gebhart/patrepeval huggingface dataset:
Neurally inspired rapid detection of sparse objects in videos (2010)

In this paper, we describe COGNIVA, a closed-loop Cognitive-Neural method and system for image and video analysis that combines recent technological breakthroughs in bio-vision cognitive algorithms and neural signatures of human visual processing. COGNIVA is an "operational neuroscience" framework for intelligent and rapid search and categorization of Items Of Interest (IOI) in imagery and video. The IOI could be a single object, group of objects, specific image regions, specific spatio-temporal pattern/sequence or even the category that the image itself belongs to (e.g., vehicle or non-vehicle). There are two main types of approach for rapid search and categorization of IOI in imagery and video. The first approach uses conventional machine vision or bio-inspired cognitive algorithms. These usually need a predefined set of IOI and suffer from high false alarm rates. The second class of algorithms is based on neural signatures of target detection. These algorithms usually break the entire image into sub-images and process EEG data from these images and classify them based on it. This approach may suffer from high false alarms and is slow because the entire image is chipped and presented to the human observer. The proposed COGNIVA overcomes the limitations of both methods by combining them resulting in a low false alarm rate and high detection with high throughput making it applicable to both image and video analysis. In the most basic form, COGNIVA first uses bioinspired cognitive algorithms for deciding potential IOI in a sequence of images/video. These potential IOI are then shown to a human and neural signatures of visual detection of IOI are collected and processed. The resulting signatures are used to categorize and provide final IOI. We will present the concept and typical results of COGNIVA for detecting Items of interest in image data.
Nanowire p–n Heterojunction Diodes Made by Templated Assembly of Multilayer Carbon‐Nanotube/Polymer/Semiconductor‐Particle Shells around Metal Nanowires (2005)

Metal nanowires coated with multilayer films of (TiO2/W12O41)3(PAN/SWNT)3PAN (12 nm thick; PAN: Polyaniline; SWNT: single-walled carbon nanotube) are synthesized using different, templated, layer-by-layer assembly techniques. Their I–V characteristics indicate a built-in p–n junction at the TiO2/PAN interface (rectification ratio >120 at 3 V). Films grown on planar substrates have similar thickness, morphology, and electrical properties.
Ontogeny of the Haemopoietic System: Yolk Sac Origin of In Vivo and In Vitro Colony Forming Cells in the Developing Mouse Embryo* (1970)

S ummary . The mouse yolk sac has been shown to contain in‐vivo colony forming cells capable of producing granulocytic, megakaryocytic and erythroid spleen colonies; in‐vitro colony forming cells producing granulocytic and mononuclear‐macrophage colonies in agar; and cells capable of repopuiating the lymphoid and myeloid tissue of lethally irradiated hosts. Similar haemopoietic precursor cells were also demonstrated in the blood at the time of initiation of the circulation and in the early embryonic liver. Organ cultures of 7 day embryos with intact yolk sacs, and embryos or yolk sacs after separation have shown the autonomous nature of the development of haemopoiesis in the yolk sac and the dependence of intra‐embryonic haemopoiesis, particularly in embryonic liver, on colonization by yolk sac haemopoietic cells. Both in‐vivo and in‐vitro colony forming cells have been involved in the first migration stream, between yolk sac and embryonic liver, and evidence has been presented for the role of local environmental factors in controlling the differentiation of these cell types. These results support the view that development of haemopoietic organs in both embryo and adult is dependent on colonization by circulating cells and that these circulating stem cells originate initially in the yolk sac. This indicates that the yolk sac is the only site of genuine de novo formation of haemopoietic stem cells.
Clinical Applications of Stem Cells for the Heart (2005)

