gebhart/patrepeval huggingface dataset:
An mRMR-SVM Approach for Opto-Fluidic Microorganism Classification (2018)

The detection of microorganisms is important in numerous applications such as water quality monitoring, blood analysis, and food testing. The conventional detection methods are tedious and labour-intensive. Establish methods involve culturing, counting and identification of the pathogen by an experienced technician which typically can take several days. The use of opto-fluidic technology to capture microorganism images offers 0 route to reduce the overall assay time. However, the detection still requires a trained technician. This paper proposes an image processing method that can be used to classify microorganism images captured by an opto-fluidic set up in an automatic manner. The proposed algorithm incorporates some of the features used in other microorganism image detection methods and proposes two new features-Entropy of Histogram of Oriented Gradients (HOG) and the filtered intensities. In addition, we propose to apply the minimal-Redundancy-Maximal-Relevance (mRMR) criterion to select and rank these features. The probability and joint probability distribution functions of the mRMR are estimated using a Gaussian model and the Kernel Density Estimation model. The performance of the proposed method was validated using SVM and data collected from an experimental setup. The results show that our proposed method outperforms existing methods and is capable of achieving a classification accuracy up to 95.8%.
Palmitoylation of the recombinant human A1 adenosine receptor: enhanced proteolysis of palmitoylation-deficient mutant receptors (1999)

Palmitoylation of the recombinant human A(1) adenosine receptor (A(1)AR) expressed in HEK-293 cells is demonstrated by showing that hexahistidine (His(6))/Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys (FLAG) (H/F) A(1)ARs, purified to homogeneity from cells metabolically labelled with [(3)H]palmitate, incorporate tritium into a 38-42 kDa receptor glycoprotein. The amount of palmitoylation is not affected by incubation of cells with the A(1)AR-selective agonist N(6)-cyclopentyladenosine (CPA). A(1)AR palmitoylation is abolished by treatment with neutral hydroxylamine or by mutation of Cys-309 to Ala (C(309)-->A). Based on Western blotting and pulse-chase experiments with [(35)S]methionine, at least 90% of wild-type receptors are palmitoylated and turn over with a t1/2 of 6.4 h. Of the C(309)-->A mutated receptors, 40% appear to turn over like wild-type receptors, with a t1/2 of 7.1 h, and 60% appear to be rapidly cleaved to form a 25 kDa receptor fragment that turns over with a t1/2 of 0.8 h. In HEK-293 cell lines expressing similar numbers of wild-type or C(309)-->A mutant A(1)Rs, there is little difference in the kinetics of CPA-induced receptor internalization (1 h), down-regulation (24 h), inhibition of forskolin-stimulated cAMP accumulation, or activation of co-transfected G-protein-activated inward rectifier K(+)/cardiac inward rectifying K(+) (GIRK1/CIR K(+)) channels. Also unaffected by palmitoylation is guanosine 5'-[gamma-thio]-triphosphate ([S]GTP)-sensitive binding to membranes by the agonist (125)I-labelled aminobenzyladenosine. The results suggest that palmitoylation has little effect on receptor-effector coupling, agonist-induced internalization or down-regulation. We speculate that palmitoylation may divert newly synthesized A(1)ARs from a pathway leading to rapid degradation.
A Self-Aligning Flip-Chip Assembly Method Using Sacrificial Positive Self-Alignment Structures (2016)

A self-aligning flip-chip assembly method is described. The method is capable of correcting up to 150 μm (five times the radius of solder balls used) of initial misalignment during flip-chip assembly. Critical components of the self-alignment are four polymeric positive self-alignment structures (PSASs), which are fabricated on a substrate, and four inverted pyramid pits, which are etched on a silicon chip in corresponding positions. The PSAS is removed using solvent after the assembly. Resistance of the solder joints is measured to be below 9 mΩ.
Ground-state properties of GaAs and AlAs (1981)

Ground-state properties of GaAs and AlAs are studied and compared using the self-consistent pseudopotential method. The calculated equilibrium lattice constant, the bulk modulus, and the cohesive energy of these compounds are in good agreement with experiment. This agreement allows for the investigation of a subtle difference in the bond strength between GaAs and AlAs. The density of states for the two compounds is found to be similar, but there exists a characteristic difference which can be used as a sensitive probe for distinguishing different species. The valence charge density and the kinetic energy density functions for these compounds are illustrated for comparison.
Comparison between pre-log and post-log statistical models in low-dose CT iterative reconstruction (2014)

