gebhart/patrepeval huggingface dataset:
Multiplex immunofluorescence staining and image analysis assay for diffuse large B cell lymphoma (2019)

With the explosion of immuno-oncology and the approval of many immune checkpoint therapies by regulatory agencies in the last few years, understanding the tumor microenvironment (TME) in the context of patients' immune status has become essential. Among available immune profiling techniques, multiplex immunofluorescence (mIF) assays offer the unique advantage of preserving the architectural features of the tumor and revealing the spatial relationships between tumor cells and immune cells. A number of mIF and image analysis assays have been described for solid tumors but most are not sufficiently suitable in lymphoma, where the lack of clear tumor-stromal boundaries and high tumor density present significant challenges. Here we describe the development and optimization of a reliable workflow using Akoya Opal staining kits to label and analyze 6 markers per slide in diffuse large B-cell lymphoma (DLBCL) tissue sections. Five panels totaling 30 markers were developed to characterize infiltrating immune cells and relevant check-point proteins such as PD1, PD-L1, ICOS, SIRP-alpha and Lag3 on 70 DLBCL sections. Multiplexed sections were scanned using an Akoya multispectral scanner. An image analysis workflow using InForm and Matlab was developed to overcome challenges inherent to the DLBCL environment. Using the assays and workflows detailed here, we were able to quantify cell densities of subsets of infiltrating immune cells and observe their spatial patterns within the tumors. We highlight heterogeneous distribution of cytotoxic T cells across tumors with similar T cell density to underscores the importance of considering spatial context when studying the effects of immunological therapies in DLBCL.
Design and Implementation of Practical Bidirectional Texture Function Measurement Devices Focusing on the Developments at the University of Bonn (2014)

Understanding as well as realistic reproduction of the appearance of materials play an important role in computer graphics, computer vision and industry. They enable applications such as digital material design, virtual prototyping and faithful virtual surrogates for entertainment, marketing, education or cultural heritage documentation. A particularly fruitful way to obtain the digital appearance is the acquisition of reflectance from real-world material samples. Therefore, a great variety of devices to perform this task has been proposed. In this work, we investigate their practical usefulness. We first identify a set of necessary attributes and establish a general categorization of different designs that have been realized. Subsequently, we provide an in-depth discussion of three particular implementations by our work group, demonstrating advantages and disadvantages of different system designs with respect to the previously established attributes. Finally, we survey the existing literature to compare our implementation with related approaches.
Cell-to-Cell Signaling and <i>Pseudomonas aeruginosa</i> Infections (1998)

Pseudomonas aeruginosa is a bacterium responsible for severe nosocomial infections, life-threatening infections in immunocompromised persons, and chronic infections in cystic fibrosis patients. The bacterium's virulence depends on a large number of cell-associated and extracellular factors. Cell-to-cell signaling systems control the expression and allow a coordinated, cell-density-dependent production of many extracellular virulence factors. We discuss the possible role of cell-to-cell signaling in the pathogenesis of P. aeruginosa infections and present a rationale for targeting cell-to-cell signaling systems in the development of new therapeutic approaches.
Super-Resolution Laser Scanning Microscopy through Spatiotemporal Modulation (2009)

Super-resolution optical microscopy has attracted great interest among researchers in many fields, especially in biology where the scale of physical structures and molecular processes fall below the diffraction limit of resolution for light. As one of the emerging techniques, structured illumination microscopy can double the resolution by shifting unresolvable spatial frequencies into the pass-band of the microscope through spatial frequency mixing with a wide-field structured illumination pattern. However, such a wide-field scheme typically can only image optically thin samples and is incompatible with multiphoton processes such as two-photon fluorescence, which require point scanning with a focused laser beam. Here, we propose two new super-resolution schemes for laser scanning microscopy by generalizing the concept of a spatially nonuniform imaging system. One scheme, scanning patterned illumination (SPIN) microscopy, employs modulation of the excitation combined with temporally cumulative imaging by a nondescanned array detector. The other scheme, scanning patterned detection (SPADE) microscopy, utilizes detection modulation together with spatially cumulative imaging, in this case by a nondescanned single-element detector. When combined with multiphoton excitation, both schemes can image thick samples with three-dimensional optical sectioning and much improved resolution.
Control Technology for a Passenger Car Diesel Engine equipped with the DPNR system (2003)

