gebhart/patrepeval huggingface dataset:
High-resolution Time-Of-Flight PET with Depth-Of-Interaction becomes feasible: a proof of principle (2012)

In this paper we prove that the choice of a suitable treatment of the scintillator surfaces, along with suitable photodetectors electronics and specific algorithms for raw data analysis, allow to achieve an optimal tradeoff between energy, time and DOI resolution, thus strongly supporting the feasibility of a prostate TOF- PET probe, MRI compatible, with the required features and performance. In numbers this means a detector element of 1.5mm x 1.5mm x 10mm, achieving at the same time energy resolution around 11.5%, time-of- flight resolution around 150 ps and DOI resolution even below 1 mm. We stress that such a time resolution allows to increase significantly the Noise Equivalent Counting Rate, and consequently improve the image quality and the lesion detection capability. These individual values correspond to the best obtained so far by other groups, but we got all of them simultaneously. In our opinion this proof of principle paves the way to the feasibility of a TOF-PET MRI compatible probe with unprecedented features and performance, not only innovative for prostate radiotracer imaging but possibly also for other organs.
Secreted protein acidic and rich in cysteine promotes glioma invasion and delays tumor growth in vivo. (2002)

Secreted protein acidic and rich in cysteine (SPARC) is highly expressed in human astrocytomas, grades II-IV. We demonstrated previously that SPARC promotes invasion in vitro using the U87MG-derived clone U87T2 and U87T2-derived SPARC-transfected clones, A2b2, A2bi, and C2a4, in the spheroid confrontation assay. Additional in vitro studies demonstrated that SPARC delays growth, increases attachment, and modulates migration of tumor cells in extracellular matrix-specific and concentration-dependent manners. Therefore, we propose that SPARC functionally contributes to brain tumor invasion and delays tumor growth in vivo, and that the effects of SPARC are related to the level of SPARC secreted into the extracellular matrix. To test these hypotheses, we stereotactically injected these clones into nude rat brains (six animals were injected per clone). Animals were sacrificed on day 7 to assess growth and invasion for all clones at the same time in tumor development. To determine whether SPARC delayed but did not inhibit growth, rats were injected with U87T2 or clone A2b2, and the animals were sacrificed on days 9 (U87T2) and 20 (A2b2), when the animals demonstrated neurological deficit. Brains were removed, fixed, photographed, paraffin embedded, and sectioned. Sections were then serially stained with H&E for morphological assessment of invasion and to measure tumor volume, immunohistochemically stained to visualize SPARC, subjected to in situ hybridization with the human AluII DNA-binding probe to identify human cells, and immunohistochemically stained with MIB-1 to measure proliferation index. The results demonstrate that SPARC promotes invasion in vivo at day 7. Both the low (A2bi) and the high (A2b2) SPARC-secreting clones produced invasive tumors, invading with fingerlike projections and satellite masses into adjacent brain, as well as along the corpus collosum. The intermediate SPARC secreting clone (C2a4) primarily migrated as a bulk tumor along the corpus collosum. SPARC significantly decreased tumor growth at day 7, as measured both by adjusted MIB-1 proliferation indices (U87T2 = 95.3 +/- 1.4 versus A2bi = 73.4 +/- 4.0, A2b2 = 30.8 +/- 6.7 and C2a4 = 15.7 +/- 13.0) and tumor volumes (U87T2 = 13.4 +/- 0.6 mm(3) versus A2bi = 4.5 +/- 0.6 mm(3), A2b2 = 1.1 +/- 0.1 mm(3), and C2a4 = 0.4 +/- 0.1 mm(3)). Furthermore, SPARC delayed but did not inhibit tumor growth. The patterns of invasion and the extent of growth delay correlated with the level of SPARC expression. We propose that the ability of SPARC to promote invasion depends on the level of its secretion and the resultant modulation of the level of adherence and motility induced. This demonstration that SPARC functionally contributes to brain tumor invasion in vivo suggests that SPARC is a candidate therapeutic target for the design of therapies directed toward inhibition of the invasive phenotype.
Molecular Genetic Analysis of V-ATPase Function in <i>Drosophila Melanogaster</i> (1997)

