gebhart/patrepeval huggingface dataset:
Role of Oxidative Stress in the Genesis of Atherosclerosis and Diabetes Mellitus: A Personal Look Back on 50 Years of Research (2016)

We have provided an overview, based on the literature and our data. In accordance with the theory of D. Harman free radical processes cause damages that can accumulate and contribute to aging of the organism. Atherosclerosis and diabetes are developing for a long time so they are manifested predominantly in old age. We found an increase in the level of free radical peroxidation products and decrease in the activity of antioxidant enzymes in the tissues of animals with experimental atherosclerosis. Similar changes were found in the blood of patients with atherosclerosis and aortic autopsy material with atherosclerotic lesions. Thus, it was revealed that oxidative stress occured under atherosclerosis, and the arteriosclerosis to "Free Radical Pathologies" was attributed. Later it was discovered by different authors that oxidized Low Density Lipoproteins (LDL) and malonyldialdehyde- modified LDL accumulated during atherogenesis, causing damages of vascular wall. Under diabetic hyperglycemia glucose co-oxidized during free radical lipoperoxidation. This process promoted the transformation of oxidative stress to carbonyl stress with accumulation of biologically active dicarbonyls, including glyoxal and methylglyoxal. We show that the glyoxal-modified LDL were captured by cultured macrophages with a higher efficiency than the MDA-modified LDL. This could facilitate the more rapid development of lipoidosis in the vessel wall (due to the formation of foam cells) and manifestation of atherosclerosis under diabetes. We found that in patients with diabetes there was a sharp decrease in the activity of antioxidant enzymes as a result of the modification of the active center under development of carbonyl stress. We expressed a hypothesis about a common molecular mechanism of vascular wall damages under atherosclerosis and diabetes. Keywords: Atherosclerosis, carbonyl stress, diabetes, free radical peroxidation, oxidized LDL, oxidative stress, reactive oxygen species.
Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy (2004)

Large, living biological specimens present challenges to existing optical imaging techniques because of their absorptive and scattering properties. We developed selective plane illumination microscopy (SPIM) to generate multidimensional images of samples up to a few millimeters in size. The system combines two-dimensional illumination with orthogonal camera-based detection to achieve high-resolution, optically sectioned imaging throughout the sample, with minimal photodamage and at speeds capable of capturing transient biological phenomena. We used SPIM to visualize all muscles in vivo in the transgenic Medaka line Arnie, which expresses green fluorescent protein in muscle tissue. We also demonstrate that SPIM can be applied to visualize the embryogenesis of the relatively opaque Drosophila melanogaster in vivo.
Daily bilateral pudendal nerve electrical stimulation improves recovery from stress urinary incontinence (2019)

Stress urinary incontinence (SUI) in women is strongly associated with childbirth which injures the pudendal nerve (PN) and the external urethral sphincter (EUS) during delivery. Electrical stimulation (ES) can increase brain-derived neurotrophic factor (BDNF) expression in injured neurons, activate Schwann cells and promote neuroregeneration after nerve injury. The aim of this study was to determine if more frequent ES would increase recovery from SUI in a rat model. Forty female Sprague-Dawley rats underwent either sham injury or pudendal nerve crush (PNC) and vaginal distention (VD) to establish SUI. Immediately after injury, electrodes were implanted at the pudendal nerve bilaterally. Each injured animal underwent sham ES, twice per week ES (2/week), or daily ES of 1 h duration for two weeks. Urethral and nerve function were assessed with leak point pressure (LPP), EUS electromyography and pudendal nerve sensory branch potential (PNSBP) recordings two weeks after injury. LPP was significantly increased after daily ES compared to 2/week ES. EUS neuromuscular junction innervation was decreased after injury with sham ES, but improved after 2/week or daily ES. This study demonstrates that daily bilateral ES to the pudendal nerve can accelerate recovery from SUI. Daily ES improved urethral function more than 2/week ES.
Thienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucomaJohn J. Baldwin, Gerald S. Ponticello, Paul S. Anderson, Marcia E. Christy, Mark A. Murcko, William C. Randall, Harvey Schwam, Michael F. Sugrue, Pierre Gautheron, and Cite this: J. Med. Chem. 1989, 32, 12, 2510–2513Publication Date (Print):December 1, 1989Publication History Published online1 May 2002Published inissue 1 December 1989https://pubs.acs.org/doi/10.1021/jm00132a003https://doi.org/10.1021/jm00132a003research-articleACS PublicationsRequest reuse permissionsArticle Views904Altmetric-Citations162LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Z-Forcing: Training Stochastic Recurrent Networks (2017)