Repair of the heart is an old dream of physicians caring for patients with cardiac disease. Experimental studies suggest that cardiac transfer of stem and progenitor cells can have a favorable impact on tissue perfusion and contractile performance of the injured heart. Some researchers favor stable stem cell engraftment by fusion or transdifferentiation into cardiomyocyte or vascular cell lineages as likely explanations for these beneficial effects. Others have proposed that transient cell retention may be sufficient to promote functional effects, eg, by release of paracrine mediators. Although the mechanistic underpinnings of stem cell therapy are still intensely debated, the concept of cell therapy has already been introduced into the clinical setting, where a flurry of small, mostly uncontrolled trials indicate that stem cell therapy may be feasible in patients. The overall clinical experience also suggests that stem cell therapy can be safely performed, if the right cell type is used in the right clinical setting. Preliminary efficacy data indicate that stem cells have the potential to enhance myocardial perfusion and/or contractile performance in patients with acute myocardial infarction, advanced coronary artery disease, and chronic heart failure. The field now is rapidly moving toward intermediate-size, double-blinded trials to gather more safety and efficacy data. Ultimately, large outcome trials will have to be conducted. We need to proceed cautiously with carefully designed clinical trials and keep in mind that patient safety must remain the key concern. At the same time, continued basic research to elucidate the underlying mechanism of stem cell therapy is clearly needed.
Characterization of sub-10-fs pulse focusing with high-numerical-aperture microscope objectives (1999)

Dispersion precompensation with a prism sequence and a third-order dispersion mirror resulted in negligible broadening of sub-10-fs pulses at subwavelength spot sizes when the pulses were focused with microscope objectives and moderate apertures. At larger apertures, lens chromaticity and spherical aberration led to an effective pulse broadening of up to 1.3x , depending on the aperture size and the detector position. The data suggest that intensities exceeding 10(14) W/cm(2) can be produced directly from femtosecond pulse oscillators.
Energy Landscape of Streptavidin−Biotin Complexes Measured by Atomic Force Microscopy (2000)

The dissociation of ligand and receptor involves multiple transitions between intermediate states formed during the unbinding process. In this paper, we explored the energy landscape of the streptavidin-biotin interaction by using the atomic force microscope (AFM) to measure the unbinding dynamics of individual ligand-receptor complexes. The rupture force of the streptavidin-biotin bond increased more than 2-fold over a range of loading rates between 100 and 5000 pN/s. Moreover, the force measurements showed two regimes of loading in the streptavidin-biotin force spectrum, revealing the presence of two activation barriers in the unbinding process. Parallel experiments carried out with a streptavidin mutant (W120F) were used to investigate the molecular determinants of the activation barriers. From these experiments, we attributed the outer activation barrier in the energy landscape to the molecular interaction of the '3-4' loop of streptavidin that closes behind biotin.
Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel “unnatural” natural products (1999)

The structures of complex polyketide natural products, such as erythromycin, are programmed by multifunctional polyketide synthases (PKSs) that contain modular arrangements of functional domains. The colinearity between the activities of modular PKS domains and structure of the polyketide product portends the generation of novel organic compounds-"unnatural" natural products-by genetic manipulation. We have engineered the erythromycin polyketide synthase genes to effect combinatorial alterations of catalytic activities in the biosynthetic pathway, generating a library of >50 macrolides that would be impractical to produce by chemical methods. The library includes examples of analogs with one, two, and three altered carbon centers of the polyketide products. The manipulation of multiple biosynthetic steps in a PKS is an important milestone toward the goal of producing large libraries of unnatural natural products for biological and pharmaceutical applications.
Current Products and Practices (2004)

The first part of this article has illustrated some of the principles in 3D imaging and the possible applications of 3D facial imaging in orthodontics. Part II explores the different techniques of 3D imaging of the teeth, as well as the recent efforts to create the ‘virtual orthodontic patient’ by using 3D soft and hard tissue data. A brief overview of some of the commercially available 3D-based technologies, such as OrthoCADTM and Invisalign® is given at the end.
Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail (2020)

Neutralizing antibodies have become an important tool in treating infectious diseases. Recently, two separate approaches yielded successful antibody treatments for Ebola-one from genetically humanized mice and the other from a human survivor. Here, we describe parallel efforts using both humanized mice and convalescent patients to generate antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, which yielded a large collection of fully human antibodies that were characterized for binding, neutralization, and three-dimensional structure. On the basis of these criteria, we selected pairs of highly potent individual antibodies that simultaneously bind the receptor binding domain of the spike protein, thereby providing ideal partners for a therapeutic antibody cocktail that aims to decrease the potential for virus escape mutants that might arise in response to selective pressure from a single-antibody treatment.
Identification of a Novel Hypoxia-Inducible Factor 1-Responsive Gene, RTP801 , Involved in Apoptosis (2002)