<div class="htmlview paragraph">A compact diesel engine with DPNR (Diesel Particulate-NOx Reduction system) has been developed. The new catalytic converter for DPNR has fine porous ceramic wall flow filter similar to a DPF (Diesel Particulate Filter), coated with NOx storage reduction catalyst. It can reduce NOx and particulate matter simultaneously. An exhaust port fuel injection system has been newly developed. It creates rich exhaust gas condition to reduce NOx and SOx, irrespective of lean engine operating conditions. In combination with the exhaust fuel injection and engine improvements, very low exhaust emission level, less than half of the European STEP4 regulation standard, is achieved.</div>
Retrofitting-new high voltage XLPE cables substituting paper-insulated power cables in steel pipes (1998)

Many utilities still have paper-insulated pipe type cables in service. In the near future they may have to replace some of these systems due to local increases in electric power demand or aged cable insulation. In many cases the steel pipes are well protected against corrosion and thus suitable for further use. For retrofitting in such installations, XLPE-insulated cables offer several advantages. Felten & Guilleaume Energietechnik AG has developed a new three-core XLPE-insulated 64/110 kV cable with reduced insulation thickness (10 mm), that can be pulled into a pipe. In co-operation with VEW ENERGIE AG, the cable performance is being investigated in a field test, that started in October 1996. This long-term loading cycle test will last for three years. The test voltage, applied between conductor and earth, amounts to 127 kV. The temperature is measured with the help of an optical-fiber measurement system. This device is computer controlled and works as a remote monitoring system.
Liver 4DMRI: A retrospective image‐based sorting method (2015)

The authors present a novel methodology to derive a patient-specific 4DMRI model to describe organ motion due to breathing, with improved image quality in 4D reconstruction.
Impact of Small-Molecule Glucokinase Activator on Glucose Metabolism and β-Cell Mass (2008)

We investigated the effect of glucokinase activator (GKA) on glucose metabolism and beta-cell mass. We analyzed four mouse groups: wild-type mice and beta-cell-specific haploinsufficiency of glucokinase gene (Gck(+/-)) mice on a high-fat (HF) diet. Each genotype was also treated with GKA mixed in the HF diet. Rodent insulinoma cells and isolated islets were used to evaluate beta-cell proliferation by GKA. After 20 wk on the above diets, there were no differences in body weight, lipid profiles, and liver triglyceride content among the four groups. Glucose tolerance was improved shortly after the GKA treatment in both genotypes of mice. beta-Cell mass increased in wild-type mice compared with Gck(+/-) mice, but a further increase was not observed after the administration of GKA in both genotypes. Interestingly, GKA was able to up-regulate insulin receptor substrate-2 (Irs-2) expression in insulinoma cells and isolated islets. The administration of GKA increased 5-bromo-2-deoxyuridine (BrdU) incorporation in insulinoma cells, and 3 d administration of GKA markedly increased BrdU incorporation in mice treated with GKA in both genotypes, compared with those without GKA. In conclusion, GKA was able to chronically improve glucose metabolism for mice on the HF diet. Although chronic GKA administration failed to cause a further increase in beta-cell mass in vivo, GKA was able to increase beta cell proliferation in vitro and with a 3-d administration in vivo. This apparent discrepancy can be explained by a chronic reduction in ambient blood glucose levels by GKA treatment.
The gene for rat atrial natriuretic factor. (1985)