Many efforts have been devoted to training generative latent variable models with autoregressive decoders, such as recurrent neural networks (RNN). Stochastic recurrent models have been successful in capturing the variability observed in natural sequential data such as speech. We unify successful ideas from recently proposed architectures into a stochastic recurrent model: each step in the sequence is associated with a latent variable that is used to condition the recurrent dynamics for future steps. Training is performed with amortized variational inference where the approximate posterior is augmented with a RNN that runs backward through the sequence. In addition to maximizing the variational lower bound, we ease training of the latent variables by adding an auxiliary cost which forces them to reconstruct the state of the backward recurrent network. This provides the latent variables with a task-independent objective that enhances the performance of the overall model. We found this strategy to perform better than alternative approaches such as KL annealing. Although being conceptually simple, our model achieves state-of-the-art results on standard speech benchmarks such as TIMIT and Blizzard and competitive performance on sequential MNIST. Finally, we apply our model to language modeling on the IMDB dataset where the auxiliary cost helps in learning interpretable latent variables. Source Code: \url{https://github.com/anirudh9119/zforcing_nips17}
Synucleins are developmentally expressed, and alpha-synuclein regulates the size of the presynaptic vesicular pool in primary hippocampal neurons. (2000)

alpha-, beta-, and gamma-Synuclein, a novel family of neuronal proteins, has become the focus of research interest because alpha-synuclein has been increasingly implicated in the pathogenesis of Parkinson's and Alzheimer's disease. However, the normal functions of the synucleins are still unknown. For this reason, we characterized alpha-, beta-, and gamma-synuclein expression in primary hippocampal neuronal cultures and showed that the onset of alpha- and beta-synuclein expression was delayed after synaptic development, suggesting that these synucleins may not be essential for synapse formation. In mature cultured primary neurons, alpha- and beta-synuclein colocalized almost exclusively with synaptophysin in the presynaptic terminal, whereas little gamma-synuclein was expressed at all. To assess the function of alpha-synuclein, we suppressed expression of this protein with antisense oligonucleotide technology. Morphometric ultrastructural analysis of the alpha-synuclein antisense oligonucleotide-treated cultures revealed a significant reduction in the distal pool of synaptic vesicles. These data suggest that one function of alpha-synuclein may be to regulate the size of distinct pools of synaptic vesicles in mature neurons.
A dynamic body discharge technique for SOI circuit applications (2003)

It has been reported (Kuang et al., 1997; Lu et al., 1997) that SOI passgate circuits suffer history effects and adverse initial-cycle parasitic bipolar currents, which cause difficulties in circuit timing and limit direct design reuse from original bulk circuits. SOI device body history can also induce transfer characteristics mismatch in dual-railed static or dynamic CMOS circuits, resulting in speed degradation or functional failures. This paper describes an efficient technique to alleviate initial-cycle bipolar currents while retaining the low-V/sub t/ floating body feature when the SOI devices concerned are on. We also present a dynamic body discharge technique to eliminate the mismatch problems in cross-coupled SOI CMOS topologies, for use in a variety of circuit families such as cascade voltage switch logic, latch-type sense amplifiers and analog operational amplifiers.
Independent Components of Magnetoencephalography: Localization (2002)

