gebhart/patrepeval huggingface dataset:
Hippocampal lesions that abolish spatial maze performance spare object recognition memory at delays of up to 48 hours (2004)

The hippocampus is widely considered to be a critical component of a medial temporal lobe memory system, necessary for normal performance on tests of declarative memory. Object recognition memory is thought to be a classic test of declarative memory function. However, previous tests of the effects of hippocampal lesions on object recognition memory have not always supported this view. One possible reason for this inconsistency is that previously reported effects of hippocampal lesions on object recognition memory tasks may have stemmed not from a deficit in object recognition memory per se, but as a result of spatial and contextual confounds in the task. Thus, in the present study, we used a spontaneous object recognition test in a modified apparatus designed to minimize spatial and contextual factors. A group of rats with complete excitotoxic lesions of the hippocampus and a group of control rats were tested on this modified spontaneous object recognition task with retention delays of up to 48 h. These rats were also tested on a spatial nonmatching-to-place task. Spatial memory performance was abolished following hippocampal lesions, whereas performance on the recognition memory task was intact at all delays tested.
Estrogen suppression of connective tissue deposition in a murine model of peritoneal adhesion formation (1996)

Estrogen's involvement in inflammation and wound healing is poorly understood. To examine the role of estrogen in peritoneal adhesion formation, we gave ovariectomized female C57BL/6 mice time-release pellets containing placebo, 0.05 mg 17 beta-estradiol (low E2), or 5 mg 17 beta-estradiol (high E2) before i.p. injection of talc in saline or saline alone. Analyses of abdominal wall connective tissue thickness and peritoneal cell populations were performed. Talc-treated mice receiving low and high E2 replacement had a decreased amount of abdominal connective tissue deposition (29% and 65% decrease, respectively) as compared with talc-treated mice receiving placebo pellets. At high E2 replacement, the difference in connective tissue deposition was significant statistically (p less than 0.01). Immunohistochemical analysis revealed that the number of macrophages in adhesion tissue was proportionate to the amount of connective tissue present, regardless of the circulating levels of E2. Northern blot analysis of abdominal wall tissue showed that five of six talc-treated animals given placebo expressed mRNA for the murine monocyte chemoattractant protein-1 (MCP-1), JE. Conversely, only one of five talc-treated animals that received E2 replacement expressed JE/MCP-1 mRNA, suggesting that the hormone may inhibit connective tissue deposition by altering the production of chemotactic factors. Furthermore, E2 suppressed talc-induced expression of JE/MCP-1 mRNA in murine macrophages. Since macrophages play a central role in the wound healing process, these studies suggest that E2 inhibition of adhesion formation could be mediated by suppressing macrophage activation and/or recruitment to inflammatory sites.
Early detection of neurodegenerative diseases (2012)

Keywords: : microRNAmild cognitive impairment (MCI)Alzheimer diseaseneurodegenerationagingbrainsynapseneurite
Airborne Particulate Matter and Human Health: A Review (2005)

Results of recent research show that particulate matter (PM) composition and size vary widely with both space and time. Despite the variability in PM characteristics, which are believed to influence human health risks, the observed relative health risk estimates per unit PM mass falls within a narrow range of values. Furthermore, no single chemical species appears to dominate health effects; rather the effects appear to be due to a combination of species. Non-PM factors such as socioeconomic status and lifestyle are also believed to affect the health risk, although accounting for these confounding factors is challenging. Airborne PM is also responsible for a number of effects aside from human health, such as alterations in visibility and climate. Because the PM problem is associated with a range of societal issues such as energy production and economic development, making progress on reducing the effects of PM will require integrated strategies that bring together scientists and decision makers from different disciplines to consider tradeoffs holistically.
Determining Antigen Specificity of Human Islet Infiltrating T Cells in Type 1 Diabetes (2019)

