gebhart/patrepeval huggingface dataset:
e-bra With Nanosensors for Real Time Cardiac Health Monitoring and Smartphone Communication (2011)

Mortality due to cardiac related ailments has been consistently higher in women as compared with men since the early 1980s in the United States. Gender related differences in specificity of regular noninvasive diagnostic tools and the lack of a clear understanding of the effect of postmenopausal hormonal changes in women have been cited as the two main reasons for this disparity. Recent advances in secondary and tertiary diagnostic information extraction techniques from signals such as electrocardiogram (ECG) through heart rate variability (HRV) analysis and wavelet domain analysis techniques have revealed many differences in autonomic nervous-cardiovascular activity regulation, between men and women. Moreover, the diagnostic tests for cardiovascular diseases usually start upon the manifestation of chest pain or angina. At this stage, disease management is the only option as opposed to preventive treatments, which is also possible with early detection based on the diagnostic information extraction techniques as stated previously. In order to truly realize the potential of such techniques, continuous and long-term monitoring is an essential requirement. This, in turn, requires sensor systems to be seamlessly mounted on day to day clothing for women. This paper describes an e-bra platform for nanosensors toward cardiovascular monitoring. The sensors, nanomaterial, or textile based dry electrodes acquire electrocardiograph, which is sent to a textile mounted wireless module. A smartphone or a wireless Bluetooth enabled PC can receive these data and store or process the information as necessary. In this paper, we wirelessly acquire ECG from subjects with the e-bra and perform HRV analysis on a PC. The use of a Smartphone as a base station for receiving data offers the advantage of cellular network connectivity to internet and consequently cloud computing resources for more complex computations such as feature extraction and automatic diagnosis. To address this capability, we further propose a protocol for response to emergencies from both the cloud backend and the smartphone itself.
Phase I trial of hydroxychloroquine with dose-intense temozolomide in patients with advanced solid tumors and melanoma (2014)

Blocking autophagy with hydroxychloroquine (HCQ) augments cell death associated with alkylating chemotherapy in preclinical models. This phase I study evaluated the maximum tolerated dose (MTD), safety, preliminary activity, pharmacokinetics, and pharmacodynamics of HCQ in combination with dose-intense temozolomide (TMZ) in patients with advanced solid malignancies. Forty patients (73% metastatic melanoma) were treated with oral HCQ 200 to 1200 mg daily with dose-intense oral TMZ 150 mg/m (2) daily for 7/14 d. This combination was well tolerated with no recurrent dose-limiting toxicities observed. An MTD was not reached for HCQ and the recommended phase II dose was HCQ 600 mg twice daily combined with dose-intense TMZ. Common toxicities included grade 2 fatigue (55%), anorexia (28%), nausea (48%), constipation (20%), and diarrhea (20%). Partial responses and stable disease were observed in 3/22 (14%) and 6/22 (27%) patients with metastatic melanoma. In the final dose cohort 2/6 patients with refractory BRAF wild-type melanoma had a near complete response, and prolonged stable disease, respectively. A significant accumulation in autophagic vacuoles (AV) in peripheral blood mononuclear cells was observed in response to combined therapy. Population pharmacokinetics (PK) modeling, individual PK simulations, and PK-pharmacodynamics (PD) analysis identified a threshold HCQ peak concentration that predicts therapy-associated AV accumulation. This study indicates that the combination of high-dose HCQ and dose-intense TMZ is safe and tolerable, and is associated with autophagy modulation in patients. Prolonged stable disease and responses suggest antitumor activity in melanoma patients, warranting further studies of this combination, or combinations of more potent autophagy inhibitors and chemotherapy in melanoma.
Michael Additions of Highly Basic Enolates toortho-Quinone Methides (2015)

