gebhart/patrepeval huggingface dataset:
Reconstructing Cortical Dynamics with Magnetoencephalography (2007)

The dynamics of neural information processing are complicated, and determining the sequence and mode of activation is equally important to determining which areas activate. Magnetoencephalography (MEG) and electroencephalography (EEG) noninvasively measure the electromagnetic fields directly generated by neuronal currents in the human brain. The potential to accurately localize these signals has emerged with the advent of dense, whole-head sensor arrays. Adaptive spatial filtering techniques such as beamforming are often used reconstruct the sources of MEG/EEG activity. I have developed extensions to apply beamforming to more experimental paradigms as well as a method for more accurate validation with intracranial EEG.Beamformers poorly resolve brain sources that are strongly correlated temporally with one another, as might be expected for an auditory experiment. I presented a method to reject the contribution of potentially interfering sources in a user-defined suppression region while allowing for source reconstruction at other specified regions. Performance of the algorithm was validated with data from simulations and an auditory MEG experiment.Few methods exist for localizing spectral power changes with MEG. I described a novel method that uses beamformers optimized for time-frequency source reconstruction from MEG data. The performance of the method was demonstrated with simulated sources and was also applied to real MEG data from a finger movement task. Modulations in both the beta band and, importantly, the high gamma band were revealed in sensorimotor cortex and found to be statistically significant across subjects. These results were additionally validated by intracranial EEG data from two epilepsy patients. Another compelling finding was high frequency activity (30-300 Hz) in the cerebellum.Finally, while intracranial recordings are considered the gold standard for validating noninvasive measurements, often electrode locations are not precisely known. One common method, CT-MRI coregistration, may result in a localization error of more than 10 mm. To address this, I developed a procedure to link preoperative MRIs, surgical photographs, and postimplant X-rays with projective transforms.
<p>Thioredoxin-Interacting Protein as a Novel Potential Therapeutic Target in Diabetes Mellitus and Its Underlying Complications</p> (2020)

Diabetes mellitus (DM) is a common metabolic disorder which is characterized by a persistent increment of blood glucose. Globally, DM affects millions of people and the prevalence is increasing alarmingly. The critical step in the pathophysiology of DM is the loss of β-cells of the pancreas, which are responsible for the secretion of insulin. Thioredoxin-interacting protein (TXNIP) is among the factors that control the production and loss of the pancreatic β-cells. TXNIP is an α-arrestin that can bind and inhibit thioredoxin (the antioxidant protein) which is produced in the pancreatic islet after glucose intake. Numerous studies illustrated that elevated TXNIP levels were found to induce β-cell apoptosis; whereas TXNIP deficiency protects against type I and type II diabetes by promoting β-cell survival. Nowadays, TXNIP depletion is becoming a key factor in pancreatic β-cell survival enhancement. In the present review, targeting TXNIP is found to be relevant as a unique therapeutic opportunity, not only to improve insulin secretion and sensitivity, but also ameliorating the long term microvascular and macrovascular complications of the disease. Thus, TXNIP inhibitors that could reduce the expression and/or activity of TXNIP to non-diabetic levels are promising agents to halt the alarming rate of diabetes and its related complications.
A General and Efficient Method for the Site-Specific Dual-Labeling of Proteins for Single Molecule Fluorescence Resonance Energy Transfer (2008)

A general strategy for the site-specific dual-labeling of proteins for single-molecule fluorescence resonance energy transfer is presented. A genetically encoded unnatural ketone amino acid was labeled with a hydroxylamine-containing fluorophore with high yield (>95%) and specificity. This methodology was used to construct dual-labeled T4 lysozyme variants, allowing the study of T4 lysozyme folding at single-molecule resolution. The presented strategy is anticipated to expand the scope of single-molecule protein structure and function studies.
ChemInform Abstract: NEUROLEPTIC ACTIVITY IN 5‐ARYLTETRAHYDRO‐Γ‐CARBOLINES (1980)