Atrial natriuretic factor (ANF), a peptide hormone recently isolated from heart atria, appears to play an important role in the regulation of extracellular fluid volume and blood pressure. Indeed, natural and synthetic ANF rapidly and markedly stimulate natriuresis and diuresis and produce smooth muscle relaxation. Consistent with the hypothesis that ANF is a novel hormone, it was recently shown that ANF is present in circulation, and high affinity membrane receptors specific for ANF have been described in renal, vascular, and adrenal tissues. These important biological activities suggest that conditions like hypertension could be associated with defective ANF gene expression. We and others have shown by cDNA cloning that ANF is part of a larger precursor, pro-natriodilatin (PND). We now describe the isolation and structural analysis of the rat PND gene. Southern blot analysis of rat genomic DNA suggests the presence of a single PND gene per haploid genome. The PND coding sequences are interrupted by two short introns. A long alternating purine-pyrimidine tract (GT)9GATG(GT)27 is found 111 base pairs downstream of the polyadenylation site; such sequences could adopt Z-DNA configuration and they have been associated with sequences that appear very active in intergenic recombination. Comparison of the rat and human PND genomic sequences shows highest homology in 5'-flanking as well as in coding sequences. The rat PND gene will be a useful model to study the physiology and pathology of this important regulator of the cardiovascular system.
Solar and Geomagnetic Activities: Are There Associations with Stroke Occurrence? (1997)

Several correlational studies have suggested an association between stroke mortality rates and geophysical parameters, but none have assessed the influence of these parameters on stroke occurrence in a general population. We conducted a population-based study (2,195 stroke patients) to determine whether there are relationships between stroke occurrence and solar and/or geomagnetic activity. A multivariable logistic regression analysis was used to estimate the odds ratio (OR) and to identify the geophysical parameters of most importance; 95% confidence intervals (CI) were calculated for the variables studied. In a multivariate analysis, large fluctuations of solar (OR = 1.21; 95% CI 1.14–1.30) and geomagnetic activity (0R = 1.20; 95% CI 1.11–1.31) on the preceding day and low level of solar activity (OR = 1.14; 95% CI 1.08–1.21) on the day of stroke onset were independent predictors of stroke occurrence.
Genetic Evidence that the α5 Helix of the Receiver Domain of PhoB Is Involved in Interdomain Interactions (2001)

Two-component signaling proteins are involved in transducing environmental stimuli into intracellular signals. Information is transmitted through a phosphorylation cascade that consists of a histidine protein kinase and a response regulator protein. Generally, response regulators are made up of a receiver domain and an output domain. Phosphorylation of the receiver domain modulates the activity of the output domain. The mechanisms by which receiver domains control the activities of their respective output domains are unknown. To address this question for the PhoB protein from Escherichia coli, we have employed two separate genetic approaches, deletion analysis and domain swapping. In-frame deletions were generated within the phoB gene, and the phenotypes of the mutants were analyzed. The output domain, by itself, retained significant ability to activate transcription of the phoA gene. However, another deletion mutant that contained the C-terminal alpha-helix of the receiver domain (alpha5) in addition to the entire output domain was unable to activate transcription of phoA. This result suggests that the alpha5 helix of the receiver domain interacts with and inhibits the output domain. We also constructed two chimeric proteins that join various parts of the chemotaxis response regulator, CheY, to PhoB. A chimera that joins the N-terminal approximately 85% of CheY's receiver domain to the beta5-alpha5 loop of PhoB's receiver domain displayed phosphorylation-dependent activity. The results from both sets of experiments suggest that the regulation of PhoB involves the phosphorylation-mediated modulation of inhibitory contacts between the alpha5 helix of its unphosphorylated receiver domain and its output domain.
Vaccination with recombinant filarial paramyosin induces partial immunity to Brugia malayi infection in jirds (1993)

Vaccination with irradiated infective larvae induces partial protective immunity to infection with the filarial nematode Brugia malayi in jirds. Prior studies have shown that such immunization stimulates a much stronger antibody response to recombinant and native filarial paramyosin than that seen after normal infection. To determine whether vaccination with recombinant paramyosin could induce protective immunity to larval challenge, jirds were immunized with either B. malayi paramyosin and maltose binding protein (BM5-MBP) (fusion protein of B. malayi paramyosin and maltose-binding protein), MBP alone, or recombinant Dirofilaria immitis paramyosin. Animals were challenged with 100 infective larvae s.c. 8 wk after the second immunization. Necropsies were performed 16 wk after challenge. Vaccination with BM5-MBP induced significant protective immunity; adult worm recoveries, worm lengths, and blood microfilaria counts were reduced in the BM5-MBP group relative to the MBP control group. The reductions in adult worm recoveries (43%) and female worm lengths (10%) were statistically significant (p < 0.05). Interestingly, protective immunity was not induced by immunization with D. immitis paramyosin. Additional studies are needed to identify mechanisms involved in protective immunity induced by BM5-MBP and to understand the differential activity of the two closely related recombinant paramyosin proteins in this model.
Global convergence of the recursive kernel regression estimates with applications in classification and nonlinear system estimation (1992)

