gebhart/patrepeval huggingface dataset:
Fabrication of symmetric sub-5 nm nanopores using focused ion and electron beams (2006)

Nanopores fabricated in solid-state membranes have previously been used for the rapid electrical detection and characterization of single biopolymer molecules. Various methods for producing solid-state nanopores have been reported, but fabricating nanopores of desired sizes controllably is still challenging. Here we report a fabrication technique which uses a focused ion beam (FIB) system to engineer nanopores precisely. This technique provides visual feedback over the formation process. The present method can produce highly symmetrical nanopores with diameters smaller than ∼5 nm and can be used to create an array of multiple nanopores simultaneously. In addition, nanopores produced using the focused ion beam sculpting technique can be tailored down to less than 1 nm in diameter using high-energy electron radiation.
Dietary Medium-Chain Fatty Acids Raise and (n-3) Polyunsaturated Fatty Acids Lower Hepatic Triacylglycerol Synthesis in Rats (1995)

The hypothesis tested was that dietary medium-chain or (n-3) polyunsaturated fatty acids, when compared with (n-6) polyunsaturated fatty acids, alter plasma triacylglycerol levels by affecting hepatic triacylglycerol synthesis as reflected by the activities of acetyl-CoA carboxylase, fatty acid synthase and diacylglycerol acyltransferase in liver. In two separate experiments rats were fed purified diets containing (n-6) polyunsaturated fatty acids in the form of corn oil and either (n-3) polyunsaturated fatty acids in the form of fish oil or medium-chain triacylglycerols (MCT). Consumption of MCT significantly raised plasma triacylglycerol concentrations, whereas fish oil feeding had a lowering effect compared with the corn oil-fed group. In individual rats, the hepatic triacylglycerol concentration was directly correlated with the plasma triacylglycerol concentration (r = 0.60, P < 0.001). The MCT oil diet vs. the corn oil diet markedly raised the activities of hepatic acetyl-CoA carboxylase, fatty acid synthase and diacylglycerol acyltransferase. In the rats fed fish oil, the activities of fatty acid synthase and diacylglycerol acyltransferase were significantly reduced, whereas the activity of acetyl-CoA carboxylase was not affected relative to activities in rats fed corn oil. The activities of the three enzymes were directly correlated with plasma triacylglycerol concentrations in individual rats (r = 0.60-0.75, P < 0.001). The type of fat in the diet probably affects the rate of hepatic triacylglycerol synthesis which is an important determinant of plasma triacylglycerol concentrations.
Synthesis, Biological Activity, and Preliminary Pharmacokinetic Evaluation of Analogues of a Phosphosulfomannan Angiogenesis Inhibitor (PI-88) (2005)

The phosphosulfomannan 1 (PI-88) is a mixture of highly sulfated oligosaccharides that is currently undergoing clinical evaluation in cancer patients. As well as its anticancer properties, 1 displays a number of other interesting biological activities. A series of analogues of 1 were synthesized with a single carbon (pentasaccharide) backbone to facilitate structural characterization and interpretation of biological results. In a fashion similar to 1, all compounds were able to inhibit heparanase and to bind tightly to the proangiogenic growth factors FGF-1, FGF-2, and VEGF. The compounds also inhibited the infection of cells and cell-to-cell spread of herpes simplex virus (HSV-1). Preliminary pharmacokinetic data indicated that the compounds displayed different pharmacokinetic behavior compared with 1. Of particular note was the n-octyl derivative, which was cleared 3 times less rapidly than 1 and may provide increased systemic exposure.
Copolymer-1 Induces Adaptive Immune Anti-inflammatory Glial and Neuroprotective Responses in a Murine Model of HIV-1 Encephalitis (2007)