Abstract Aus den Hydrazinhydrochloriden (I) erhält man mit dem Piperidinon (II) nach dem Schema der Fischerschen Indolsynthese das heterocyclische System (III).
An Assay to Monitor HIV-1 Protease Activity for the Identification of Novel Inhibitors in T-Cells (2010)

The emergence of resistant HIV strains, together with the severe side-effects of existing drugs and lack of development of effective anti-HIV vaccines highlight the need for novel antivirals, as well as innovative methods to facilitate their discovery. Here, we have developed an assay in T-cells to monitor the proteolytic activity of the HIV-1 protease (PR). The assay is based on the inducible expression of HIV-1 PR fused within the Gal4 DNA-binding and transactivation domains. The fusion protein binds to the Gal4 responsive element and activates the downstream reporter, enhanced green fluorescent protein (eGFP) gene only in the presence of an effective PR Inhibitor (PI). Thus, in this assay, eGFP acts as a biosensor of PR activity, making it ideal for flow cytometry based screening. Furthermore, the assay was developed using retroviral technology in T-cells, thus providing an ideal environment for the screening of potential novel PIs in a cell-type that represents the natural milieu of HIV infection. Clones with the highest sensitivity, and robust, reliable and reproducible reporter activity, were selected. The assay is easily adaptable to other PR variants, a multiplex platform, as well as to high-throughput plate reader based assays and will greatly facilitate the search for novel peptide and chemical compound based PIs in T-cells.
Au-Nanoparticle Nanowires Based on DNA and Polylysine Templates (2002)

A crop of gold circles and lines: Psoralen-functionalized Au nanoparticles incorporated into DNA, and Au-nanoparticle-functionalized poly-L-lysine, yield linear and circular nanowires, respectively, on mica surfaces (see atomic force microscopy images).
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles (2001)

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.
Spin-label studies of the sulfhydryl environment in bovine plasma albumin. 1. The N-F transition and acid expansion (1978)

The environment of the sulfhydryl group in plasma albumin was previously characterized by employing spin-labels of varying chain lengths (Hull, H. H., Chang, R., & Kaplan, L. J. (1975) Biochim. Biophys. Acta 400, 132). It was established that the sulfhydryl is in a crevice approximately 10 A deep but this crevice was not identified further. We now report the results of titrating albumin through the acidic conformational transitions while monitoring the electron-spin resonance of the bound nitroxide. With short spin-labels a general change is observed as the pH is lowered but the N--F transition is not discernible. However, with a spin label previously shown to project to the lip on the crevice a clear N--F transition as well as the subsequent acid expansion are observed. These results indicate that the sulfhydryl is in the crevice, formed by the domains of albumin, which opens during the N--F transition. Further results indicate that bound fatty acids do not influence the integrity of the sulfhydryl environment at neutral pH.
The P, T phase and reaction diagram for elemental carbon, 1979 (1980)

A brief history of the many investigations of the pressure/temperature phase diagrams of elemental carbon is given. The strengths and weaknesses of the various proposed diagrams are discussed, and the areas where additional or better experimental data are needed are pointed out. Many questions still remain about linear solid carbons; about the low‐pressure/high‐temperature solid/liquid/vapor triple point; about the melting line of diamond; about the existence of a high‐pressure metallic phase; and about the existence of two liquid phases, one insulator and the other metallic.
Combined Biomarkers for Early Alzheimer Disease Diagnosis (2007)

Few public health problems have captured the attention of the biomedical and lay communities alike as has Alzheimer Disease (AD). Several questions remain still open in disease management, as the necessity to delineate disease process from "normal ageing". In the last few years, Mild Cognitive Impairment (MCI) has received significant attention, thus it represents the major risk factor for AD. Not all people diagnosed as having MCI, however, will develop AD, hence there is a need to reliably predict progression. To this aim, different biomarkers have been proposed with the attempt to identify MCI people who already have pre-clinical AD. Neuropsychological assessment, peripheral and CSF biomarkers as well as neuroimaging findings (both structural and functional) have reported variable accuracy values, but better results have been obtained by combined biomarker approach. In this review, we summarise the most recent findings on combined biomarkers and their usefulness in clinical practice for the early and preclinical diagnosis of AD.
Electrophysiologic Properties and Antiarrhythmic Actions of a Novel Antianginal Agent (2004)