Hypoxia is an important factor that elicits numerous physiological and pathological responses. One of the major gene expression programs triggered by hypoxia is mediated through hypoxia-responsive transcription factor hypoxia-inducible factor 1 (HIF-1). Here, we report the identification and cloning of a novel HIF-1-responsive gene, designated RTP801. Its strong up-regulation by hypoxia was detected both in vitro and in vivo in an animal model of ischemic stroke. When induced from a tetracycline-repressible promoter, RTP801 protected MCF7 and PC12 cells from hypoxia in glucose-free medium and from H(2)O(2)-triggered apoptosis via a dramatic reduction in the generation of reactive oxygen species. However, expression of RTP801 appeared toxic for nondividing neuron-like PC12 cells and increased their sensitivity to ischemic injury and oxidative stress. Liposomal delivery of RTP801 cDNA to mouse lungs also resulted in massive cell death. Thus, the biological effect of RTP801 overexpression depends on the cell context and may be either protecting or detrimental for cells under conditions of oxidative or ischemic stresses. Altogether, the data suggest a complex type of involvement of RTP801 in the pathogenesis of ischemic diseases.
Synthetic triterpenoids enhance transforming growth factor beta/Smad signaling. (2003)

We have studied the effects of two new synthetic triterpenoids, 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid (CDDO) and its derivative, 1-(2-cyano-3,12-dioxooleana-1,9-dien-28-oyl) imidazole (CDDO-Im), on transforming growth factor (TGF)-beta/Smad signaling. These agents, at nanomolar concentrations, increase the expression of TGF-beta-dependent genes, such as those for plasminogen activator inhibitor 1 and the type II TGF-beta receptor, and they synergize with TGF-beta in this regard. They prolong the activation of Smad2 induced by TGF-beta and markedly enhance the ability of Smad3 to activate a Smad binding element, CAGA-luciferase. In transfection assays, they reverse the inhibitory effects of Smad7. CDDO and CDDO-Im also enhance Smad signaling in the pathways of two other members of the TGF-beta superfamily, namely, activin and bone morphogenetic protein. Finally, these triterpenoids induce expression of the transcriptional coactivator p300-CBP-associated factor and synergize with TGF-beta in this regard. These are the first studies to report enhancement of Smad signaling by synthetic triterpenoids and should further their optimal use for applications in prevention or treatment of diseases in which there is aberrant function of TGF-beta.
Hydroxylase Cofactor Activity in Cerebrospinal Fluid of Normal Subjects and Patients with Parkinson's Disease (1979)

A method for measuring hydroxylase cofactor activity in human cerebrospinal fluid is described. The hydroxylase cofactor content of cerebrsopinal fluid from Parkinsonian patients is approximately 50 percent that of normal subjects. A significant correlation between hydroxylase cofactor and the concentration of homovanillic acid in the cerebrospinal fluid was observed.
The National Eye Institute Visual Function Questionnaire in the Macular Telangiectasia (MacTel) Project (2008)

This is the first cross-sectional cohort study to assess vision targeted HR-QOL in patients with MacTel type 2. Patients with MacTel type 2 reported markedly reduced visual functioning compared to reports of a normal reference group. These findings provide support to the use of the NEI-VFQ-25 in patients with MacTel type 2 to measure the effect of disease and potential therapies on vision-targeted HR-QOL.
A gene for a new lipoprotein in the dapA-purC interval of the Escherichia coli chromosome (1991)

Cloning and sequence analysis of the region located downstream of the dapA gene of Escherichia coli has revealed the presence of an open reading frame that is cotranscribed with dapA. This gene codes for a 344-amino-acid polypeptide with a potential signal sequence characteristic of a lipoprotein. When this gene, called nlpB, is expressed from a multicopy plasmid in bacteria grown in the presence of [3H]palmitate, a labeled 37-kDa protein is produced. A slightly larger precursor molecule is detected when minicells expressing nlpB are treated with globomycin, a specific inhibitor of lipoprotein signal peptidase. Therefore, the nlpB gene encodes a new lipoprotein, designated NlpB. This lipoprotein is detected in outer membrane vesicles prepared from osmotically lysed spheroplasts and appears to be nonessential, since a strain in which the nlpB gene is disrupted by insertion of a chloramphenicol resistance gene is still able to grow and shows no discernible NlpB phenotype. The putative transcription termination signals of the dapA-nlpB operon overlap the promoter of the adjacent purC gene.
Activation of phosphatidylinositol 3-kinase, Akt, and mammalian target of rapamycin is necessary for hypoxia-induced pulmonary artery adventitial fibroblast proliferation (2004)

