chlorofumarate 24a following a 1 h continuous infusion at 10-20 microg/kg/min (95-100% block) was ca. 5 min which is similar to that observed following a 0.2 mg/kg bolus dose of this compound and indicates a lack of cummulative effects. Preliminary studies with chlorofumarate 24a in whole human blood revealed that mixed-onium thiazolidine 29 was the major metabolite and that plasma cholinesterases do not play the primary role in duration of NMB effect. The NMB properties of 24a in rhesus monkeys led to its clinical evaluation as a possible alternative to succinylcholine.
Interferon-α, but not the ABL-kinase inhibitor imatinib (STI571), induces expression of myeloblastin and a specific T-cell response in chronic myeloid leukemia (2002)

Chronic myeloid leukemia (CML) is a clonal disease of hematopoietic stem cells caused by a reciprocal translocation of the long arms of chromosomes 9 and 22. In human leukocyte antigen A*0201(+) (HLA-A*0201(+)) individuals, response after interferon-alpha (IFN-alpha) was shown to be associated with the emergence of CML-specific cytotoxic T cells that recognize PR-1, a myeloblastin (MBN)-derived nonapeptide. In contrast, imatinib potently induces remissions from CML by specific inhibition of the ABL tyrosine kinase. Here, we explored molecular regulations associated with CML responses under different treatment forms using cDNA-array. Expression of MBN was found to be down-regulated in remission under imatinib therapy (0 of 7 MBN(+) patients). In contrast, MBN transcription was readily detectable in the peripheral blood in 8 of 8 tested IFN-alpha patients in complete remission (P =.0002). IFN-alpha-dependent MBN transcription was confirmed in vitro by stimulation of peripheral blood mononuclear cells (PBMCs) with IFN-alpha and by IFN-alpha-mediated activation of the MBN promoter in reporter gene assays. Finally, with the use of HLA-A*0201-restricted, MBN-specific tetrameric complexes, it was demonstrated that all of 4 IFN-alpha-treated patients (100%), but only 2 of 11 imatinib patients (19%), in complete hematological or cytogenetic remission developed MBN-specific cytotoxic T cells (P =.011). Together, the induction of MBN expression by IFN-alpha, but not imatinib, may contribute to the specific ability of IFN-alpha to induce an MBN-specific T-cell response in CML patients. This also implies that the character of remissions achieved with either drug may not be equivalent and therefore a therapy modality combining IFN-alpha and imatinib may be most effective.
Suppression of azoxymethane-induced rat colon carcinogenesis by dietary administration of naturally occurring xanthophylls astaxanthin and canthaxanthin during the postinitiation phase (1995)

The modulating effects of dietary feeding of two xanthophylls, astaxanthin (AX) and canthaxanthin (CX) during the postinitiation phase on colon carcinogenesis initiated with azoxymethane (AOM) were investigated in male F344 rats. Animals were initiated with AOM by weekly s.c. injections of 15 mg/kg body wt for 3 weeks and then they were fed the diets containing AX or CX at concentrations of 100 and 500 p.p.m. for 34 weeks. The others contained the groups of rats treated with AX or CX alone and untreated. At the end of the study (week 37), the incidence and multiplicity of neoplasms (adenoma and adenocarcinoma) in the large intestine of rats initiated with AOM and followed by AX or CX containing diet at a high dose (500 p.p.m.) were significantly smaller than those of rats given AOM alone (P < 0.001). In addition, AX or CX feeding significantly inhibited the development of aberrant crypt foci induced by AOM. Dietary exposure to AX or CX also decreased cell proliferation activity as revealed by measuring 5'-bromodeoxyuridine-labeling index as crypt cells, colonic mucosal ornithine decarboxylase activity and blood polyamine levels. These results indicate that AX and CX are possible chemopreventers for carcinogenesis of colon in addition to urinary bladder and oral cavity and such effects may be partly due to suppression of cell proliferation.
The Relationship of Food Conversion Efficiency and Growth Potential in Juvenile Mosquitofish, Gambusia affinis (1980)