Ranolazine is a novel antianginal agent capable of producing anti-ischemic effects at plasma concentrations of 2 to 6 microM without a significant reduction of heart rate or blood pressure. This review summarizes the electrophysiologic properties of ranolazine. Ranolazine significantly blocks I(Kr) (IC(50) = 12 microM), late I(Na), late I(Ca), peak I(Ca), I(Na-Ca) (IC(50) = 5.9, 50, 296, and 91 microM, respectively) and I(Ks) (17% at 30 microM), but causes little or no inhibition of I(to) or I(K1). In left ventricular tissue and wedge preparations, ranolazine produces a concentration-dependent prolongation of action potential duration (APD) in epicardium, but abbreviation of APD of M cells, leading to either no change or a reduction in transmural dispersion of repolarization (TDR). The result is a modest prolongation of the QT interval. Prolongation of APD and QT by ranolazine is fundamentally different from that of other drugs that block I(Kr) and induce torsade de pointes in that APD prolongation is rate-independent (ie, does not display reverse rate-dependent prolongation of APD) and is not associated with early after depolarizations, triggered activity, increased spatial dispersion of repolarization, or polymorphic ventricular tachycardia. Torsade de pointes arrhythmias were not observed spontaneously nor could they be induced with programmed electrical stimulation in the presence of ranolazine at concentrations as high as 100 microM. Indeed, ranolazine was found to possess significant antiarrhythmic activity, acting to suppress the arrhythmogenic effects of other QT-prolonging drugs. Ranolazine produces ion channel effects similar to those observed after chronic exposure to amiodarone (reduced late I(Na), I(Kr), I(Ks), and I(Ca)). Ranolazine's actions to reduce TDR and suppress early after depolarization suggest that in addition to its anti-anginal actions, the drug possesses antiarrhythmic activity.
Synthesis, Crystal Structures, Magnetic, and Thermal Properties of Divalent Metal Formate–Formamide Layered Compounds. (2013)

A series of layered divalent metal formate compounds, [M(HCOO)2(HCONH2)2] (M = Mn (1Mn), Ni (2Ni), Cu(3Cu), Zn(4Zn), Mg(5Mg)), have been prepared by solvothermal synthesis and their room temperature (RT) and low-temperature (LT) crystal structures, and thermal and magnetic properties determined. All the compounds contain octahedral metal ions connected by four anti-anti formato ligands to form (4,4) nets with the composition of M(HCOO)2. The oxygen atoms from two coordinating formamide ligands above and below the layer complete the MO6 distorted octahedral coordination. Order-disorder phase transformations involving the formamide ligands were observed in the 1Mn, 2Ni, and 4Zn compounds. Like transitions in related formate structures with perovskite like topology, the transitions correspond to the ordering of the amine groups of the terminating formamide ligands which are disordered at ambient temperature. The magnetic properties of the three magnetic members of the series 1Mn, 2Ni, and 3Cu were investigated using microcrystalline samples, over the temperature range of 2 K-300 K under different applied fields. All compounds belong to antiferromagnetic square lattices with S = 5/2, 1, and 1/2. Exchange constants for a nearest neighbor model are presented here. Specific heat measurements indicate magnetic long-range order at lower temperatures, S = 5/2 (antiferromagnetic) and S = 1 (ferrimagnetic).
Highly Sensitive Detection of Dengue Virus Nucleic Acid in Samples from Clinically Ill Patients (2009)