In contrast to cell types in which exposure to hypoxia causes a general reduction of metabolic activity, a remarkable feature of pulmonary artery adventitial fibroblasts is their ability to proliferate in response to hypoxia. Previous studies have suggested that ERK1/2, phosphatidylinositol 3-kinase (PI3K), Akt, and mammalian target of rapamycin (mTOR) are activated by hypoxia and play a role in a variety of cell responses. However, the pathways involved in mediating hypoxia-induced proliferation are largely unknown. Using pharmacological inhibitors, we established that PI3K-Akt, mTOR-p70 ribosomal protein S6 kinase (p70S6K), and EKR1/2 signaling pathways play a critical role in hypoxia-induced adventitial fibroblast proliferation. We found that exposure of serum-starved fibroblasts to 3% O2 resulted in a time-dependent activation of PI3K and transient phosphorylation of Akt. However, activation of PI3K was not required for activation of ERK1/2, implying a parallel involvement of these pathways in the proliferative response of fibroblasts to hypoxia. We found that hypoxia induced significant increases in mTOR, p70S6K, 4E-BP1, and S6 ribosomal protein phosphorylation, as well as dramatic increases in p70S6K activity. The activation of p70S6K/S6 pathway was sensitive to inhibition by rapamycin and LY294002, indicating that mTOR and PI3K/Akt are upstream signaling regulators. However, the magnitude of hypoxia-induced p70S6K activity and phosphorylation suggests involvement of additional signaling pathways. Thus our data demonstrate that hypoxia-induced adventitial fibroblast proliferation requires activation and interaction of PI3K, Akt, mTOR, p70S6K, and ERK1/2 and provide evidence for hypoxic regulation of protein translational pathways in cells exhibiting the capability to proliferate under hypoxic conditions.
Exploring the effect of xenon on biomembranes. (2005)

We report the initial findings of 100 ns molecular dynamics simulations of the role of cellular membranes in general anaesthesia. The effect of xenon on hydrated dipalmitoylphosphatidylcholine bilayers is described. The xenon atoms were found to prefer the interfacial and central regions of the bilayer. The presence of xenon was observed to lead to a small increase in the surface area, membrane thickness, and order of the acyl chains.
Analysis of Aroma Components of Kiwifruit (Actinidia chinensis Planch.)by Gas Chromatography-Mass Spectrometry (2002)

Aroma components in the kiwifruit var ″ Zaoxian″ were extracted by solvent extraction. According to the analysis of gas chromatography-mass spectrometry, 45 components in the kiwifruit were identified. These constituents represent 95.9% of the total peak areas. The main aroma components with higher relative content in the kiwifruit include hexadecanoic acid, octanoic acid, oleic acid, 3 _ hydroxy _ butanoic acid ethyl ester,(Z,Z) _ 9,12 _ octadecadienoic acid, 1,2,4 _ trihydroxy _ p _ menthane, (E) _ 2 _ hexenal, 1,2 _ benzenedicarboxylic acid bis(2 _ methoxyethyl) ester, octadecanoic acid and 2 _ hexenal, etc.
Systemic Linoleic and γ-Linolenic Acid Therapy in Dry Eye Syndrome With an Inflammatory Component (2003)

Therapy with LA and GLA and tear substitutes reduces ocular surface inflammation and improves dry eye symptoms. Long-term studies are needed to confirm the role of this new therapy for keratoconjunctivitis sicca.
LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration (2007)