An improved exponential bound on the L/sub 1/ error for the recursive kernel regression estimates is derived. It is shown, using the martingale device, that weak, strong and complete L/sub 1/ consistencies are equivalent. Consequently the conditions on a certain smoothing sequence are necessary and sufficient for strong L/sub 1/ consistency of the recursive kernel regression estimate. The rates of global convergence are also given. Obtained results are applied to recursive classification rules and to nonlinear time series estimation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High‐Resolution Mapping of Tachycardia Originating from the Superior Vena Cava: Evidence of Electrical Heterogeneity, Slow Conduction, and Possible Circus Movement Reentry (2002)

Superior Vena Cava Reentry. High-resolution mapping of a tachycardia originating from the superior vena cava (SVC) in a patient with atrial fibrillation is described. Unidirectional circuitous repetitive activation encompassing the full tachycardia cycle length was documented around a line of block within the myocardial sleeve of the SVC. Intermittent conduction to the right atrium resulted in an irregular atrial tachycardia. Evidence of electrical heterogeneity and slow conduction persisted in sinus rhythm and was exaggerated by premature stimulation but did not reproduce the activation pattern during tachycardia. All the available evidence is best compatible with circus movement reentry within the SVC, with marked slow and anisotropic conduction responsible for the restricted dimensions of the reentrant circuit. These findings may suggest a similar substrate and arrhythmia mechanism in the myocardium of the pulmonary veins.
Efficient code diversification for network reprogramming in sensor networks (2010)

As sensors in a network are mostly homogeneous in software and hardware, a captured sensor can easily expose its code and data to attackers and further threaten the whole network. To increase the survivability of a sensor network, code diversification has been shown to be an effective solution. However, disseminating many diversified code images is very costly in current network reprogramming systems, as it does not take advantage of the epidemic propagation of network reprogramming. New mechanisms need to be studied for integrating code diversification with network reprogramming. This paper proposes an efficient code diversification scheme for network reprogramming in sensor networks. The scheme uses Deluge to disseminate code images of sensor applications that carry diversification information and allows sensors to randomize the layout of their own executables. Such diversification can defeat a wide range of attacks that exploit the knowledge of code layout, as no sensors have the same code layout in their executables. Except the cost determined by the code size, the computational overhead of diversification in sensors can be reduced to 60%, while sacrificing only 10% of security.
Alstrom's syndrome: further evidence of autosomal recessive inheritance and endocrinological dysfunction. (1990)

We report a case of Alstrom's syndrome with hypothyroidism in addition to the cardinal features of blindness, deafness, obesity, and insulin dependent diabetes mellitus. The parents were first cousins once removed which strengthens the case for autosomal recessive inheritance.
Intensive Lipid Lowering by Statin Therapy Does Not Improve Vasoreactivity in Patients With Type 2 Diabetes (2002)