Dengue virus (DENV) is a major cause of febrile illness and hemorrhagic fever in tropical and subtropical regions. Typically, patients presenting with acute dengue disease are viremic but may not have yet developed detectable titers of antibody. Therefore, early diagnosis depends mostly on detection of viral components, such as the RNA. To define the potential use of transcription-mediated amplification (TMA) DENV RNA as a diagnostic tool, we first compared its analytic sensitivity using a routine real-time reverse transcription (RT)-PCR and found that TMA is approximately 10 to 100 times more sensitive. In addition, we tested acute-phase serum samples (<5 days post-symptom onset) submitted as part of laboratory-based surveillance in Puerto Rico and determined that among patients with serologically confirmed dengue infection, TMA detected DENV RNA in almost 80% of serum specimens that were negative by the RT-PCR test used for diagnosis and in all specimens with positive RT-PCR results. We conclude that TMA is a highly sensitive method which can detect DENV RNA in approximately 89% of clinical, acute-phase serum specimens.
Sex, capacity and forensic cotton wool: IM v LM [2014] EWCA Civ 37 (2014)

The laws governing the sex lives of men and women with intellectual and cognitive disabilities and mental health problems are fraught with difficulty. Sexual activity with a person who lacks the me...
Phosphorylation of serine 59 of p56lck in activated T cells. (1993)

p56lck, a member of the src family of non-receptor protein tyrosine kinases, is expressed almost exclusively in cells of lymphoid origin. Recent evidence has implicated p56lck in a critical role both in T cell development and activation. A variety of T cell stimuli induce a shift in the electrophoretic mobility of p56lck from an apparent molecular mass of 56 kDa (p56lck) to 60 kDa (p60lck). This shift in electrophoretic mobility correlates with an increase in the phosphoserine content of the p60lck. We have shown that both 4 alpha-phorbol 12 beta-myristate acetate and OKT3 treatment of Jurkat cells, as well as 4 alpha-phorbol 12 beta-myristate acetate treatment of 171.CD4 and LSTRA cells, induced phosphorylation of serine-59 on p56lck in vivo, which correlated with the shift to p60lck. We also demonstrated that the same serine residue could be phosphorylated in vitro with mitogen-activated protein kinases and that this event was capable of reducing p56lck activity in vitro. Combined, these data suggest a novel pathway for the in vivo regulation of p56lck activity.
Neuroinflammation mediated by IL-1β increases susceptibility of dopamine neurons to degeneration in an animal model of Parkinson's disease (2008)

These data provide insight into the etiology of PD and support a role for inflammation as a risk factor for the development of neurodegenerative disease.
SP645QUANTITATIVE COMPUTED TOMOGRAPHY RESULTS FOR BONE MASS AND ABDOMINAL AORTIC VASCULAR CALCIFICATION IN HEMODIALYSIS SUBJECTS TREATED WITH ESCALATING DOSE LEVELS OF SOTATERCEPT: INTERIM ANALYSIS OF ACE-011-REN-001 (2015)

• Renal osteodystrophy (ROD) and vascular calcification (VC) are integral components of chronic kidney disease-mineral/bone disorder (CKD-MBD). CKD-MBD is strongly associated with greatly increased morbidity and mortality in end-stage kidney disease (ESKD).1 • Activin A is a transforming growth factor-β superfamily protein that is found at high levels in bone; its signaling is through the type II activin A receptor (ActRIIA).2-4 Inhibin, an inhibitor of activin A signaling, is produced in the ovaries and stimulates bone growth.2,5 Decreased inhibin expression is associated with post-menopausal bone loss.5
Injectable Hyaluronic Acid Gel for Soft Tissue Augmentation (1998)

Stabilized, non-animal, hyaluronic acid gel is well tolerated and effective in augmentation therapy of soft tissues of the face. This material presents several advantages in comparison to previously used injectable biomaterials and expands the arsenal of therapeutic tools in the field of soft tissue augmentation.
Cell Encapsulation Technology and Therapeutics (1999)

excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use of general descriptive names, trade names, trademarks, etc., in this publication, even if the former are not especially identified, is not to be taken as a sign that such names, as understood by the Trade Marks and Merchandise Marks Act, may accordingly be used freely by anyone.
Tunneling spectroscopy using a probe qubit (2013)