V-ATPases are phylogenetically widespread, highly conserved, multisubunit proton pumps. Originally characterised in endomembranes, they have been found to energise transport across plasma membranes in a range of animal cells and particularly in certain epithelia. While yeast is the model of choice for the rapid generation and identification of V-ATPase mutants, it does not allow their analysis in a plasma membrane context. For such purposes, Drosophila melanogaster is a uniquely suitable model. Accordingly, we have cloned and characterised genes encoding several V-ATPase subunits in D. melanogaster and, using P-element technology, we have succeeded in generating multiple new alleles. Reporter gene constructs reveal ubiquitous expression, but at particularly high levels in those epithelial thought to be energised by V-ATPases, and several of the alleles have lethal recessive phenotypes characterised by epithelial dysfunction. These results, while providing the first gene knockouts of V-ATPases in animals, also illustrate the general utility of D. melanogaster as a model for the genetic analysis of ion transport and its control in epithelia.
Types of Assays for SARS-CoV-2 Testing: A Review (2020)

Clinical laboratory testing routinely provides actionable results, which help direct patient care in the inpatient and outpatient settings. Since December 2019, a novel coronavirus (SARS-CoV-2) has been causing disease (COVID-19 [coronavirus disease 2019]) in patients, beginning in China and now extending worldwide. In this context of a novel viral pandemic, clinical laboratories have developed multiple novel assays for SARS-CoV-2 diagnosis and for managing patients afflicted with this illness. These include molecular and serologic-based tests, some with point-of-care testing capabilities. Herein, we present an overview of the types of testing available for managing patients with COVID-19, as well as for screening of potential plasma donors who have recovered from COVID-19.
Haplotype Reconstruction from SNP Alignment (2004)

In this paper, we describe a method for statistical reconstruction of haplotypes from a set of aligned SNP fragments. We consider the case of a pair of homologous human chromosomes, one from the mother and the other from the father. After fragment assembly, we wish to reconstruct the two haplotypes of the parents. Given a set of potential SNP sites inferred from the assembly alignment, we wish to divide the fragment set into two subsets, each of which represents one chromosome. Our method is based on a statistical model of sequencing errors, compositional information, and haplotype memberships. We calculate probabilities of different haplotypes conditional on the alignment. Due to computational complexity, we first determine phases for neighboring SNPs. Then we connect them and construct haplotype segments. Also, we compute the accuracy or confidence of the reconstructed haplotypes. We discuss other issues, such as alternative methods, parameter estimation, computational efficiency, and relaxation of assumptions.
Development of a Dynamic Skin Permeation System for Long-Term Permeation Studies (1984)

A dynamic skin permeation system was developed aiming to eliminate the deficiencies observed in the apparatus currently available. It consists of two half-cells in mirror image, each contains a stirring platform to permit a starhead magnet to rotate at a synchronous speed. The solution chamber is equipped with a sampling port, which can be tightly closed with glass stopper. The design characteristics of this new system was calibrated, using the commercially available Franz diffusion cell as the reference. The results clearly suggested that this newly developed skin permeation system shows consistently superior than the Franz diffusion cell in terms of the control of skin surface temperature and the efficiency of solution mixing. To investigate the potential effect of environment, the temperature on the stratum corneum surface was varied, while the dermal solution was maintained at constant body temperature, and its effect on the kinetics of skin permeation was studied. The energy requirements for various steps of skin permeation were determined. The results suggested that the skin permeation system developed in this investigation can be useful for the mechanistic analysis of long-term skin permeation kinetics.
B-PMIPv6: PMIPv6 with bicasting for soft handover (2009)

This paper proposes an extension of Proxy Mobile IPv6 (PMIPv6) with bicasting for soft handover, named B-PMIPv6. The proposed scheme is compared with the existing PMIPv6 handover scheme by the theoretical analysis and the network simulator. From the experimental results, we can see that the proposed B-PMIPv6 scheme can provide smaller handover latency and reduce packet loss than the existing schemes.
Synchronous model for Fieldbus applications (2002)