Type 1 diabetes, the immune mediated form of diabetes, represents a prototypical organ specific autoimmune disease in that insulin producing pancreatic islets are specifically targeted by T cells. The disease is now predictable in humans with the measurement of type 1 diabetes associated autoantibodies (islet autoantibodies) in the peripheral blood which are directed against insulin and beta cell proteins. With an increasing incidence of disease, especially in young children, large well-controlled clinical prevention trials using antigen specific immunotherapy have been completed but with limited clinical benefit. To improve outcomes, it is critical to understand the antigen and T cell receptor repertoires of those cells that infiltrate the target organ, pancreatic islets, in human type 1 diabetes. With international networks to identify organ donors with type 1 diabetes, improved immunosequencing platforms, and the ability to reconstitute T cell receptors of interest into immortalized cell lines allows antigen discovery efforts for rare tissue specific T cells. Here we review the disease pathogenesis of type 1 diabetes with a focus on human islet infiltrating T cell antigen discovery efforts, which provides necessary knowledge to define biomarkers of disease activity and improve antigen specific immunotherapy approaches for disease prevention.
Microphone Arrays : A Tutorial (2001)

This report presents a tutorial of fundamental array processing and beamforming theory relevant to microphone array speech processing. A microphone array consists of multiple microphones placed at different spatial locations. Built upon a knowledge of sound propagation principles, the multiple inputs can be manipulated to enhance or attenuate signals emanating from particular directions. In this way, microphone arrays provide a means of enhancing a desired signal in the presence of corrupting noise sources. Moreover, this enhancement is based purely on knowledge of the source location, and so microphone array techniques are applicable to a wide variety of noise types. Microphone arrays have great potential in practical applications of speech processing, due to their ability to provide both noise robustness and hands-free signal acquisition. This report has been extracted from my PhD thesis, and can be referenced as:
Putting its fingers on stressful situations: the heavy metal‐regulatory transcription factor MTF‐1 (2001)

It has been suggested that metallothioneins, discovered about 45 years ago, play a central role in heavy metal metabolism and detoxification, and in the management of various forms of stress. The metal-regulatory transcription factor-1 (MTF-1) was shown to be essential for basal and heavy metal-induced transcription of the stress-responsive metallothionein-I and metallothionein-II. Recently it has become obvious that MTF-1 has further roles in the transcriptional regulation of genes induced by various stressors and might even contribute to some aspects of malignant cell growth. Furthermore, MTF-1 is an essential gene, as mice null-mutant for MTF-1 die in utero due to liver degeneration. We describe here the state of knowledge on the complex activation of MTF-1, and propose a model with MTF-1 as an interconnected cellular stress-sensor protein involved in heavy metal metabolism, hepatocyte differentiation and detoxification of toxic agents.
Magnetic Field-Assisted Gene Delivery: Achievements and Therapeutic Potential (2012)

The discovery in the early 2000's that magnetic nanoparticles (MNPs) complexed to nonviral or viral vectors can, in the presence of an external magnetic field, greatly enhance gene transfer into cells has raised much interest. This technique, called magnetofection, was initially developed mainly to improve gene transfer in cell cultures, a simpler and more easily controllable scenario than in vivo models. These studies provided evidence for some unique capabilities of magnetofection. Progressively, the interest in magnetofection expanded to its application in animal models and led to the association of this technique with another technology, magnetic drug targeting (MDT). This combination offers the possibility to develop more efficient and less invasive gene therapy strategies for a number of major pathologies like cancer, neurodegeneration and myocardial infarction. The goal of MDT is to concentrate MNPs functionalized with therapeutic drugs, in target areas of the body by means of properly focused external magnetic fields. The availability of stable, nontoxic MNP-gene vector complexes now offers the opportunity to develop magnetic gene targeting (MGT), a variant of MDT in which the gene coding for a therapeutic molecule, rather than the molecule itself, is delivered to a therapeutic target area in the body. This article will first outline the principle of magnetofection, subsequently describing the properties of the magnetic fields and MNPs used in this technique. Next, it will review the results achieved by magnetofection in cell cultures. Last, the potential of MGT for implementing minimally invasive gene therapy will be discussed.
Internet search behavior as an economic forecasting tool: The case of inflation expectations (2011)