New information concerning respiratory metabolic rates of juvenile mosquitofish (i = 915 mg 02 kg-1 h-1 at 20° C) was applied to existing data on mosquitofish respiration and combined with findings on growth and food consumption rates to determine percentages of net ingested energy used for growth and respiration over a 10- 35° C temperature range. The energy percentage used by mosquitofish for respiration was minimized at 25-30° C while that used for growth (= food conversion efficiency) was maximized at the same temperature. A calculated growth potential index, derived from an overall energy balance equation, was also maximized at the 25 to 30° C range and proved to be closely correlated with food conversion efficiency (r = 0.98). Possible future applications of the growth potential index for estimating food conversion efficiencies in field populations of fishes are suggested.
Sildenafil Is a Pulmonary Vasodilator in Awake Lambs with Acute Pulmonary Hypertension (2000)

Sildenafil is a selective pulmonary vasodilator in an ovine model of acute pulmonary hypertension. Sildenafil induces pulmonary vasodilation via a NO-dependent mechanism. In contrast to zaprinast, sildenafil did not prolong the pulmonary vasodilator action of inhaled NO.
Alignment of full and partial CT thoracic scans using bony structures (2006)

Diagnostic thoracic procedures using computed tomography (CT) often include comparisons of scans acquired with different slice thicknesses. In this manuscript, we investigated the potential for alignment of different CT scans from the same patient using skeletal knowledge of the thoracic region. Skeletal matching was selected because it is expected to be less susceptible to differences associated with patient breath hold, positioning and cardiac motion. Our method utilized the positioning of the ribs relative to the vertebra for matching. It also included matching the scapula when visible in the scans. Rib positioning was described by the angles formed between the vertebra centroid and combinations of pairs of rib centroids visible on each CT slice; this was used as the primary matching mechanism. Scapula morphology was described using a feature based on the local maxima of the distance transform. Since the scapula is not visible in all slices of a full scan, its description was limited to only defining the potential range of slices. A cost function incorporating the difference of features from rib positioning and scapula morphology between two slices was derived and used to match slices. The method was evaluated on an independent set of 10 pairs of full and partial CT scans. Assessment was based on whether or not slices containing known nodules between each pair of scans were overlapping after the alignment procedure. Results showed that the proposed metric correctly aligned 9 out of 10 scans. The preliminary results are encouraging for using this method as a first step towards temporal analysis of lung nodules.
Pyrrolidine-Catalyzed Homo-Aldol Condensation Reactions of Aldehydes (1999)

The first example of synthetically useful pyrrolidine-catalyzed homocoupling reaction of aliphatic aldehydes accelerated by benzoic acid is presented together with a plausible reaction mechanism.
<title>Differential geometry of the cortical surface</title> (1995)

The cortical fold is one of the most striking features of the brain and it plays a tremendously important role in understanding brain function. In this paper we build a precise mathematical representation of a typical cortical surface. This representation will allow us to make statements about the geometry of the surface and will enable us to compute intrinsic geometrical properties such as the Mean and the Gaussian curvature of the surface.
Activated photothermal heating using croconaine dyes (2013)

Laser-induced photothermal heating is promoted by dyes or nanoparticles that strongly absorb light and convert it into heat. The best known near-infrared absorbing systems are gold nanorods and nanocages. The alternative strategy of using organic dyes to absorb the laser light has several inherent advantages due to the small molecular size and potential synthetic flexibility, but a major drawback is rapid photothermal bleaching. Here, we report three important findings: (a) near-infrared croconaine dyes exhibit outstanding properties for high performance photothermal heating; including an intense and narrow absorption band at around 800 nm, high chemical, photo- and thermal stability, very efficient relaxation to the ground state, and very low oxygen photosensitization ability. (b) Photothermal heating obeys the Beer–Lambert law (1 − 10−A) and sample heating reaches an asymptotic limit when chromophore absorbance values are greater than ∼1. (c) Croconaine dyes form red-shifted encapsulation complexes which allows the realization of molecular recognition induced activated photothermal heating, a broadly applicable nanoscale design concept that employs chemical or supramolecular processes to switch on laser-induced hyperthermia.
The Impact of Efflux Pump Inhibitors on the Activity of Selected Non-Antibiotic Medicinal Products against Gram-Negative Bacteria (2017)