We applied second-order blind identification (SOBI), an independent component analysis method, to MEG data collected during cognitive tasks. We explored SOBI's ability to help isolate underlying neuronal sources with relatively poor signal-to-noise ratios, allowing their identification and localization. We compare localization of the SOBI-separated components to localization from unprocessed sensor signals, using an equivalent current dipole modeling method. For visual and somatosensory modalities, SOBI preprocessing resulted in components that can be localized to physiologically and anatomically meaningful locations. Furthermore, this preprocessing allowed the detection of neuronal source activations that were otherwise undetectable. This increased probability of neuronal source detection and localization can be particularly beneficial for MEG studies of higher-level cognitive functions, which often have greater signal variability and degraded signal-to-noise ratios than sensory activation tasks.
Bayesian on-line learning of driving behaviors (2011)

This paper presents a novel self-supervised online learning method to discover driving behaviors from data acquired with an inertial measurement unit (IMU) and a camera. Both sensors where mounted in a car that was driven by a human through a typical city environment with intersections, pedestrian crossings and traffic lights. The presented system extracts motion segments from the IMU data and relates them to visual cues obtained from camera data. It employs a Bayesian on-line estimation method to discover the motion segments based on change-point detection and uses a Dirichlet Compound Multinomial (DCM) model to represent the visual features extracted from the camera images. By incorporating these visual cues into the on-line estimation process, labels are computed that are equal for similar motion segments. As a result, typical traffic situations such as braking maneuvers in front of a red light can be identified automatically. Furthermore, appropriate actions in form of observed motion changes are associated to the discovered traffic situations. The approach is evaluated on a real data set acquired in the center of Zurich.
An Integrated System for Simultaneous, Multichannel Neuronal Stimulation and Recording (2007)

Precision electronics that provide multi-electrode stimulation and recording capabilities are an important tool for the experimental study of neuronal development and plasticity. Towards this end, we present a custom analog integrated circuit (IC), fabricated in a 0.35-mum process, incorporating stimulation buffers and recording preamplifiers for multiple electrodes onto a single die. The architecture of the IC allows for arbitrary, independent configuration of electrodes for stimulation or recording, and the IC includes artifact-elimination circuitry that returns the stimulation electrode to its previous voltage following stimulation, minimizing the interference with recording. We analyze the thermal noise levels in the recording preamplifiers and experimentally measure input-referred noise as low as 4.77 muV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> in the frequency range of 30 Hz-3 kHz at a power consumption of 100 muW from a total power supply of 3.8 V. We also consider the temporal response and stability of the artifact elimination circuitry. We demonstrate that the use of the artifact-elimination circuitry with a 30-mum diameter stimulation electrode permits a return to recording mode in les 2 ms after stimulation, facilitating near-simultaneous stimulation and recording of neuronal signals. (Patent applied for, U.S. No. 2007/0178579.)
Modified mRNA/lipid nanoparticle-based vaccines expressing respiratory syncytial virus F protein variants are immunogenic and protective in rodent models of RSV infection (2020)

The RSV Fusion (F) protein is a target for neutralizing antibody responses and is a focus for vaccine discovery; however, the process of RSV entry requires F to adopt a metastable prefusion form and transition to a more stable postfusion form, which displays less potent neutralizing epitopes. mRNA vaccines encode antigens that are translated by host cells following vaccination, which may allow conformational transitions similar to those observed during natural infection to occur. Here we evaluate a panel of chemically modified mRNA vaccines expressing different forms of the RSV F protein, including secreted, membrane associated, prefusion-stabilized, and non-stabilized structures, for conformation, immunogenicity, protection, and safety in rodent models. Vaccination with mRNA encoding native RSV F elicited antibody responses to both prefusion- and postfusion-specific epitopes, suggesting that this antigen may adopt both conformations in vivo. Incorporating prefusion stabilizing mutations further shifts the immune response toward prefusion-specific epitopes, but does not impact neutralizing antibody titer. mRNA vaccine candidates expressing either prefusion stabilized or native forms of RSV F protein elicit robust neutralizing antibody responses in both mice and cotton rats, similar to levels observed with a comparable dose of adjuvanted prefusion stabilized RSV F protein. In contrast to the protein subunit vaccine, mRNA-based vaccines elicited robust CD4+ and CD8+ T-cell responses in mice, highlighting a potential advantage of the technology for vaccines requiring a cellular immune response for efficacy.
Improvement of Western Blot Test Specificity for Detecting Equine Serum Antibodies to Sarcocystis Neurona (2000)