A protocol by which ketone or ester enolates and ortho-quinone methides (o-QMs) are generated in situ in a single reaction flask from silylated precursors under the action of anhydrous fluoride is reported. The reaction partners are joined to give a variety of β-(2-hydroxyphenyl)-carbonyl compounds in 32-94% yield in a single laboratory operation. The intermediacy of o-QMs is supported by control experiments utilizing enolate precursors and conventional alkyl halides as competitive alkylating agents and the isolation of 1,5-dicarbonyl products resulting from conjugate additions that do not restore the aromatic system.
Community services: a toolkit for rapid deployment of network services (2003)

Advances in packaging and interface technologies have made it possible for software components to be shared across the network through encapsulation and offered as network services. They allow end-users to focus on their applications and obtain remote services when needed simply by invoking them across the network. Many groups have built significant infrastructures for providing domain-specific high performance services. However, transforming high performance applications into network services is labor intensive and time consuming because there is little existing infrastructure to utilize. In this paper, we propose a software toolkit and runtime infrastructure for rapid deployment of network services.
Detection of harmonic sets (1995)

We examine the detection problem of signals with narrowband, harmonically related components received by a passive sensor array. We investigate detector structures based on the Fourier method. The harmonic detector estimates the total signal power by combining the DFT coefficients from harmonic frequency bins. This power estimate is normalized by the estimated background noise power and then compared to a threshold. We investigate two harmonic detector structures: one that operates with coherent, correlated signals and the other with uncorrelated harmonic signals. We derive statistical laws governing both detector structures that facilitate setting a power threshold for a given probability of false alarm; and present upper- and lower-bounds for the probability of detection. The results developed and presented demonstrate the inherent advantage of the harmonic detector. At operating conditions characterized by low signal-to-noise power ratio values the harmonic detector exhibits enhanced detection performance by combining the estimated signal power from harmonic frequency bins. We generalize results from single-bin and harmonic detector structures and present them as special cases of a unifying framework.
l -Amino acid sensing by the extracellular Ca 2+ -sensing receptor (2000)

The extracellular calcium (Ca(2+)(o))-sensing receptor (CaR) recognizes and responds to (i.e., "senses") Ca(2+)(o) as its principal physiological ligand. In the present studies, we document that the CaR is activated not only by extracellular calcium ions but also by amino acids, establishing its capacity to sense nutrients of two totally different classes. l-Amino acids, especially aromatic amino acids, including l-phenylalanine and l-tryptophan, stereoselectively mobilized Ca(2+) ions in the presence of the CaR agonists, Ca(2+)(o), gadolinium (Gd(3+)(o)), and spermine in fura-2-loaded human embryonic kidney (HEK-293) cells stably transfected with the human CaR. l-amino acid-dependent effects were observed above, but not below, a threshold level of Ca(2+)(o) of approximately 1.0 mM. l-Amino acids, particularly aromatic amino acids, also stereoselectively enhanced the sensitivity of the CaR to its agonists, Ca(2+)(o) and spermine. Branched-chain amino acids were almost inactive, and charged amino acids, including arginine and lysine, were much less effective than aromatic and other amino acids. l-amino acid mixtures emulating the amino acid composition of fasting human plasma reproduced the effects of high concentrations of individual l-amino acids on Ca(2+) mobilization and enhanced the sensitivity of the CaR to Ca(2+)(o). The data presented herein identify the CaR as a molecular target for aromatic and other l-amino acids. Thus, the CaR can integrate signals arising from distinct classes of nutrients: mineral ions and amino acids. The actions of l-amino acids on the CaR may provide explanations for several long recognized but poorly understood actions of dietary protein on calcium metabolism.
The POSTGRES next generation database management system (1991)

article Free Access Share on The POSTGRES next generation database management system Authors: Michael Stonebraker Univ. of California, Berkeley Univ. of California, BerkeleyView Profile , Greg Kemnitz Univ. of California, Berkeley Univ. of California, BerkeleyView Profile Authors Info & Claims Communications of the ACMVolume 34Issue 10Oct. 1991 pp 78–92https://doi.org/10.1145/125223.125262Published:01 October 1991Publication History 308citation3,492DownloadsMetricsTotal Citations308Total Downloads3,492Last 12 Months912Last 6 weeks281 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Methylation of APC and GSTP1 in Non-Neoplastic Tissue Adjacent to Prostate Tumour and Mortality from Prostate Cancer (2013)

