gebhart/patrepeval huggingface dataset:
Spectral absorbance, structure, and population density of photoreceptors in the retina of the lake sturgeon (Acipenser fulvescens) (2007)

Lake sturgeon ( Acipenser fulvescens Rafinesque, 1817) photoreceptors were studied with scanning electron microscopy and microspectrophotometry. The retina contains both rods and cones, with cones estimated composing about 30% of the photoreceptor population. Only large single cones were identified and they are similar to those found in other species of the order Acipenseriformes. The rods are large, with long, broad outer segments, and are similar to the dominant rod found in other sturgeons and the North American paddlefish ( Polyodon spathula (Walbaum, 1792)). Mean (SD) rod packing density at 22 624 ± 3 509 rods/mm 2 is low compared with those of other animals that function primarily in dim light. The visual pigment of the rods has a mean (SD) peak absorbance (λ max ) at 541 ± 2 nm. Three different cone populations were identified: a long wavelength sensitive cone containing a visual pigment with λ max at 619 ± 3 nm; middle wavelength sensitive cone with λ max at 538 ± 1 nm; and short wavelength sensitive cone with λ max at 448 ± 1 nm. All the visual pigments are based on the vitamin A 2 chromophore.
Utilizing adenovirus vectors for gene delivery in cancer (2014)

The fusion of bioengineering and biopharmaceutical technologies can provide solutions to the obstacles encountered during systemic delivery of Ads. The in vivo transgene expression efficiency of Ad nanocomplex systems is typically high, and animal tumor models demonstrate that systemic administration of these Ad complexes can arrest tumor growth. However, further optimization of these smart Ad nanocomplex systems is needed to increase their effectiveness and safety for clinical application in cancer gene therapy.
B lymphocytes in Treatment-Naïve Pediatric Lupus Patients are Epigenetically Distinct from Healthy Children (2022)

Abstract Background Systemic lupus erythematosus (SLE) is a complex disease likely triggered by gene-environment interactions. We have shown that most of the SLE-associated haplotypes encompass genomic regions enriched for epigenetic marks associated with enhancer function in neutrophils, and T and B cells, suggesting that genetic risk is exerted through altered gene regulation. Data remain scarce on how epigenetic variance contributes to disease risk in pediatric SLE (pSLE). We aim to identify differences in epigenetically-regulated chromatin architecture in treatment-naïve pSLE patients compared to healthy children. Methods Using the assay for transposase-accessible chromatin with sequencing (ATACseq), we surveyed open chromatin in 8 treatment-naïve pSLE patients, with at least moderate disease severity, and 5 healthy children. We investigated whether regions of open chromatin unique to pSLE patients demonstrate enrichment for specific transcriptional regulators, using standard computational approaches to identify unique peaks and a false discovery rate of &lt;0.05. Further analyses for differential transcription factor binding, histone modification enrichment, and variant calling were performed using multiple bioinformatics packages in R and Linux. Results There were 30,139 differentially accessible regions (DAR) identified unique to pSLE B cells, of which 64.3% are more accessible in pSLE than B cells from healthy children. Many of these DAR are found in distal, intergenic regions, and are enriched for enhancer histone marks (p=0.027). When we compared B cells from pSLE patients to those of untreated adults, we found more regions of inaccessible chromatin, and fewer DAR within 10-100kb of known SLE haplotypes. In pSLE B cells, 65.2% of the DAR are located within or near known SLE haplotypes. Further analysis revealed enrichment of several transcription factor binding motifs within these DAR that may regulate genes involved in the pro-inflammatory responses and cellular adhesion. Conclusions This is the first report describing differences in chromatin architecture between pSLE patients and healthy children. We demonstrate an epigenetically-distinct profile in pSLE B cells when compared to those from healthy children and adults with lupus, indicating that pSLE B cells are predisposed for disease onset and development. Increased chromatin accessibility in non-coding genomic regions controlling activation of inflammation and the immune response suggest that transcriptional dysregulation by regulatory elements that control B cell activation plays an important role in the pathogenesis of pSLE.
Supplementary Figure 2 from Brain Tumor Cells in Circulation Are Enriched for Mesenchymal Gene Expression (2023)

&lt;p&gt;STEAM cocktail staining specifically identifies GBM cells.&lt;/p&gt;
LIGNITE FUEL ENHANCEMENT (2005)