The potential role of non-antibiotic medicinal products in the treatment of multidrug-resistant Gram-negative bacteria has recently been investigated. It is highly likely that the presence of efflux pumps may be one of the reasons for the weak activity of non-antibiotics, as in the case of some non-steroidal anti-inflammatory drugs (NSAIDs), against Gram-negative rods. The activity of eight drugs of potential non-antibiotic activity, active substance standards, and relevant medicinal products were analysed with and without of efflux pump inhibitors against 180 strains of five Gram-negative rod species by minimum inhibitory concentration (MIC) value determination in the presence of 1 mM MgSO₄. Furthermore, the influence of non-antibiotics on the susceptibility of clinical strains to quinolones with or without PAβN (Phe-Arg-β-naphthylamide) was investigated. The impacts of PAβN on the susceptibility of bacteria to non-antibiotics suggests that amitriptyline, alendronate, nicergoline, and ticlopidine are substrates of efflux pumps in Gram-negative rods. Amitriptyline/Amitriptylinum showed the highest direct antibacterial activity, with MICs ranging 100-800 mg/L against all studied species. Significant decreases in the MIC values of other active substances (acyclovir, atorvastatin, and famotidine) tested with pump inhibitors were not observed. The investigated non-antibiotic medicinal products did not alter the MICs of quinolones in the absence and in the presence of PAβN to the studied clinical strains of five groups of species.
Estimating the list size for BEAST-APP decoding (2005)

The BEAST-APP decoding algorithm is a low-complexity bidirectional algorithm that searches code trees to find the list of the most likely codewords, which are used to compute approximate a posteriori probabilities (APPs) of the transmitted symbols. It can be applied to APP-decoding of any linear block code, as well as in iterative structures for decoding concatenated block codes. Previous work has shown that the list size sufficient to achieve the performance of true-APP decoding is very small. This paper aims at providing a theoretical justification for this result. The sufficient list size is estimated first via the minimum list distance - a parameter that is defined and analyzed as a key factor that governs the performance of list-based algorithms. Additionally, statistical properties of the codeword likelihoods are investigated and the typical list structure is presented. Preliminary simulation results for iterative BEAST decoding confirm the list-size estimates obtained from both approaches.
Using Semantic Web Ontology for Intercloud Directories and Exchanges. (2010)

The concept of a cloud operated by one service provider or enterprise interoperating with a clouds operated by another is a powerful idea. So far that is limited to use cases where code running on one cloud explicitly references a service on another cloud. There is no implicit and transparent interoperability. This interoperability should be more than cloud to cloud, it should embody 1-to-many and many-to-many models. Working groups have proposed building a layered set of protocols to solve this interoperability challenge called “Intercloud Protocols”. Instead of each cloud provider establishing connectivity with another cloud provider in a Point-to-Point manner resulting into n 2 complexity problem, Intercloud Directories and Exchanges will help facilitate as mediators for enabling connectivity and collaboration among disparate cloud providers. This paper proposes a mechanism for such mediation utilizing a resources catalog approach, defined using the Semantic Web Resource Definition Framework (RDF) and a common Ontology of Cloud Computing Resources across heterogeneous cloud providers.
Size-dependent charge storage in amorphous silicon quantum dots embedded in silicon nitride (2003)

Size-dependent charge storage was observed in metal–insulator–semiconductor structures containing amorphous Si quantum dots (a-Si QDs) grown by plasma-enhanced chemical vapor deposition. For a-Si QDs as large as 2 nm in diameter, one electron or one hole was stored in each a-Si QD. For small-sized a-Si QDs of 1.4 nm in diameter, however, the width of capacitance–voltage hysteresis was decreased, indicating that the charge density in the a-Si QDs was reduced. This can be attributed to the lowered tunneling barrier in the small-sized a-Si QDs resulting from a large quantum confinement effect. Long-term charge storage was observed in the fully charged a-Si QDs; this is attributed to a suppression of the discharge process by electrostatic repulsion among the charged dots.
AT<sub>2</sub> Receptor Stimulation May Halt Progression of Pheochromocytoma (2006)

Two patients with pheochromocytoma are described in whom treatment with a high dose of an angiotensin receptor blocker was associated with cessation of tumor growth as assessed by serial CT scanning and plasma norepinephrine estimation. If the association with drug treatment is causal, the mechanism may be through stimulation of the AT2 receptor consequent upon the elevation of plasma angiotensin II levels induced by AT1 receptor blockade. Similar observations in further patients should lead to a placebo-controlled study in patients with malignant or familial pheochromocytoma, or other tumors found to express the AT2 receptor.