We describe a quantum tunneling spectroscopy technique that requires only low-bandwidth control. The method involves coupling a probe qubit to the system under study to create a localized probe state. The energy of the probe state is then scanned with respect to the unperturbed energy levels of the probed system. Incoherent tunneling transitions that flip the state of the probe qubit occur when the energy bias of the probe is close to an eigenenergy of the probed system. Monitoring these transitions allows the reconstruction of the probed system eigenspectrum. We demonstrate this method on an rf SQUID flux qubit.
Conversion of corn fiber to ethanol by recombinant E. coli strain FBR3 (1999)

We have developed a novel ethanologenic Escherichia coli strain FBR3 that is an efficient biocatalyst for converting mixed sugar streams (eg, arabinose, glucose, and xylose) into ethanol. In this report, the strain was tested for conversion of corn fiber hydrolysates into ethanol. Corn fiber hydrolysates with total sugar concentrations of 7.5% (w/v) were prepared by reacting corn fiber with dilute sulfuric acid at 145 degrees C. Initial fermentations of the hydrolysate by strain FBR3 had lag times of approximately 30 h judged by ethanol production. Further experiments indicated that the acetate present in the hydrolysate could not solely account for the long lag. The lag phase was greatly reduced by growing the pre-seed and seed cultures on corn fiber hydrolysate. Ethanol yields for the optimized fermentations were 90% of theoretical. Maximum ethanol concentrations were 2.80% w/v, and the fermentations were completed in approximately 50 h. The optimal pH for the fermentation was 6.5. Below this pH, sugar consumption was incomplete and above it, excess base addition was required throughout the fermentation. Two alternative neutralization methods (overliming and overliming with sulfite addition) have been reported for improving the fermentability of lignocellulosic hydrolysates. These methods further reduced the lag phase of the fermentation, albeit by a minor amount.
Analysis of individual biochemical events based on artificial synapses using ultramicroelectrodes: cellular oxidative burst (2000)

Carbon fiber platinized ultramicroelectrodes placed within micrometres of a single living cell are used to monitor cellular events. This artificial synapse is used here to collect and examine the very nature of the massive oxidative bursts produced by human fibroblasts when their membrane is locally depolarized by a puncture made with a micrometre sized sealed pipette. The electrochemical analysis of the response indicates that oxidative bursts consist of a mixture of a few femtomoles of highly cytotoxic chemicals: hydrogen peroxide, nitrogen monoxide and peroxynitrite, together with nitrite ions, which may result from a partial spontaneous decomposition of peroxynitrite prior to its release by the cell.
Cyclooxygenase‐independent actions of cyclooxygenase inhibitors (2001)

Several studies have demonstrated unequivocally that certain nonsteroidal anti-inflammatory drugs (NSAIDs) such as sodium salicylate, sulindac, ibuprofen, and flurbiprofen cause anti-inflammatory and antiproliferative effects independent of cyclooxygenase activity and prostaglandin synthesis inhibition. These effects are mediated through inhibition of certain transcription factors such as NF-kappaB and AP-1. The respective NSAIDs might interfere directly with the transcription factors, but their effects are probably mediated predominantly through alterations of the activity of cellular kinases such as IKKbeta, Erk, p38 MAPK, or Cdks. These effects apparently are not shared by all NSAIDs, since indomethacin failed to inhibit NF-kappaB and AP-1 activation as well as Erk and Cdk activity. In contrast, indomethacin was able to activate PPARgamma, which was not affected by sodium salicylate or aspirin. The differences in cyclooxygenase-independent mechanisms may have consequences for the specific use of these drugs in individual patients because additional effects may either enhance the efficacy or reduce the toxicity of the respective compounds.
How similar is a molecule to another? An electron density measure of similarity between two molecular structures (1980)

Abstract A matching measure between two molecular structures based on density functions is described. Some examples related with an alarm pheromone activity are given; the results encourage the possible use of similarity density concepts in molecular engineering.
A comparative study of Fas and Fas-ligand expression during melanoma progression (2000)

These results suggest that downregulation of CD95 and upregulation of Fas-L in melanoma might be considered as concomitant with disease progression.