Copolymer-1 (COP-1) elicits neuroprotective activities in a wide range of neurodegenerative disorders. This occurs, in part, by adaptive immune-mediated suppression of microglial inflammatory responses. Because HIV infection and immune activation of perivascular macrophages and microglia drive a metabolic encephalopathy, we reasoned that COP-1 could be developed as an adjunctive therapy for disease. To test this, we developed a novel animal model system that reflects HIV-1 encephalitis in rodents with both innate and adaptive arms of the immune system. Bone marrow-derived macrophages were infected with HIV-1/vesicular stomatitis-pseudotyped virus and stereotactically injected into the basal ganglia of syngeneic mice. HIV-1 pseudotyped with vesicular stomatitis virus envelope-infected bone marrow-derived macrophages induced significant neuroinflammation, including astrogliosis and microglial activation with subsequent neuronal damage. Importantly, COP-1 immunization reduced astro- and microgliosis while diminishing neurodegeneration. Hippocampal neurogenesis was, in part, restored. This paralleled reductions in proinflammatory cytokines, including TNF-alpha and IL-1beta, and inducible NO synthase, and increases in brain-derived neurotrophic factor. Ingress of Foxp3- and IL-4-expressing lymphocytes into brains of COP-1-immunized animals was observed. We conclude that COP-1 may warrant therapeutic consideration for HIV-1-associated cognitive impairments.
Small-angle X-Ray scattering from polyurethane elastomers (1968)

Abstract Small-angle X-ray scattering is shown to be an effective technique, complementary to mechanical and thermal methods, for the study of structural ordering in polyurethane elastomers. Wide variations in intensity were found for different sample compositions and are interpreted in terms of the degree of hard segment aggregation. The results support previous conclusions regarding the organization in these samples based on analysis by scanning thermal methods. The polyether polyurethanes studied showed a higher degree of organization than the equivalent polyesters, and longer urethane segments enhance the extent of domain structure. Studies of the temperature dependence of scattering strengthen the previous assignment of a transition at about 150°C to the disordering of domain structure.
Synthetic peptide with cell attachment activity of fibronectin. (1983)

Four synthetic peptides that together constitute the cell attachment domain of fibronectin [Pierschbacher, M.D., Ruoslahti, E., Sundelin, J., Lind, P. & Peterson, P. (1982) J. Biol. Chem. 257, 9593-9597] were constructed and tested for their ability to induce cell attachment and spreading. One of these peptides, consisting of the 30 amino acid residues nearest the COOH terminus of the domain, contained all of the cell attachment activity of the whole domain. Under suitable conditions the peptide was approximately as active as intact fibronectin on a molar basis. The activity could be demonstrated by binding the peptide to polystyrene directly, or via albumin, or by coupling it to agarose beads. This synthetic peptide will be useful in the elucidation of the molecular details of the attachment of cells to fibronectin and could allow manipulation of the adhesive properties of cell culture surfaces and prosthetic materials.
Interactions through L-selectin between leukocytes and adherent leukocytes nucleate rolling adhesions on selectins and VCAM-1 in shear flow. (1996)

We demonstrate an additional step and a positive feedback loop in leukocyte accumulation on inflamed endothelium. Leukocytes in shear flow bind to adherent leukocytes through L-selectin/ligand interactions and subsequently bind downstream and roll on inflamed endothelium, purified E-selectin, P-selectin, L-selectin, VCAM-1, or peripheral node addressin. Thus adherent leukocytes nucleate formation of strings of rolling cells and synergistically enhance leukocyte accumulation. Neutrophils, monocytes, and activated T cell lines, but not peripheral blood T lymphocytes, tether to each other through L-selectin. L-selectin is not involved in direct binding to either E- or P-selectin and is not a major counterreceptor of endothelial selectins. Leukocyte-leukocyte tethers are more tolerant to high shear than direct tethers to endothelial selectins and, like other L-selectin-mediated interactions, require a shear threshold. Synergism between leukocyte-leukocyte and leukocyte-endothelial interactions introduces novel regulatory mechanisms in recruitment of leukocytes in inflammation.
A nanobody targeting the F-actin capping protein CapG restrains breast cancer metastasis (2013)