The aim of this paper is to show how the synchronous approach that is used in classical distributed systems can be adopted for designing Fieldbus applications. Generally, control applications can be classified into two different hierarchy levels, namely control loop at lower and supervisory control at higher level. The lower level systems are sampled systems and the higher level systems handle the logical part of the control that cannot be treated by the sampled systems. In this paper, the authors concentrate on applications that belong to the class of sampled systems. Typically, these applications have short response times (few milliseconds) and therefore, impose hard real-time constraints on the Fieldbus. The synchronous model that the authors propose is kept simple in order to permit efficient implementations. As a second contribution, the authors study the influence of real-time aspects of the application on the proposed synchronous model. Examples demonstrate the practical utility of the authors' model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modification of Starch by Dry Heating with Ionic Gums (2002)

ABSTRACT Waxy maize (native and hydroxypropylated [HP]) and potato starches were impregnated with ionic gums (sodium alginate, CMC, and xanthan, 1% based on starch solids) and heat‐treated in a dry state for 0, 2, or 4 hr at 130°C. Effects of the dry heating on paste viscosity (RVA) and clarity (light transmittance) were examined. Heat treatment with sodium alginate and CMC raised the paste viscosities of native and HP waxy maize starches, but decreased that of potato starch. Xanthan provided the most substantial changes in paste viscosity among the tested gums. It appeared to heavily restrict granule swelling of the waxy maize starches, but it increased swelling of potato starch granules. Dry heating raised the paste viscosity of all the starch‐gum mixtures tested, except the potato starchalginate mixture. The final viscosity at 50°C of a 7% paste was raised in all other starches by ≈500–1,000 cP by this treatment. The paste of waxy maize starch‐gum products became opaque and shorter textured by the heat treatment, regardless of the gum type, whereas potato starch‐gum products did not show any obvious change in paste clarity. Ionic gums could behave as cross‐linking agents as well as form graft copolymers through heatinduced ester formation. This simple heating process with ionic gums could be used as a modification method for starch.
The role of sirtuin 1 in osteoblastic differentiation in human periodontal ligament cells (2011)

These data suggest that SIRT1 is a potent regulator of differentiation of human periodontal ligament cells and may have clinical implications for periodontal bone regeneration.
Pilot Scale Studies of Geosmin and 2-Methylisoborneol Removal (1988)

Water blooms of O.bornettii, a producer of off-flavour compounds, occasionally occur in Lake Mjoesa. Accordingly a new water works is planned to alleviate the associated taste and odour problems. A pilot plant was constructed in 1985 and a continuous water treatment study was performed over a one year period. Granular activated carbon (GAC) was compared with ozonation-GAC. Filtrasorb-400 was used and the empty-bed contact-time of the GAC-filters was 21 min. The ozone dosage varied from 2 to 5 mg O3/l. To simulate water blooms, commercially produced geosmin and 2-methyliso-borneol (MIB) were added to the water in concentrations from 10 to 190 ng/l. A slightly higher TOC-uptake was seen in the ozonation-GAC combination. This may indicate that the ozonation process is forming organic oxidation products that are competing with the geosmin and MIB for adsorption sites in the GAC-filter.
Biocompatible microcapsules with enhanced mechanical strength (2001)

A block copolymer, (short-chain alginate)-co-MPEG, was synthesized and used for coating the capsular membranes of the photosensitive microcapsules. The resulted microcapsules exhibited an excellent mechanical strength. The permeability test results revealed that the capsular membrane was freely permeable to cytochrome C and myoglobin, less permeable to serum albumin, and almost impermeable to IgG. In the cell attachment test, the results showed that the surface formed by (short-chain alginate)-co-MPEG copolymer could effectively reduce cell adhesion as compared to poly(L-lysine) and alginate. The microcapsules were evaluated by intraperitoneal implantation experiment of mice. The results demonstrated that microcapsules coated with (short-chain alginate)-co-MPEG were more biocompatible than the conventional alginate/PLL/alginate microcapsules.
Evaluation of microsatellite instability and immunohistochemistry for the prediction of germ-line MSH2 and MLH1 mutations in hereditary nonpolyposis colon cancer families. (2002)