This paper proposes a measure of real-time inflation expectations based on metadata, i.e., data about data, constructed from internet search queries performed on the search engine Google. The forecasting performance of the Google Inflation Search Index (GISI) is assessed relative to 37 other indicators of inflation expectations – 36 survey measures and the TIPS spread. For decades, the academic literature has focused on three measures of inflation expectations: the Livingston Survey, Survey of Professional Forecasters, and the Michigan Survey. While useful in developing models of forecasting inflation, these low frequency measures appear anachronistic in the modern era of higher frequency and real-time data. I demonstrate that higher frequency measures tend to outperform lower frequency measures in tests of accuracy, predictive power, and rationality. Furthermore, Granger Causality tests indicate that the GISI metadata indicator anticipates the inflation rate by 12 months, and out-of-sample forecasts show that the GISI has the lowest forecast error of all the inflation expectations indicators tested.
WebNC: efficient sharing of web applications (2009)

WebNC is a system for efficiently sharing, retrieving and viewing web applications. Unlike existing screencasting and screensharing tools, WebNC is optimized to work with web pages where a lot of scrolling happens. WebNC uses a tile-based encoding to capture, transmit and deliver web applications, and relies only on dynamic HTML and JavaScript. The resulting webcasts require very little bandwidth and are viewable on any modern web browser including Firefox and Internet Explorer as well as browsers on the iPhone and Android platforms.
In VINI veritas (2006)

This paper describes VINI , a virtual network infrastructure that allows network researchers to evaluate their protocols and services in a realistic environment that also provides a high degree of control over network conditions. VINI allows researchers to deploy and evaluate their ideas with real routing software, traffic loads, and network events. To provide researchers flexibility in designing their experiments, VINI supports simultaneous experiments with arbitrary network topologies on a shared physical infrastructure. This paper tackles the following important design question: What set of concepts and techniques facilitate flexible, realistic, and controlled experimentation ( e.g. , multiple topologies and the ability to tweak routing algorithms) on a fixed physical infrastructure? We first present VINI's high-level design and the challenges of virtualizing a single network. We then present PL-VINI , an implementation of VINI on PlanetLab, running the "Internet In a Slice". Our evaluation of PL-VINI shows that it provides a realistic and controlled environment for evaluating new protocols and services.
Pressure induced magnetic, electronic and mechanical properties of SmX (X = Se, Te) (2009)

The magnetic, structural, elastic and electronic properties of Sm-chalcogenides in the stable [Formula: see text] and high pressure [Formula: see text] phase have been analyzed using an ab initio pseudo-potential method with a spin-polarized GGA based on exchange-correlation energy optimization, as implemented in SIESTA code. The magnetic phase stability has been determined from the total energy calculations in non-magnetic and magnetic phases, which clearly indicate that at ambient and high pressures, these compounds are ferromagnetically stable. Also, the Sm ion is described in both five and six localized f electrons. Under compression the Sm chalcogenides undergo a first-order transformation from Sm(2+) to a stable valence state (Sm(3+)) with delocalization of the 4f electrons into the 5d states of Sm followed by a structural transition from the B1 to the B2 phase. The structural properties namely, equilibrium lattice constant, bulk modulus, its pressure derivative, transition pressure and volume collapse agree well with the experimental results. We have also computed the electronic structure at different volumes.
Sumoylation of the P Protein at K254 Plays an Important Role in Growth of Parainfluenza Virus 5 (2011)