The Design Team continued to conference this quarter. Their primary task during this timeframe was to finalize the dryer design based on information learned from the NDIC Pilot work and detailed design discussions at Barr offices in August. Heyl-Patterson was tasked with incorporating all comments and drafting drawings. They submitted a preliminary proposal which spawned detailed discussions about tube bundle, air locks, and fire suppression systems. The type of fire protection specified dictated the final structural arrangement. Three meetings were spent discussing the pro's and con's of suppression vs. ventilation systems. In the end, the dryer and bucket elevator will have suppression systems and the remaining equipment will be explosion vented. This is in agreement with GRE's current insurer, FM Global. Three inlet airlocks were reduced to two and four outlets were reduced to three. The inlet plenum was subdivided for greater flexibility and sparging air added in the outlet plenum. It was also decided to use bundles with varied material, diameter, and tube & fin spacing. This will be completed in an effort to identify for us which configuration has the best heat transfer characteristics using coal as the fluidizing medium. The dryer will also be delivered in four pieces. This will allow for installation through the current access door on the Air Heater deck. The Input/Output list and functional description was completed and forwarded to Honeywell to finalize controls. Major pieces of equipment received this quarter were the Bucket Elevator, Liewell Screen, conveyors, and Motor Control Center. ICI completed removal of the wall separating Silo 28 from the dryer area; handrail and grating between the two areas has also been removed. They relocated a blowdown line. They moved an Air Heater basket access hatch.
Investigation of porphyrin-forming reactions. Part 3. The origin of scrambling in dipyrromethane + aldehyde condensations yielding trans-A2B2-tetraarylporphyrins (2001)

The dipyrromethane + aldehyde condensation is a common method for the synthesis of trans-A2B2-porphyrins, but is often plagued by scrambling processes that lead to a mixture of porphyrins. The problem of scrambling is more pronounced with unhindered dipyrromethanes (e.g., 5-phenyldipyrromethane) than with hindered dipyrromethanes (e.g., 5-mesityldipyrromethane). We have characterized the oligomer composition (by LD-MS), yield of porphyrin (by UV–Vis), yield of N-confused porphyrin (by HPLC), and level of unreacted aldehyde (by TLC) in dipyrromethane + aldehyde condensations leading to trans-A2B2-porphyrins. Reaction conditions known to suppress scrambling in reactions involving 5-phenyldipyrromethane (PDPM) were compared to conditions known to provide extensive scrambling. The low-scrambling conditions were found to suppress scrambling by inhibiting reaction of oligomer fragments generated by acid-induced cleavage of the dipyrromethane, rather than by inhibiting acidolysis itself. However, such reaction conditions were also found to inhibit the condensation, leading to low yields (<10%) of porphyrin. The condensation of PDPM + aldehyde was also compared to reactions involving 5-mesityldipyrromethane (MDPM) to understand why trans-A2B2-porphyrins can be prepared in good yield devoid of scrambling from reactions using MDPM. The absence of scrambling in MDPM + aldehyde condensations was due to the resistance of MDPM to acidolysis. Taken together, these studies provide insight into the origin of scrambling with different types of substrates under different reaction conditions in the dipyrromethane + aldehyde route to trans-A2B2-porphyrins.
Genetic and Pharmacological Analyses of Syk Function in IIbβ3 Signaling in Platelets (1999)

Agonists induce inside-out IIbβ3signaling resulting in fibrinogen binding and platelet aggregation. These in turn trigger outside-in signaling resulting in further platelet stimulation. Because the Syk tyrosine kinase is activated during both phases of integrin signaling, we evaluated its role in IIbβ3 function in murine platelets rendered null for Syk by gene targeting and in human platelets incubated with piceatannol, a tyrosine kinase inhibitor reportedly selective for Syk. Both Syk null murine platelets and piceatannol-treated human platelets exhibited a partial, but statistically significant defect in activation of IIbβ3 by adenine diphosphate (ADP) ± epinephrine as assessed by fibrinogen binding. Syk null platelets adhered normally to immobilized fibrinogen, and mice with these platelets exhibited normal tail bleeding times. In contrast, piceatannol treatment of human platelets completely inhibited platelet adhesion to immobilized fibrinogen. The discrepancy in extent of integrin dysfunction between murine and human platelet models may be due to lack of specificity of piceatannol, because this compound inhibited the activity of Src and FAK as well as Syk and also reduced tyrosine phosphorylation of multiple platelet proteins. These results provide genetic evidence that Syk plays a role in IIbβ3 signaling in platelets and pharmacological evidence that, although piceatannol also inhibits IIbβ3 signaling, it does so by inhibtion of multiple protein tyrosine kinases.
Abstract P767: Understanding the Role of Microglial Il-1α After Stroke (2021)