CapG inhibition strongly reduces breast cancer metastasis. A nanobody-based approach offers a fast track for gauging the therapeutic merit of drug targets. Mapping of the nanobody-CapG interface may provide a platform for rational design of pharmacologic compounds.
Data Triage: An Adaptive Architecture for Load Shedding in TelegraphCQ (2005)

Many of the data sources used in stream query processing are known to exhibit bursty behavior. Data in a burst often has different characteristics than steady-state data, and therefore may be of particular interest. In this paper, we describe the Data Triage architecture that we are adding to TelegraphCQ to provide low latency results with good accuracy under such bursts.
Aerosolized Ribavirin Treatment of Infants with Respiratory Syncytial Viral Infection (1983)

We evaluated a new antiviral agent, ribavirin, in the treatment of infants hospitalized with lower-respiratory-tract disease from respiratory syncytial virus. Ribavirin or placebo was administered to 33 infants in a double-blind manner by continuous aerosol for three to six days. Seventeen infants were treated with placebo, and 16 with ribavirin. By the end of treatment, infants receiving ribavirin had significantly greater improvement in their overall score for severity of illness, in lower-respiratory-tract signs, and in arterial oxygen saturation. Viral shedding was also diminished in the treated groups as compared with the placebo group. No side effects or toxicity were associated with the aerosol therapy. Isolates of respiratory syncytial virus obtained from the infants over the course of therapy showed no change in sensitivity to ribavirin.
Histopathologic Analysis of Sixteen Autopsy Cases of Chronic Hypersensitivity Pneumonitis and Comparison With Idiopathic Pulmonary Fibrosis/Usual Interstitial Pneumonia (2009)

Hypersensitivity pneumonitis (HP) is an interstitial lung disease caused by the inhalation of organic substances and certain inorganic chemicals. The histopathologic features of chronic HP (CHP) have not been studied extensively. We examined the pathologic characteristics of 16 autopsy cases of clinically confirmed CHP and compared them with 11 cases of idiopathic pulmonary fibrosis/usual interstitial pneumonia (IPF/UIP). To clarify the exact intralobular location of the fibrotic lesions, we conducted 3-dimensional reconstruction of fibrosis of CHP and IPF/UIP. Granuloma was not detected in any CHP case. Similar to IPF/UIP, honeycombing lesions were found dominantly in the lower lobes in most CHP cases; upper lobe dominance and asymmetrical distribution of honeycomb lesions were more frequent in CHP than in IPF/UIP. In all lungs affected by CHP, centrilobular fibrosis was outstanding, often connecting to the perilobular areas in the appearance of "bridging fibrosis," which was clearly demonstrated by 3-dimensional imaging. Centrilobular and bridging fibrosis were significantly more conspicuous in CHP than IPF/UIP; however, considerable overlap was found. It is important to thoroughly explore the possibility of antigen exposure in cases of lungs with UIP with centrilobular fibrosis to discriminate CHP from IPF/UIP.
The Safety and Lack of Efficacy of Vinpocetine in Alzheimer's Disease (1989)

Fifteen Alzheimer patients were treated with increasing doses of vinpocetine (30, 45, and 60 mg per day) in an open-label pilot trial during a one-year period. Patients were assessed seven times both on and off drug with: the Buschke Selective Reminding Task, a letter fluency test, a category fluency test, the Boston Naming Test, a cognitive capacity screening examination, and a clinical global impression. Vinpocetine failed to improve cognition on psychometric testing or overall functioning, as measured by the clinical global impression, at any dose tested. Patients showed significant decline in most measures during the course of the study, at the same rate as a matched control group, consistent with progressive dementia. There were no significant side effects from drug therapy. We conclude that vinpocetine is ineffective in improving cognitive deficits and does not slow the rate of decline in individuals with Alzheimer's disease.
Risk of Interference from Transcutaneous Electrical Nerve Stimulation on the Sensing Function of Implantable Defibrillators (2008)