Equine protozoal myeloencephalitis (EPM) is a neurological disease of horses and ponies caused by the apicomplexan protozoan parasite Sarcocystis neurona. The purposes of this study were to develop the most stringent criteria possible for a positive test result, to estimate the sensitivity and specificity of the EPM Western blot antibody test, and to assess the ability of bovine antibodies to Sarcocystis cruzi to act as a blocking agent to minimize false-positive results in the western blot test for S. neurona. Sarcocystis neurona merozoites harvested from equine dermal cell culture were heat denatured, and the proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in a 12-20% linear gradient gel. Separated proteins were electrophoretically transferred to polyvinylidene fluoride membranes and blocked in 1% bovine serum albumin and 0.5% Tween-Tris-buffered saline. Serum samples from 6 horses with S. neurona infections (confirmed by culture from neural tissue) and 57 horses without infections (horses from the Eastern Hemisphere, where S. neurona does not exist) were tested by Western blot. Horses from both groups had reactivity to the 62-, 30-, 16-, 13-, 11-, 10.5-, and 10-kD bands. Testing was repeated with another step. Blots were treated with bovine S. cruzi antibodies prior to loading the equine samples. After this modification of the Western blot test, positive infection status was significantly associated with reactivity to the 30- and 16-kD bands (P<0.001, Fisher's exact test). The S. cruzi antibody-blocked Western blot had a sample sensitivity of 100% and sample specificity of 98%. It is concluded that the specificity of the Western blot test is improved by blocking proteins not specific to S. neurona and using reactivity to the 30- and 16-kD bands as the criterion for a positive test.
Single nucleotide polymorphisms and risk of hepatocellular carcinoma in cirrhosis (2012)

Liver carcinogenesis is a complex and multi-factorial process, in which both environmental and genetic features interfere and contribute to malignant transformation. Patients with cirrhosis are particularly exposed and justify periodical screenings in order to detect the early development of hepatocellular carcinoma (HCC). The risk of HCC is, however, not identical from one patient to another. The identification of host factors that may also play an important role in HCC development may improve our understanding of the implications of the various biological pathways involved in liver carcinogenesis; such progress may as well help refine the selection of patients who could benefit from specific preventative measures or could be given adapted screening policies. Numerous candidate-gene studies have reported associations between single nucleotide polymorphisms (SNPs) and the presence of HCC. Some of these publications unfortunately suffer from major methodological drawbacks because of their case-control, retrospective and monocentric aspect. Prospective cohort studies conducted in large homogeneous populations and comprising a sufficient number of events during follow-up may overcome these pitfalls, but require a long time to be conducted and are still scarce. More recently, the first Genome Wide Association studies (GWAs) have enabled the identification of unsuspected loci that may be involved in various steps implicated in liver tumourigenesis. Taken together, these studies highlight variants that modulate oxidative stress, iron metabolism, inflammatory and immune responses, DNA repair mechanisms or systems involved in cell-cycle regulation as genetic traits susceptible to modify the natural history of cirrhotic patients and partly explain the observed differences in the risk of HCC occurrence. However, large genetic epidemiology studies in the field of cancer diseases have suggested the limited ability of polymorphic traits, alone, to refine individual prognosis. The integration of various panels of genes into clinical scores may in the near future define a "genomic risk prediction" specific to liver cancer developed in cirrhotic patients.
Linear Superclusters of Colloidal Gold Particles by Electrostatic Assembly on DNA Templates (2001)