Cardiovascular disease is the most important cause of morbidity and mortality in patients with type 2 diabetes. Endothelial dysfunction predicts cardiovascular outcome. Type 2 diabetes is characterized by endothelial dysfunction, which may be caused by dyslipidemia. Statin therapy restores endothelial function in hyperlipidemic patients. Therefore, we hypothesize a beneficial effect of atorvastatin on NO-dependent vasodilation in patients with type 2 diabetes and mild dyslipidemia (low density lipoproteins >4.0 mmol/L and/or triglycerides >1.8 mmol/L). We evaluated the effect of intensive lipid lowering (4 weeks of 80 mg atorvastatin once daily) on vasoreactivity in 23 patients with type 2 diabetes by using venous occlusion plethysmography. Twenty-one control subjects were matched for age, sex, body mass index, blood pressure, and smoking habits. The ratio of blood flows in the infused (measurement [M]) and noninfused (control [C]) arm was calculated for each recording (M/C ratio), and M/C% indicates the percentage change from the baseline M/C ratio. Serotonin-induced NO-dependent vasodilation was significantly blunted (52+/-30 versus 102+/-66 M/C%, P<0.005), and nitroprusside-induced endothelium-independent vasodilation was modestly reduced (275+/-146 versus 391+/-203 M/C%, P<0.05) in patients with type 2 diabetes compared with control subjects. Despite significant reduction of total cholesterol, low density lipoproteins, and triglycerides (5.8+/-1.0 to 3.2+/-0.6 [P<0.0001], 4.1+/-1.1 to 1.8+/-0.7 [P<0.0001], and 2.2+/-1.3 to 1.4+/-0.5 [P<0.05] mmol/L, respectively), no effect on NO-dependent (59+/-44 M/C%) and endothelium-independent (292+/-202 M/C%) vasodilation was demonstrated. These data suggest that intensive lipid lowering by atorvastatin has no effect on NO availability in forearm resistance arteries in type 2 diabetic patients. Other factors, such as hyperglycemia, may be a more important contributing factor regarding impaired vasoreactivity in this patient group.
Evidence for a new spinocerebellar ataxia locus (1997)

The autosomal dominant ataxias (ADA) are a diverse group of multisystem, neurodegenerative disorders characterized by mutations at several chromosomal loci (SCA types 1-5, SCA type 7, DRPLA). We excluded all the known SCA loci by mutational and linkage analyses is an American family of British origin with ADA and document that an additional ataxia locus must exist. The clinical characteristics and ethnic origin of our family are similar to the British Drew family of Walworth with the SCA type 3 mutation and differ from other families without a known ataxia locus. Individuals in our family and the Drew family initially show signs of ataxia but may develop variable degrees of ophthalmoplegia, Parkinsonian features and central demyelination. The phenotypic diversity in families without a known ataxia locus suggests that there may be several other undefined ataxia loci.
A novel screening system for secretion of heterologous proteins in <i>Bacillus subtilis</i> (2011)

High-level production of secretory proteins in Bacillus subtilis leads to a stress response involving the two-component system CssRS and its target genes htrA and htrB. Here, we used this sensing system in a reporter strain in which gfp is under control of P(htrA) , the secretion stress responsive promoter of htrA. Overexpression of heterologous secretory proteins in this strain results in green fluorescent cells, which can be separated from non-secreting, low fluorescent cells using a fluorescence-activated cell sorter (FACS). Using this principle, genomic libraries of uncharacterized prokaryotic organisms, expressed in the reporter strain, can be screened for genes encoding secretory proteins.
Patellar prosthesis positioning in total knee arthroplasty. A roentgenographic study. (1988)

Patellar prosthesis positioning in 40 primary total knee replacements was evaluated with regard to (1) patellar tilt, (2) angle between the patellar component and patellar bony remnant, (3) lateral versus medial placement, (4) patellar height, and (5) size of the patellar component versus patellar length. Two different designs were evaluated. Twenty knees that were resurfaced with a patellar button prosthesis and implanted with conventional surgical technique constituted Group A. Twenty knees that were resurfaced with a new biconvex prosthesis and implanted with specially designed instrumentation constituted Group B. For Group A, the patellar tilt averaged 4.25 degrees preoperative and 8.35 degrees postoperative. For Group B the patellar tilt averaged 4.60 degrees preoperative and 1.83 degrees postoperative. In Group B, there was significant improvement in patellar position, with only two patients showing values exceeding the neutral range (p = 0.0409). The angle between the patellar component and the bony remnant in Group A averaged 5.975 degrees, and in Group B, 1.447 degrees. Two patients in Group A and 18 patients in Group B had values in the normal range for patellar tilt and the angle between the prosthesis and the bone. The prosthesis was inserted medial to the patellar center in six patients in Group A and one patient in Group B. A significant decrease in patellar height was noted for both groups, but values were still within the normal range. Both groups showed significant increase in the postoperative articular length, indicating that oversized prostheses were inserted and excess bone removed.