Noise reversion and undersensing might prevent the ICD from delivering shock when it should and the interpretation as VT/VF could result in inappropriate shocks. Because of the potentially serious consequences of interference we do not recommend the use of TENS in patients with ICD.
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms (2012)

DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
Solubility and Molecular Conformations of n-Alkane Chains in Water (2009)

We employ molecular dynamics simulations to study the solubility and molecular conformations of n-alkane chains in water. We find nearly exponential decrease in solubility with carbon number up to n-eicosane (C(20)), and excellent agreement with experiment up to n-dodecane (C(12)). We detect no sharp break in the dependence of the solubility upon carbon number. A free energy landscape analysis of the chain conformations reveals remarkable similarities between the ideal gas and solvated phase landscapes, suggesting that solvated chain conformations are driven primarily by ideal gas statistics. We find no evidence for hydrophobic collapse of n-alkane chains shorter than n-eicosane (C(20)). The primary effect of the solvent is the appearance of a barrier on the order k(B)T, not present in the ideal gas, between the free energy basins corresponding to compact and extended chain conformations, and destabilization of the most extended conformations. Our findings are robust to nontrivial modification of the potential model, suggesting that the absence of strong solvent effects on the free energy landscapes is fundamental to relatively short (<or=20-mer) chains composed of small hydrophobic monomers, and does not depend on the precise nature of the chain interactions.
Should losartan be administered following brain injury? (2014)

Brain injury is a major health concern and associated with delayed neurological complications, including post-injury epilepsy, cognitive and emotional disabilities. Currently, there is no strategy to prevent post-injury delayed complications. We recently showed that dysfunction of the blood-brain barrier, often reported in brain injuries, can lead to epilepsy and neurodegeneration via activation of inflammatory TGF-β signaling in astrocytes. We further showed that the FDA approved angiotensin II type 1 receptor antagonist, losartan, blocks brain TGF-β signaling and prevents epilepsy in the albumin or blood-brain barrier breakdown models of epileptogenesis. Here we discuss the potential of losartan as an anti-epileptogenic and a neuroprotective drug, the rationale of its use following brain injury and the challenges of designing clinical trials. We highlight the urgent need to develop reliable biomarkers for epileptogenesis (and other complications) after brain injury as a pre-requisite to challenge neuroprotective therapies.
HLA matching in unrelated donor bone marrow transplantation (1996)

The availability of an HLA-matched sibling donor in only 30% to 35% of patients requiring allogeneic bone marrow transplantation (BMT) has led to the proposal of unrelated donors as an alternative source of bone marrow. The greater HLA incompatibility, which, although present, was undetected until recently in many unrelated donor BMT cases, has resulted in a higher rate of posttransplant complications and impaired acturial survival when compared with HLA-matched sibling BMT. Molecular HLA typing enables us to evaluate the impact of incompatibility at each locus in the outcome of unrelated donor BMT. The overall retrospective data would recommend that HLA-A, -B and -C allelic molecular matching should be implemented in addition to HLA-DR allelic matching. Further retrospective analysis is needed in order to assess which incompatibility or combinations are better tolerated than others. Only the definitive knowledge at the sequence level of the donor and the recipient HLA allelic diversity involved in controlling the allogeneic immune response will allow us to understand the precise biologic rationale of the graft-versus-host disease. Knowledge and control of the HLA incompatibilities should allow us to offset the detrimental effects of histoincompatibility while developing strategies to take advantage of the beneficial graft-versus-leukemia effect. Also the role of minor histocompatibility antigens remains largely unknown and will require careful evaluation before minor antigens can be used as a selection criterion in BMT. Carefully designed prospective studies will enable us to test the impact of each HLA locus. HLA typing and BMT represent a successful example of productive cooperation between basic and clinical sciences that should be pursued for the improvement of the clinical outcome of unrelated donor BMT.
Candida albicans Als3p is required for wild-type biofilm formation on silicone elastomer surfaces (2006)