Forty-eight hereditary nonpolyposis colorectal carcinoma (HNPCC) families for which a tumor sample was available were evaluated for the presence of germ-line mutations in MSH2 and MLH1, tumor microsatellite instability (MSI), and where possible, expression of MSH2 and MLH1 in tumors by immunohistochemistry. Fourteen of 48 of the families had a germ-line mutation in either MSH2 or MLH1 that could be detected by genomic DNA sequencing, and 28 of 48 of the families had MSI-H tumors. Four additional families showed loss of expression of MSH2, and one additional family showed loss of expression of MLH1 but did not have germ-line mutations in MSH2 or MLH1 that could be detected by DNA sequencing. MSI-H, as defined using the National Cancer Institute recommended five-microsatellite panel, had a 100% sensitivity for identifying samples having MSH2 or MLH1 mutations or loss of expression. In contrast, loss of MSH2 and MLH1 expression did not identify all samples having germ-line mutations in MSH2 or MLH1, because in five cases, a mutant protein product was expressed that could be detected by IHC. A combination of the Bethesda criteria for HNPCC and an MSI-H phenotype defined the smallest number of cases having all of the germ-line MSH2 and MLH1 mutations that could be detected by DNA sequencing.
The First Stereoselective Total Synthesis of Quinine (2001)

The first entirely stereoselective total synthesis of (-)-quinine is reported.
Process-Planning for Layered Manufacturing of Heterogeneous Objects Using Direct Metal Deposition (2002)

Layered manufacturing (LM) is emerging as a new technology that enables the fabrication of three-dimensional heterogeneous objects such as multimaterials and functionally gradient materials (FGMs). The necessary steps for LM fabrication of heterogeneous objects include representation and process planning of material information inside an object. This paper introduces a new processing planning method that takes into account the processing of material information. The detailed tasks are pre-processing (discretization), orientation (build direction selection), and adaptive slicing of heterogeneous objects. In particular, this paper focuses on the discretization process that converts all of the material information inside a heterogeneous object into material features like geometric features. It is thus possible to choose an optimal build direction among various preselected ones by approximately estimating build time. This is because total build time depends on the complexity of features. This discretization process also allows adaptive slicing of heterogeneous objects to minimize surface finish and material composition error. In addition, tool path planning can be simplified into fill pattern generation. Examples are shown to illustrate the overall procedure.
Aerosol MALDI mass spectrometry for bioaerosol analysis (2008)

In the thesis Aerosol MALDI mass spectrometry for bioaerosol analysis is described how the aerosol mass spectrometer of the TU Delft has been further developed for the on-line analysis of bioaerosols. Due to the implemented improvements mass spectra with high resolution and a high mass range can be obtained from single protein containing aerosol particles. Fluorescence is used to select the biological fraction of an aerosol: when a particle emits fluorescence when irradiated with UV-laser light the particle is ionised. The ions formed are detected and form the final mass spectrum. With an off-line sample preparation method has been demonstrated that bacteria particles can be analysed with the aerosol mass spectrometer. With an on-line sampler preparation method three bacterial species have been analysed and could be discriminated from each other. However, the resolution and the mass range of the on-line prepared bacteria particles is not the same as obtained with off-line prepared bacteria particles, due to a not (yet) optimal on-line sample preparation method. The on-line sample preparation method can be optimized by using a solvent in which the MALDI matrix and the proteins are soluble. An aerosol mass spectrometer capable of the analysis of single bioaerosol particles can be used for the detection of a biological attack, in sterile production processes and in microbiology to study processes within a single bacterial cell for instance.
Induction of Treg by monocyte‐derived DC modulated by vitamin D<sub>3</sub> or dexamethasone: Differential role for PD‐L1 (2009)