LEDGF/p75 directly interacts with lentiviral integrase proteins and can modulate their enzymatic activities and chromosomal association. A novel genetic knockout model was established that allowed us for the first time to analyze HIV-1 integration in the absence of LEDGF/p75 protein. Supporting a crucial role for the cofactor in viral replication, HIV-1 vector integration and reporter gene expression were significantly reduced in LEDGF-null cells. Yet, integrase processed the viral cDNA termini normally and maintained its local target DNA sequence preference during integration. Preintegration complexes extracted from knockout cells moreover supported normal levels of DNA strand transfer activity in vitro. In contrast, HIV-1 lost its strong bias toward integrating into transcription units, displaying instead increased affinity for promoter regions and CpG islands. Our results reveal LEDGF/p75 as a critical targeting factor, commandeering lentiviruses from promoter- and/or CpG island-proximal pathways that are favored by other members of Retroviridae. Akin to yeast retrotransposons, disrupting the lentiviral targeting mechanism significantly perturbs overall integration.
Increased activity of surviving locus ceruleus neurons in Alzheimer's disease (1999)

In Alzheimer's disease (AD) there is neuronal loss in the locus ceruleus (LC), and the noradrenergic system may be even more affected in depressed AD patients. However, this neuronal loss may go together with an increase in activity of the remaining noradrenergic neurons. We prospectively evaluated 16 AD patients (6 depressed, 5 transiently depressed, and 5 nondepressed) and 10 controls. We determined norepinephrine and its metabolite 3-methoxy-4-hydroxyphenylglycol (MHPG) in various brain areas, and compared these data with previously established neuron numbers in the LC in the same patients. We could not confirm earlier studies reporting lower norepinephrine concentrations in depressed than in nondepressed dementia patients. The mean norepinephrine concentrations in AD patients were significantly lower than those in control patients, whereas the mean concentrations of MHPG were not different. Moreover, we found significant inverse relationships between the number of remaining pigmented LC neurons and the MHPG/norepinephrine ratio in the frontal cortex and LC. These data are the first to provide direct evidence for the hypothesis that remaining LC neurons are activated to compensate for decreased cerebral norepinephrine levels in AD, by demonstrating that the MHPG/norepinephrine ratio is significantly higher in AD, indicating increased metabolism.
Effects of Zinc Sulphate Pretreatment on Gastric Acid Secretion and Lesion Formation in Rats Infused Intravenously with Graded Doses of Methacholine (1978)

The effects of intraperitoneal pretreatment with zinc sulphate (22, 44 or 88 mg/kg) were studied on gastric acid secretion and lesion formation induced by methacholine (125, 250 or 500 microgram/kg/h) infused intravenously in rats with stomachs perfused in situ. Graded infusions of methacholine produced dose-dependent increases in gastric acid secretion and lesion incidence in saline-pretreated control rats. These effects were progressively reduced by increasing pretreatment doses of zinc sulphate. The relationship between these findings and the action of zinc on gastric mast cells is discussed.
Osteoprotegerin Reverses Osteoporosis by Inhibiting Endosteal Osteoclasts and Prevents Vascular Calcification by Blocking a Process Resembling Osteoclastogenesis (2000)

High systemic levels of osteoprotegerin (OPG) in OPG transgenic mice cause osteopetrosis with normal tooth eruption and bone elongation and inhibit the development and activity of endosteal, but not periosteal, osteoclasts. We demonstrate that both intravenous injection of recombinant OPG protein and transgenic overexpression of OPG in OPG(-/-) mice effectively rescue the osteoporotic bone phenotype observed in OPG-deficient mice. However, intravenous injection of recombinant OPG over a 4-wk period could not reverse the arterial calcification observed in OPG(-/-) mice. In contrast, transgenic OPG delivered from mid-gestation through adulthood does prevent the formation of arterial calcification in OPG(-/-) mice. Although OPG is normally expressed in arteries, OPG ligand (OPGL) and receptor activator of NF-kappaB (RANK) are not detected in the arterial walls of wild-type adult mice. Interestingly, OPGL and RANK transcripts are detected in the calcified arteries of OPG(-/-) mice. Furthermore, RANK transcript expression coincides with the presence of multinuclear osteoclast-like cells. These findings indicate that the OPG/OPGL/RANK signaling pathway may play an important role in both pathological and physiological calcification processes. Such findings may also explain the observed high clinical incidence of vascular calcification in the osteoporotic patient population.