Changes in gene methylation are an early event in prostate carcinogenesis and may play a role in cancer progression. Gene methylation in NTAT is a possible prognostic marker to be evaluated in clinical studies.
Etanercept Therapy for Immune-mediated Cochleovestibular Disorders: Preliminary Results in a Pilot Study (2001)

Our limited data suggest that etanercept therapy is safe and may be efficacious in carefully selected patients with IMCVDs, at least on a short-term basis. These preliminary efficacy and safety results appear encouraging enough to warrant further follow-up and studies for better determination of the potential clinical utility of etanercept for IMCVDs.
The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells. (2001)

Histone deacetylase (HDACs) regulate histone acetylation by catalyzing the removal of acetyl groups on the NH(2)-terminal lysine residues of the core nucleosomal histones. Modulation of the acetylation status of core histones is involved in the regulation of the transcriptional activity of certain genes. HDAC activity is generally associated with transcriptional repression. Aberrant recruitment of HDAC activity has been associated with the development of certain human cancers. We have developed a class of HDAC inhibitors, such as suberoylanilide hydroxamic acid (SAHA), that were initially identified based on their ability to induce differentiation of cultured murine erythroleukemia cells. Additional studies have demonstrated that SAHA inhibits the growth of tumors in rodents. In this study we have examined the effects of SAHA on MCF-7 human breast cancer cells. We found that SAHA causes the inhibition of proliferation, accumulation of cells in a dose-dependent manner in G(1) then G(2)-M phase of the cell cycle, and induction of milk fat globule protein, milk fat membrane globule protein, and lipid droplets. Growth inhibition was associated with morphological changes including the flattening and enlargement of the cytoplasm, and a decrease in the nuclear:cytoplasmic ratio. Withdrawal of SAHA led to reentry of cells into the cell cycle and reversal to a less differentiated phenotype. SAHA induced differentiation in the estrogen receptor-negative cell line SKBr-3 and the retinoblastoma-negative cell line MDA-468. We propose that SAHA has profound antiproliferative activity by causing these cells to undergo cell cycle arrest and differentiation that is dependent on the presence of SAHA. SAHA and other HDAC inhibitors are currently in Phase I clinical trials. These findings may impact the clinical use of these drugs.
Bone repair with a form of BMP‐2 engineered for incorporation into fibrin cell ingrowth matrices (2004)

Most growth factors naturally involved in development and regeneration demonstrate strong binding to the extracellular matrix and are retained there until being locally mobilized by cells. In spite of this feedback between cell activity and growth factor mobilization in the extracellular matrix, this approach has not been extensively explored in therapeutic situations. We present an engineered bone morphogenetic protein-2 (BMP-2) fusion protein that mimics such function in a surgically relevant matrix, fibrin, incorporated into the matrix until it is locally liberated by cell surface-associated proteases. A tripartite fusion protein, denoted TG-pl-BMP-2, was designed and produced recombinantly. An N-terminal transglutaminase substrate (TG) domain provides covalent attachment to fibrin during coagulation under the influence of the blood transglutaminase factor XIIIa. A central plasmin substrate (pl) domain provides a cleavage site for local release of the attached growth factor from the fibrin matrix under the influence of cell-activated plasmin. A C-terminal human BMP-2 domain provides osteogenic activity. TG-pl-BMP-2 in fibrin was evaluated in vivo in critical-size craniotomy defects in rats, where it induced 76% more defect healing with bone at 3 weeks with a dose of 1 mug/defect than wildtype BMP-2 in fibrin. After a dosing study in rabbits, the engineered growth factor in fibrin was evaluated in a prospective clinical study for pancarpal fusion in dogs, where it induced statistically faster and more extensive bone bridging than equivalent treatment with cancellous bone autograft. The strong healing response shown by fibrin including a bound BMP-2 variant suggests that with the combination of bound growth factor and ingrowth matrix, it may be possible to improve upon the natural growth factor and even upon tissue autograft.
Coarse Master Equations for Peptide Folding Dynamics (2008)