The role of inflammation driven by the pro-inflammatory cytokine interleukin-1 (IL-1) during poststroke injury has been the focus of intense research. Indeed, pre-clinical studies have demonstrated the deleterious actions of IL-1 after stroke, whilst blocking its actions is beneficial in pre-clinical and clinical settings. Whilst most studies have focused on the role of IL-1β, the role of IL-1α during poststroke inflammation has been largely overlooked and very little has been done to examine the selective contribution of each IL-1 isoform in ischaemic stroke. In this study, we have investigated the contribution of IL-1α to ischaemic and haemorrhagic stroke. Methods : in vivo model of middle cerebral artery thrombosis through topical application of FeCl3 (40%) (n=4/group (4, 24, 72h) histology, n=6 /group (4, 24, 72 ) qPCR) in vivo model of haemorrhagic stroke induced by using the collagenase model (intra-striatal injection of collagenase VII-S, 0.045U) (n=4/group (4, 24h) histology). We first investigated the spatio-temporal expression of IL-1 in the brain after ischaemic stroke using an in vivo model of middle cerebral artery thrombosis through topical application of FeCl3 (n=4-6/group). We observed IL-1α positive microglia as early as 4 hours after ischaemic stroke. At 24 hours we observed IL-1α and also IL-1β positive microglia, moreover, IL-1β was also expressed by neutrophils and monocytes. These results have been confirmed by qPCR. Interestingly, we observed similar results after haemorrhagic stroke, induced by using the collagenase model, whereby IL-1α expression in microglia precedes IL-1β expression (n=4/group). The early expression of IL-1α in microglia in both models suggest a critical role for the microglial response during sterile inflammation. To further investigate the role of microglial IL-1α, we have generated a conditional IL-1α mouse mutant crossed with CX3CR1 Cre-ERT2 mice to induce a specific deletion of IL-1α in microglia. Future experiments using this genetic model will clarify the role of IL-1α during the acute phase of strokes.
Ultraviolet Photolithographic Development of Polyphosphazene Hydrogel Microstructures for Potential Use in Microarray Biosensors (2006)

Polyphosphazenes that bear both methoxyethoxyethoxy and cinnamyl side groups were synthesized and evaluated for use as hydrogels incorporated into micrometer-scale biosensor arrays. Polymers with the general formula [NPRxR‘y]n where R = OCH2CH2OCH2CH2OCH3 and R‘ = OCHCHCH2Ph (x = y = 1; x = 2, y = 0) were synthesized. The polymers were cross-linked to form hydrogels by exposure to ultraviolet radiation (λ = 320−480 nm) in the presence of a photoinitiator. Hydrogel microstructures in the size range 50−500 μm were fabricated using standard photolithographic techniques. The resolution and dimensions of these microstructures were examined by optical microscopy, scanning electron microscopy, and profilometry. The resultant three-dimensional hydrogel microstructures were used to encapsulate enzymes for biosensor applications. The enzymatic activity of encapsulated horseradish peroxidase (HRP) was examined as a model system. The HRP catalyzed reaction between H2O2 and Amplex Red to produce a fluorescent product, resorufin, was confirmed by fluorescence microscopy.
MWIR optical modulation using structured silicon membranes (2016)

We have used near IR pump – Mid IR probe techniques to compare the feasibility and potential of using free standing nano-porous and micro-porous silicon (ordered hole arrays) as optically controlled modulators operating in the Mid-Wave Infrared (MWIR) covering the range from 3.3-5 <i>&mu;</i>m. We employed 800 nm pumping pulses with the duration of 60 fs to reduce 4 <i>&mu;</i>m light transmission modulation to about 25% and 45% for both silicon structures, respectively, at excitation powers of 50mW (4 <i>mJ=cm<sup>2</sup></i>). However, at 5 <i>&mu;</i>m both structures shown similar contrast of about 60%. The time resolved measurements revealed a fast sub-picosecond rise time for both structures suggesting that the optically generated carriers are a dominant mechanism for the modulation. However, the measurements demonstrated a significant difference in the relaxation dynamics. The nanoporous silicon demonstrated recovery as fast as a few tens of picoseconds and a possibility to effectively work in the GHz regime, while hole arrays shown almost three orders of magnitude slower response making it suitable for the MHz regime.
Search for new physics in final states with a lepton and missing transverse energy inppcollisions at the LHC (2013)