Specific therapy with modulated DC may restore immunological tolerance, thereby obviating the need for chronic immunosuppression in transplantation or autoimmunity. In this study we compared the tolerizing capacity of dexamethasone (Dex)- and 1 alpha,25-dihydroxyvitamin D3 (VD3)-modulated DC. Treatment of monocytes with either VD3 or Dex resulted in DC with stable, semi-mature phenotypes compared with standard DC, with intermediate levels of co-stimulatory and MHC class II molecules, which remained unaltered after subsequent pro-inflammatory stimulation. IL-12p70 secretion was lost by VD3- and Dex-DC, whereas IL-10 secretion was unaffected. VD3-DC distinctly produced large amounts of TNF-alpha. Both VD3- and Dex-DC possessed the capacity to convert CD4 T cells into IL-10-secreting Treg potently suppressing the proliferation of responder T cells. However, only Treg induced by VD3-DC exhibited antigen specificity. VD3-, but not Dex-, DC expressed significant high levels of PD-L1 (programmed death-1 ligand), upon activation. Blockade of PD-L1 during priming redirected T cells to produce IFN-gamma instead of IL-10 and abolished acquisition of regulatory capacity. Our findings demonstrate that both VD3- and Dex-DC possess durable but differential tolerogenic features, acting via different mechanisms. Both are potentially useful to specifically down-regulate unwanted immune responses and induce immune tolerance. These modulated DC appear suitable as adjuvant in antigen-specific clinical vaccination intervention strategies.
Focused-electron-beam-induced deposition of freestanding three-dimensional nanostructures of pure coalesced copper crystals (2002)

We report on direct writing of three-dimensional freestanding nanostructures of Cu by use of a focused electron beam (FEB) and the metalorganic precursor hfac-Cu-TMVS. Freestanding horizontal rods were deposited over about 10 μm length and consist of small 2–5 nm Cu nanocrystals dispersed in an amorphous matrix containing carbon, fluorine, silicon, and oxygen. The freestanding horizontal rods were used as support for further vertical deposits resulting in tips of coalesced facetted Cu nanocrystals of up to 100 nm in size. The almost constant deposition rate of 5–6 nm/s is in contrast to vertical tips on bulk supports, which show a deposition rate decreasing from 23 to 10 nm/s. The above results suggest a thermal decomposition process induced by electron energy absorption.
Some Applications of Organic Corrosion Inhibitors In the Petroleum Industry (1951)

The application of organic inhibitors for the abatement of corrosion in the petroleum industry is a relatively recent development. The history of this development is briefly reviewed, with particular emphasis on the application of corrosion preventives in oil and gas wells. The mechanics of inhibitor use and recommended methods of application are discussed. Corrosion rate data are presented for a number of typical systems in which organic corrosion inhibitors are used. These systems include oil wells, gas condensate wells, gas lines, water injection systems, gasoline plant stripping columns and refinery processing units. The question of the mechanism of the action of organic inhibitors in reducing corrosion rates of metals is briefly considered. Laboratory and field data on the relation between inhibitor concentration and corrosion rate are analyzed and compared with the predictions of corrosion rate derived from adsorption theory.
Probabilistic Packet Scheduling Scheme for Hybrid Pull-Push P2P Live Streaming Protocols (2011)

Hybrid pull-push P2P live streaming protocols are proposed to reduce the delay and the overhead of mesh based protocols and to improve the robustness of tree based protocols. In conventional hybrid protocols such as Cool streaming, the partition of a given stream into several sub streams is conducted in a static manner and each peer selects its parents without considering their upload availability. In this paper, we propose a new packet scheduling scheme for hybrid protocols based on the notion of randomization. Our scheme attaches a pseudo random number to each packet, and associates a sub range of random numbers to each parent and-child pair so that a packet attached a random number will be forwarded through a link associated with a sub range containing the random number. The size of each sub range is determined by considering the upload availability of each parent. By taking such a dynamic, probabilistic approach, we could improve the efficiency of resource utilization, as well as the stability, flexibility, and the robustness against peer churns.