We construct coarse master equations for peptide folding dynamics from atomistic molecular dynamics simulations. A maximum-likelihood propagator-based method allows us to extract accurate rates for the transitions between the different conformational states of the small helix-forming peptide Ala5. Assigning the conformational states by using transition paths instead of instantaneous molecular coordinates suppresses the effects of fast non-Markovian dynamics. The resulting master equations are validated by comparing their analytical correlation functions with those obtained directly from the molecular dynamics simulations. We find that the master equations properly capture the character and relaxation times of the entire spectrum of conformational relaxation processes. By using the eigenvectors of the transition rate matrix, we are able to systematically coarse-grain the system. We find that a two-state description, with a folded and an unfolded state, roughly captures the slow conformational dynamics. A four-state model, with two folded and two unfolded states, accurately recovers the three slowest relaxation process with time scales between 1.5 and 7 ns. The master equation models not only give access to the slow conformational dynamics but also shed light on the molecular mechanisms of the helix-coil transition.
Speaker-independent vowel recognition: spectrograms versus cochleagrams (2002)

The ability of multilayer perceptrons (MLPs) trained with backpropagation to classify vowels excised from natural continuous speech is examined. Two spectral representations are compared: spectrograms and cochleagrams. The features used to train the MLPs include discrete Fourier transform (DFT) or cochleagram coefficients from a single frame in the middle of the vowel, or coefficients from each third of the vowel. The effects of estimates of pitch, duration, and the relative amplitude of the vowel were investigated. The experiments show that with coefficients alone, the cochleagram is superior to the spectrogram in classification performance for all experimental conditions. With the three additional features, however, the results are comparable. Perceptual experiments with trained human listeners on the same data revealed that MLPs perform much better than humans on vowels excised from context.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A. (1982)

C-peptide, which contains the 13 NH2-terminal residues of RNase A, shows partial helix formation in water at low temperature (1 degree C, pH 5, 0.1 M NaCl), as judged by CD spectra; the helix is formed intramolecularly [Brown, J. E. & Klee, W. A. (1971) Biochemistry 10, 470-476]. We find that helix stability depends strongly on pH: both a protonated histidine (residue 12) and a deprotonated glutamate (residue 9 or 2 or both) are required for optimal stability. This information, together with model building, suggests that the salt bridge Glu-9- ... His-12+ stabilizes the helix. Formation of the helix is enthalpy driven [van't Hoff delta H, - 16Kcal/mol (1 cal = 4.18 J)] and the helix is not observed above 30 degrees C. Proton NMR data indicate that several side chains adopt specific conformations as the helix is formed. These results have two implications for the mechanism of protein folding. First, they indicate that short alpha-helices, stabilized by specific side-chain interactions within the helix, can be stable enough in water to function as folding intermediates. Second, they suggest that similar experiments with peptides of controlled amino acid sequence could be used to catalogue the intrahelix interactions that stabilize or destabilize alpha-helices in aqueous solution. These data might provide the code relating amino acid sequence to the locations of alpha-helices in proteins.
NF-κB Antiapoptosis: Induction of TRAF1 and TRAF2 and c-IAP1 and c-IAP2 to Suppress Caspase-8 Activation (1998)

Tumor necrosis factor alpha (TNF-alpha) binding to the TNF receptor (TNFR) potentially initiates apoptosis and activates the transcription factor nuclear factor kappa B (NF-kappaB), which suppresses apoptosis by an unknown mechanism. The activation of NF-kappaB was found to block the activation of caspase-8. TRAF1 (TNFR-associated factor 1), TRAF2, and the inhibitor-of-apoptosis (IAP) proteins c-IAP1 and c-IAP2 were identified as gene targets of NF-kappaB transcriptional activity. In cells in which NF-kappaB was inactive, all of these proteins were required to fully suppress TNF-induced apoptosis, whereas c-IAP1 and c-IAP2 were sufficient to suppress etoposide-induced apoptosis. Thus, NF-kappaB activates a group of gene products that function cooperatively at the earliest checkpoint to suppress TNF-alpha-mediated apoptosis and that function more distally to suppress genotoxic agent-mediated apoptosis.
Vpu-induced degradation of CD4: requirement for specific amino acid residues in the cytoplasmic domain of CD4 (1993)