The P protein of parainfluenza virus 5 (PIV5) is an essential cofactor of the viral RNA-dependent RNA polymerase. Phosphorylation of the P protein can positively or negatively regulate viral gene expression, depending on the precise phosphorylation sites. Sumoylation, a process of adding small ubiquitin-like modifier (SUMO) to proteins posttranslationally, plays an important role in regulating protein function. In this study, we have found that the P protein of PIV5 was sumoylated with SUMO1 in both transfected and infected cells. The K254 residue of the P protein is within a consensus sumoylation motif. Mutation of the P protein at K254 to arginine (P-K254R) reduced PIV5 minigenome activity, as well as the sumoylation level of the P protein. Incorporation of K254R into a recombinant PIV5 (rPIV5-P-K254R) resulted in a virus that grew to a lower titer and had lower levels of viral RNA synthesis and protein expression than wild-type PIV5, suggesting that sumoylation of the P protein at K254 is important for PIV5 growth. Biochemical studies did not reveal any defect of P-K254R in its interactions with viral proteins NP and L or formation of homotetramers. We propose that sumoylation of the P protein at K254 regulates PIV5 gene expression through a host protein.
High-Efficiency FLP and ΦC31 Site-Specific Recombination in Mammalian Cells (2007)

DNA site-specific recombinases (SSRs) such as Cre, FLPe, and phiC31, are powerful tools for analyzing gene function in vertebrates. While the availability of multiple high-efficiency SSRs would facilitate a wide array of genomic engineering possibilities, efficient recombination in mammalian cells has only been observed with Cre recombinase. Here we report the de novo synthesis of mouse codon-optimized FLP (FLPo) and PhiC31 (PhiC31o) SSRs, which result in recombination efficiencies similar to Cre.
Single-bubble and multibubble cavitation in water triggered by laser-driven focusing shock waves (2018)

In this study a single laser pulse spatially shaped into a ring is focused into a thin water layer, creating an annular cavitation bubble and cylindrical shock waves: an outer shock that diverges away from the excitation laser ring and an inner shock that focuses towards the center. A few nanoseconds after the converging shock reaches the focus and diverges away from the center, a single bubble nucleates at the center. The inner diverging shock then reaches the surface of the annular laser-induced bubble and reflects at the boundary, initiating nucleation of a tertiary bubble cloud. In the present experiments, we have performed time-resolved imaging of shock propagation and bubble wall motion. Our experimental observations of single-bubble cavitation and collapse and appearance of ring-shaped bubble clouds are consistent with our numerical simulations that solve a one-dimensional Euler equation in cylindrical coordinates. The numerical results agree qualitatively with the experimental observations of the appearance and growth of large bubble clouds at the smallest laser excitation rings. Our technique of shock-driven bubble cavitation opens interesting perspectives for the investigation of shock-induced single-bubble or multibubble cavitation phenomena in thin liquids.
Fine Chemical Manipulations of Microscopic Liquid Samples. 1. Droplet Loading with Chemicals (1999)

Physically and chemically stable microscopic aqueous droplets of nano-, pico-, and femtoliter volumes were made and kept under heptane. Such droplets can contain chemicals of interest in pico-, femto-, and attomole amounts or less. Their fine chemical manipulation was achieved by a diffusional microburet (DMB), which consists of a pulled glass capillary whose microscopic tip is filled with a tiny diffusion membrane of agar or polyacrylamide gel. Once this tip is moved into a target droplet by a fine micromanipulator under a microscope, diffusional reagent delivery from the DMB body begins, driven by the concentration gradient within the tip. This system was tested in this work by delivering an inert fluorescent dye, Lucifer Yellow CH, into buffer droplets while fluorescence intensity in each droplet was recorded. An exponential decay of delivery rate was observed corresponding to an exponential saturation process for the accumulation of the delivered chemical inside the target droplet.
Interactions of T Cells with Fibroblast-Like Synoviocytes: Role of the B7 Family Costimulatory Ligand B7-H3 (2008)