This Letter describes the search for an enhanced production rate of events with a charged lepton and a neutrino in high-energy pp collisions at the LHC. The analysis uses data collected with the CMS detector, with an integrated luminosity of 5:0 fb 1 at ffiffi ffi s p 7 TeV, and a further 3:7 fb 1 at ffiffi ffi s p 8 TeV. No evidence is found for an excess. The results are interpreted in terms of limits on a heavy charged gauge boson (W 0 ) in the sequential standard model, a split universal extra dimension model, and contact interactions in the helicity-nonconserving model. For the last, values of the binding energy below 10.5 (8.8) TeV in the electron (muon) channel are excluded at a 95% confidence level. Interpreting the ' final state in terms of a heavy W 0 with standard model couplings, masses below 2.90 TeV are excluded.
Effect offurmutation on acid-tolerance response and in vivo virulence of avian septicemicEscherichia coli (2002)

The Fur (ferric uptake regulator) protein is a master regulator of iron metabolism in gram-negative bacteria. In the present study, the effect of a partial deletion of the fur gene on the acid-tolerance response and in vivo virulence of avian Escherichia coli was examined. The fur mutant was unable to trigger the acid-tolerance response as observed in the wild-type parent strain. However, the mutant was as virulent as the wild-type parent strain when tested in 1-day-old chickens by subcutaneous inoculation. These data indicate that the fur gene is involved in the acid-tolerance response but not involved in the virulence of E. coli, as detected by the ability to cause septicemia in our experimental infection.
How to get away with liver innate immunity? A viruses’ tale (2021)

In their never-ending quest towards persistence within their host, hepatitis viruses have developed numerous ways to counteract the liver innate immunity. This review highlights the different and common mechanisms employed by these viruses to (i) establish in the liver (passive entry or active evasion from immune recognition) and (ii) actively inhibit the innate immune response (ie modulation of pattern recognition receptor expression and/or signalling pathways, modulation of interferon response and modulation of immune cells count or phenotype).
Abstract 2361: MYC-driven breast cancer tumorigenesis is dependent on normal mitochondrial function (2022)

Abstract While the transcription factor MYC is amplified in all breast cancer subtypes, nearly 60% of patients with triple-negative tumors have elevated MYC copy number and expression. Patients with triple-negative breast cancer (TNBC) typically have increased metastasis, decreased response to therapies, and poor outcomes, highlighting MYC’s causal association with disease aggressiveness and low survival rates. Unfortunately, MYC is not considered directly pharmacologically tractable. Therefore, we sought to identify collateral “genetic dependencies,” downstream of oncogenic MYC. Using comparative genome-scale CRISPR/Cas9 screening in isogenic human mammary epithelial cells (HMECs), we have identified two mitochondrial membrane transporter genes, TIMM17A and MTCH2, specifically required for MYC-dependent proliferation and survival. Since MYC is suspected to drive metabolic reprogramming in cancers, we assessed how MYC affected mitochondrial protein content by quantitative mass spectrometry. This revealed an increase in N-acetylaspartate (NAA) in HMECs with MYC amplification compared to other genetic backgrounds. Interestingly, increased NAA levels are dependent on TIMM17A and MTCH2 presence. Loss of either of these genes results in cell death coupled with decreased NAA. NAA supplementation in the media of MYC-HMECs following loss of TIMM17A or MTCH2 can rescue the cell death. Importantly, NAA supplementation in cells with guides targeting GFP (negative control) or general essential gene RPL11 did not show increased cell growth/viability - showing that the NAA supplementation is specifically compensating for loss of mitochondrial transport function in MYC-HMECs. Based on these data, it appears that MYC-amplified TNBCs are uniquely dependent on TIMM17A and MTCH2 mitochondrial transporter function because they drive metabolic reprogramming resulting in addiction to N-acetylaspartate production. To conclude these studies, we are evaluating the dependence on mitochondrial transport and NAA synthesis in MYC-amplified TNBCs by assessing the function of TIMM17A and MTCH2 as MYC-specific genetic dependencies in patient derived xenografts of TNBC and determining if TNBCs are addicted to increased NAA synthesis by overexpressing aspartoacylase to breakdown NAA. Successful completion of this work will provide novel drug targets required for survival of aggressive MYC-amplified breast cancers. Citation Format: Sydney M. Moyer, Nina Ilic, Sydney Gang, Taylor E. Arnoff, William C. Hahn. MYC-driven breast cancer tumorigenesis is dependent on normal mitochondrial function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2361.
Seamless Stitching using Multi-Perspective Plane Sweep (2004)