Candida albicans ALS3 encodes a large cell-surface glycoprotein that has adhesive properties. Immunostaining of cultured C. albicans germ tubes showed that Als3p is distributed diffusely across the germ tube surface. Two-photon laser scanning microscopy of model catheter biofilms grown using a PALS3-green fluorescent protein (GFP) reporter strain showed GFP production in hyphae throughout the biofilm structure while biofilms grown using a PTPI1-GFP reporter strain showed GFP in both hyphae and yeast-form cells. Model catheter biofilms formed by an als3 Delta/als3 Delta strain were weakened structurally and had approximately half the biomass of a wild-type biofilm. Reintegration of a wild-type ALS3 allele restored biofilm mass and wild-type biofilm structure. Production of an Als3p-Ag alpha 1p fusion protein under control of the ALS3 promoter in the als3 Delta/als3 Delta strain restored some of the wild-type biofilm structural features, but not the wild-type biofilm mass. Despite its inability to restore wild-type biofilm mass, the Als3p-Ag alpha 1p fusion protein mediated adhesion of the als3 Delta/als3 Delta C. albicans strain to human buccal epithelial cells (BECs). The adhesive role of the Als3p N-terminal domain was further demonstrated by blocking adhesion of C. albicans to BECs with immunoglobulin reactive against the Als3p N-terminal sequences. Together, these data suggest that portions of Als3p that are important for biofilm formation may be different from those that are important in BEC adhesion, and that Als3p may have multiple functions in biofilm formation. Overexpression of ALS3 in an efg1 Delta/efg1 Delta strain that was deficient for filamentous growth and biofilm formation resulted in growth of elongated C. albicans cells, even under culture conditions that do not favour filamentation. In the catheter biofilm model, the ALS3 overexpression strain formed biofilm with a mass similar to that of a wild-type control. However, C. albicans cells in the biofilm had yeast-like morphology. This result uncouples the effect of cellular morphology from biofilm formation and underscores the importance of Als3p in biofilm development on silicone elastomer surfaces.
Arabic Handwritten Words Recognition Based on a Planar Hidden Markov Model. (2005)

Off-line recognition of handwritten words is a difficult task due to the high variability and uncertainty of human writing. The majority of the recent systems are constrained by the size of the lexicon to deal with and the number of writers. In this paper, we propose an approach for multi-writers Arabic handwritten words recognition. The developed method uses multiple sources of information at the description and the classification levels. A hybrid planar Markovien modelling permitting to follow the horizontal and vertical variations of the writing has been adopted. This modelling is based on different levels of segmentation: horizontal, natural and vertical. The process of segmentation conducts to the decomposition of the writing in a limited set of elementary entities, with simplified morphologies specific to every horizontal band. The choice of different type of primitives is then imposed in order to assure an efficient description. Different architectures of modelling proved also to be indispensable. The classification is finally achieved using a Planar Hidden Markov Model.
In vitro circularization of RNA (2016)

Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.
Analysis of Wafer Sojourn Time in Dual-Arm Cluster Tools With Residency Time Constraint and Activity Time Variation (2010)

When scheduling cluster tools under wafer residency time constraints, wafer sojourn time in a processing module should be carefully controlled such that it is in a permissive range. Activity time variation often results in wafer sojourn time fluctuation and makes an originally feasible schedule infeasible. Thus, it is very important to know how the wafer sojourn time changes when activity time varies. With bounded activity time variation considered, this paper conducts a detailed analysis of wafer sojourn time variation in dual-arm cluster tools. To do so, a Petri net (PN) model and a real-time control policy are presented. Based on the PN model, real-time operational architecture, and real-time control policy, this paper analyzes the effect of activity time variation on wafer sojourn time delay at a process module and presents its upper bounds. The upper bounds are given in an analytical form and can be easily evaluated. With the wafer sojourn time analysis, it is possible to develop an effective method for schedulability analysis and optimal steady-state scheduling. An example is used to show the applications of the proposed approach.