The organization of nanoparticles into superstructures of predefined geometry is an important challenge in the area of nanoscale architecture. Attractive Coulombic interaction between positively charged amine groups on gold particle surfaces and negatively charged phosphate backbones of DNA molecules (see Figure) drives the self-assembly of gold nanoparticles into linear supercluster structures.
Conservation of the C5a peptidase genes in group A and B streptococci (1996)

The chromosome of group B streptococci (GBS) contains a gene which is related to the C5a peptidase gene (scpA) of group A streptococci (GAS). scpA encodes a surface-associated peptidase (group A streptococcal C5a peptidase [SCPA]) which specifically cleaves C5a, a major chemoattractant generated in serum by activation of complement. The entire scpA-like gene (scpB) was cloned from a GBS strain and sequenced. The gene encodes an open reading frame of 3,450 bp, which corresponds to a deduced protein (SCPB) of 1,150 amino acids with a molecular weight of 126,237 Da. Nucleotide and deduced amino acid sequences of SCPB were found to be highly homologous to those of SCPAs from GAS. Unexpectedly, scpA12 is more similar to scpB than to another GAS gene, scpA49. The sequence 5' of the open reading frame, including transcription start and a termination site in the signal sequence, is also similar to that of scpA, although less conserved than the coding sequences. The near identity of GBS and GAS peptidases is consistent with horizontal transmission of the scp gene between these species. Recombinant SCPB was expressed in Escherichia coli by using the expression vector plasmid pGEX-4T-1 and was shown to be identical in size to the enzyme extracted from the parental GBS strain 78-471.
Serum CYFRA 21-1 (cytokeratin-19 fragments) is a useful tumour marker for detecting disease relapse and assessing treatment efficacy in breast cancer (2004)

The usefulness of serum CYFRA 21-1 (cytokeratin-19 fragments) in monitoring the recurrence of breast cancer and in evaluating therapeutic effects was studied retrospectively. The sera from 173 patients with primary breast cancer or recurrent disease were measured for CYFRA 21-1, carcinoembryonic antigen (CEA), and carbohydrate antigen 15-3 (CA 15-3) levels. The positive rates of serum CYFRA 21-1 for stage IV (n=12) or recurrent disease (n=26) were 83.3 and 84.6%, respectively, while those of serum CEA were 41.7 and 26.9%, and those of serum CA 15-3 were 83.3 and 34.6%. The elevated preoperative levels of serum CYFRA 21-1 decreased to normal levels after curative operation, whereas the levels remained abnormally high after noncurative operation. There was a significantly high frequency of recurrence in patients with elevated levels of serum CYFRA 21-1 preoperatively compared to those with normal levels of the marker preoperatively. The serum CYFRA 21-1 levels were well correlated with response to chemotherapy. The positive rate of serum CYFRA 21-1 alone was higher than that of an assay combining CEA with CA 15-3, in both primary and recurrent cases (28.8 vs 18.8 and 84.6 vs 46.2%, respectively). These observations suggest that serum CYFRA 21-1 may be a reliable marker of recurrence or therapeutic efficacy.
Experiences with GroupLens: marking usenet useful again (1997)

Collaborative filetering attempts to alleviate information overload by offering recommendations on whether information is valuable based on the opinions of those who have already evaluated it. Usenet news is an information source whose value is being severely diminished by the volume of low-quality and uninteresting information posted in its newsgroups. The GroupLens system applies collaborative filtering to Usenet news to demonstrate how we can restore the value of Usenet news by sharing our judgements of articles, with our identities protected by pseudonyms.

This paper extends the original GroupLens work by reporting on a significantly enhanced system and the results of a seven week trial with 250 users and over 20,000 news articles. GroupLens has an open and flexible architecture that allows easy integration of new newsreader clients and ratings bureaus. We show ratings and prediction profiles for three news-groups, and assess the accuracy of the predictions.