Withdigitalcamerasbecomingincreasinglycheaperandmoreaccessibletoconsumers,thereexistsastrongneedforbetterautomateddigitalimageprocessing. Red-eye removalandcolorcorrectionaretwo of the more popular image processing capabilities that have been incorporated into commercialsoftware packages aimed at photographers. Another popular application is
The fabrication and characterization of fiber Bragg gratings in highly birefringent photonic crystal fibers for sensing applications (2008)

The combination of the functionalities of Fiber Bragg Gratings (FBGs) and Photonic Crystal Fibers (PCFs) has unveiled new potential for FBG based sensors. The fabrication of FBGs in PCFs has been reported in literature. However, using dedicated PCFs to improve the sensitivity of FBG-based sensors has received only limited attention. In this report we therefore show how to eliminate some of the drawbacks of FBGs in conventional step-index fibers for sensor applications by exploiting the design flexibility of PCFs. The added value of PCFs stems from the ability to design an optical fiber in which an FBG acts as a sensor with a selective sensitivity, e.g. a sensor that is sensitive to strain but not to temperature. For this purpose we use a PCF with a birefringence on the order of 10<sup>-3</sup>, which is one order of magnitude larger than for conventional birefringent fibers. The two FBG reflection peaks are therefore significantly separated from each other, e.g. 2 nm, which makes these FBGs suited for sensing purposes since both peaks can be unambiguously and accurately identified. As a conclusion we summarize the advantages and disadvantages of our approach to design and fabricate selective FBG-based sensors.
Atomically Flat Silicon Surface and Silicon/Insulator Interface Formation Technologies for (100) Surface Orientation Large-Diameter Wafers Introducing High Performance and Low-Noise Metal–Insulator–Silicon FETs (2009)

Technology to atomically flatten the silicon surface on (100) orientation large-diameter wafer and the formation technology of an atomically flat insulator film/silicon interface are developed in this paper. Atomically flat silicon surfaces composed of atomic terraces and steps are obtained on (100) orientation 200-mm-diameter wafers by annealing in pure argon ambience at 1200 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">deg</sup> C for 30 min. Atomically flat surfaces with various terrace widths and step structures are observed by atomic force microscopy. It is found that the atomic terrace width changes widely with an off angle of the wafer surface from the (100) lattice plane. It is also found that the direction of the off angle significantly affects the atomically flat surface morphology, i.e., when the directions of the off angles are parallel to the <110> directions, the step structure is composed of alternating pairs of straight and triangular steps. When the directions of the off angles are parallel to the <100> directions, the step structure is composed of only straight steps. By precise control of the off angle and the direction toward the <100> directions for a 200-mm-diameter silicon wafer, we have succeeded in fabricating an atomically flat surface with straight atomic steps and a very uniform terrace width of 140-150 nm on the entire surface of a large-diameter silicon wafer. Furthermore, it is found that only radical-reaction-based insulator film formation technology, such as oxidation utilizing oxygen radicals carried out at a low temperature (400 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">deg</sup> C ), preserves the atomic flatness of the insulator film/silicon interface. Finally, when MOSFETs are fabricated with an atomically flat interface, they exhibit near ideal subthreshold swing factors, with much smaller fluctuation, extremely lower 1/ <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</i> noise, and higher MOS dielectric breakdown field intensity compared with MOSFETs fabricated with conventional technologies.
On Six Species Of Koenenia: With Remarks On The Order Palpigradi (2009)

to belong to the Italian species.He kindly sent me a copy of the paper, and instantly I saw from his description and figures that it was a new species.Later