Fibroblast-like synoviocytes (FLS) and T cells can activate each other in vitro, and in vivo interactions between these cells may be important in rheumatoid arthritis (RA), yet FLS lack significant expression of CD28 ligands. We sought to identify molecules homologous to CD28 ligands that are strongly expressed by FLS, and documented strong B7-H3 expression on FLS and by fibroblasts of other tissues, which was unaffected by a variety of cytokines. Western blot analysis of FLS lysates showed predominant expression of the larger, four Ig-like domain isoform of B7-H3. Immunohistological sections of RA synovial tissue showed strong staining for B7-H3 on FLS. Cells expressing B7-H3 were distinct from but in close proximity to cells that expressed CD45, CD20, and CD3. Confocal microscopy of FLS and T cell cocultures showed localization of B7-H3 in the region of the T cell-FLS contact point, but distinct from the localization of T cell CD11a/CD18 (LFA-1) and FLS CD54 (ICAM-1). Reduction of B7-H3 expression on FLS by RNA interference affected interactions of FLS with resting T cells or cytokine-activated T cells. Resting T cells showed increased production of TNF-alpha, IFN-gamma, and IL-2, whereas cytokine-activated T cells showed reduced cytokine production relative to control. However, cytokine production by T cells activated through their TCR was not notably altered by knock down of B7-H3. These observations suggest that B7-H3 may be important for the interactions between FLS and T cells in RA, as well as other diseases, and the outcome of such interactions depends on the activation state of the T cell.
Involvement of RNA and DNA in the staining of Escherichia coli by SYTO 13 (2002)

The results confirm the efficacy of SYTO 13 for labelling bacteria and for assessing the distinct physiological status. A better knowledge of the parameters implicated in its fluorescence emission has been achieved.
Bench-to-bedside review: the role of nitric oxide in sepsis (2009)

Sepsis is a state of systemic inflammation directed at microbes or their toxins in blood or tissues. Nitric oxide (NO) is one of many vasoactive molecules released from a variety of cell types during sepsis. Almost two decades ago, NO emerged as a potential therapeutic target in sepsis. NO produced by the constitutive NO synthase (NOS) isoform (endothelial NOS and neuronal NOS) in the vascular endothelium and elsewhere acts as a nonadrenergic, noncholinergic neurotransmitter, an inhibitor of platelet aggregation and a vasodilator. During sepsis, activation of inducible NOS (iNOS) in the lung epithelium and other organs occurs, leading to NO overproduction. The result of excessive circulating NO is enhanced bacterial destruction, but also profound vasodilatation, activation of inflammatory cascades and depression of cardiac function. Trials of nonselective NOS inhibitors have shown increased mean arterial pressure, but also increased pulmonary artery pressure and reduced cardiac output. Small animal studies of iNOS selective inhibition have produced dichotomous results, but larger clinical studies assessing mortality are lacking. Inhaled NO has been touted as a therapeutic option to improve systemic oxygenation in the acute lung injury of sepsis (hypoxic pulmonary vasoconstriction and pulmonary hypertension); however, studies of inhaled NO in acute respiratory distress syndrome have not shown survival efficacy. Further investigation into the role of NO in human sepsis, and the development of methods to assess NO balance in patients with sepsis is essential in this field. In this review, we outline the effects of NO in sepsis, and summarize the therapeutic outcomes of NOS inhibitors, and inhaled NO in sepsis and acute respiratory distress syndrome.
Computer-aided surgery planning and rehearsal at Mayo Clinic (1996)

The Biomedical Imaging Resource at the Mayo Clinic has been involved in the design and implementation of computer-based techniques for comprehensive and fully-interactive display and analysis of biomedical images since the 1970s. The algorithms and programs Mayo Clinic has developed have been integrated into a software system called Analyze. This system has been used in the planning and rehearsal of numerous operations, including some special surgeries, such as the separation of joined twins. More than 10 years' experience using computers to plan operations has led Mayo Clinic to design the Virtual Reality Assisted Surgery Program (VRASP) for eventual use during craniofacial, orthopedic, prostate and neurological surgery. VRASP lets surgeons view 3D renderings of CT and MRI data and permits interactive virtual display manipulation. In essence, as doctors use interactive technology and computer-generated 3D images of patients' bodies to plan and rehearse surgery, so the program brings pre-surgery planning and rehearsal into line with what happens on the operating table, to make the surgical procedure more effective, less risky and less expensive.