Two functions have been attributed to the product of the human immunodeficiency virus type 1 vpu open reading frame: it increases virion release from infected cells and induces rapid degradation of CD4 shortly after its synthesis. In the absence of Vpu, newly synthesized gp160 and CD4 associate in the endoplasmic reticulum (ER), forming a complex whose further maturation is blocked and which is eventually degraded. In studies using NL4-3-based expression vectors, it has been previously shown that Vpu induces the release of gp160 from the complex that it forms with CD4 in the ER. This release, which appears to be due to the rapid degradation of CD4 induced by Vpu, allows gp160 to transit to the Golgi, where it matures further. We investigated which regions of CD4 are important for its susceptibility to Vpu-induced degradation by transfecting HeLa cells with isogenic vpu-positive and vpu-negative proviruses and vectors expressing various truncated or mutated CD4 molecules. The results suggested that the cytoplasmic domain of CD4 contains a determinant lying within amino acids 418 to 425 that is critical for susceptibility to Vpu-induced degradation. Neither the phosphorylation sites in the cytoplasmic domain nor the Lck interaction region was required for the effect. Vpu-induced degradation was specific for CD4, since CD8, even when retained in the ER, was not degraded. In addition, under conditions of high-level Vpu expression, CD4 degradation could be observed in the absence of gp160 or other means of retaining CD4 in the ER.
Efeitos de giberelina e ethephon na anatomia de plantas de cana-de-açúcar (1999)

O presente trabalho teve como finalidade analisar os efeitos da aplicação de giberelina (GA) e do ethephon (CEPA) na anatomia de plantas de cana-de-açúcar. Para o estudo da anatomia de caules e folhas foi realizada pulverização de plantas jovens a partir de sementes. Após 216 dias da semeadura, realizaram-se cortes das folhas +4, da região do nó +10 e dos entrenós +10 e montagem de lâminas permanentes. Observou-se que o tratamento com GA 50 mg L-1 manteve intensa atividade meristemática, havendo contínua formação de feixes vasculares com menor quantidade de fibras de esclerênquima. O GA 50 mg L-1 provocou diminuição em número e tamanho de células buliformes nas folhas +4. Verificou-se que CEPA 1.200 mg L-1, inibiu a atividade meristemática na região do nó +10, reduziu a quantidade de fibras de esclerênquima dos feixes vasculares e aumentou o número de células buliformes.
Glucocorticoid receptor‐mediated reduction of IgG‐fusion protein aggregation in Chinese hamster ovary cells (2010)

Formation of high molecular weight (HMW) species is a common issue encountered during manufacture of protein therapeutics. With advanced purification techniques, efficient removal of protein aggregates is no longer a challenging task, but it is important to minimize protein aggregation level at the culture stage to reduce the downstream burden and improve overall process yield. In this regard, our recent effort on medium optimization has led us to unexpectedly discover that glucocorticoids can significantly reduce the formation of HMW species in IgG-fusion protein produced by CHO cells. First, the effectiveness of dexamethasone can be seen at nanomolar concentrations, which allows this glucocorticoid analog to be a cost-efficient chemical for reducing protein aggregation in cell cultures. Second, this reduction is mediated through glucocorticoid receptors (GR) as it is antagonized by GR antagonist RU486. Third, GR activation upregulates expression of glutathione reductase but not protein disulfide-isomerase, which may help with providing a balanced redox condition in the cells. Last, the beneficial effect of dexamethasone is not limited to one cell line, and it can be repeated in a different cell line, indicating that glucocorticoids are also applicable to other DG44 cell lines for reducing protein aggregation.