X-ray detectors in clinical computed tomography (CT) operate in energy-integrating mode. Their signal statistics is complicated by a cascade of random processes which prevent a highly accurate model of signal statistics from being practical for CT iterative reconstruction algorithms. Since all models are approximations, it is natural to ask whether incremental refinement of their accuracy may be beneficial in practice. In the design of CT model-based iterative reconstruction (MBIR), pre-log and post-log models are the two major categories of statistical models being considered, but it is rather uncertain whether one model could lead to notably improved image quality over the other in realistic situations. In this study, we compare pre-log and post-log MBIR methods using real phantom data acquired on a GE Discovery CT750 HD system over a wide range of x-ray dose levels. The pre-log MBIR included Beer's law, beam-hardening effects, and all major data calibration factors in a nonlinear forward model to perform three-dimensional image reconstruction directly from raw multi-slice CT measurements, whereas the post-log MBIR used pre-corrected and log-converted data so that a simpler linear forward model was used. We found that pre-log MBIR achieved better CT number accuracy in low dose settings when compared to post-log MBIR, but the two methods produced very similar images at high and medium dose settings. Although a few potentially attractive options remain to be explored to further improve the image quality of both pre-log and post-log methods, we conclude that accurate noise models may be important for iterative reconstruction of very low dose CT datasets, and careful design and optimization of the models should not be overlooked in the design of CT MBIR.
Project Title: Radiochemical Analysis by High Sensitivity Dual-Optic Micro X-ray Fluorescence (2003)

A novel dual-optic micro X-ray fluorescence instrument will be developed to do radiochemical analysis of high-level radioactive wastes at DOE sites such as Savannah River Site and Hanford. This concept incorporates new X-ray optical elements such as monolithic polycapillaries, which focus X-rays. The polycapillary optic can be used to focus X-rays emitted by the X-ray tube thereby increasing the X-ray flux on the sample over 1000 times. The polycapillary optic will also be used to collect the X-rays from the excitation site. This will effectively screen the radiation background from the radioactive species in the specimen. This dual-optic approach significantly reduces the background and increases the analyte signal thereby increasing the sensitivity of the analysis. This dual-capillary design is essentially a confocal (having the same foci) design, i.e. the detected X-rays are only emitted from the overlap of the two focal spots. This increases spatial resolution and reduce s background. The integration of the X-ray optics increases the signal-to-noise and thereby increases the sensitivity of the analysis for low-level analytes. This work will address a key need for radiochemical analysis of high-level waste using a non-destructive, multi-element, and rapid method in a radiation environment. There is significant potential that this instrumentation could be capable of on-line analysis for process waste stream characterization at DOE sites.
Rational Design of Lower‐Temperature Solid Oxide Fuel Cell Cathodes via Nanotailoring of Co‐Assembled Composite Structures (2014)

Abstract A novel in situ co‐assembled nanocomposite LSM‐Bi 1.6 Er 0.4 O 3 (ESB) (icn‐LSMESB) was obtained by conjugated wet‐chemical synthesis. It showed an enhancement of the cathode polarization at 600 °C by &gt;140 times relative to conventional LSM‐Y 0.08 Zr 0.84 O 1.92 (YSZ) cathodes and exceptional solid oxide fuel cell (SOFC) performance of &gt;2 W cm −2 below 750 °C. This demonstrates that this novel cost‐effective and broadly applicable process provides new opportunities for performance enhancement of energy storage and conversion devices by nanotailoring of composite electrodes.
Placing Two Fractures Consecutively in Close Proximity to Significantly Increase Revenue-to-Cost Ratio (2008)

Abstract Though fractures caused by stimulation will likely propagate away from high-permeability areas, the stimulation often provides a significant production improvement because of the large flow-path increase created by the fracture. This fact can be hard for many to accept. Placing two fractures consecutively in close proximity to each other may offer a tremendous benefit. With this approach, the first fracture is placed conventionally into the maximum stress direction. After a short delay, the second fracture is then placed, taking advantage of the temporary stress modification caused by the opening of the first fracture. This delay is computed so the stress modification at the tip of the second fracture is always maximized. This is done so that the second fracture will extend into the original (natural) minimum stress direction, meaning the fracture will extend into highly permeable areas and, therefore, production expectations from the second fracture will potentially be much larger than production of the first fracture. This leads to a significant increase in the revenue-to-cost ratio. In other words, a significant revenue increase can be achieved with an incremental cost increase. This new approach uses conventional pin-point stimulation methods; therefore, even though it is "new," it carries a very minimal risk with a potentially large payout. This paper discusses how the new process can be effectively performed by harnessing a pseudo-Maxwell/Kelvin-Voigt, creep phenomenon that is normally present in rock. The paper will also examine formation geology, reservoir aspects, best practices, better completion schemes, simulation data, and different stimulation and perforating techniques that would be best used for achieving maximum productivity.
Air-ground channel measurements and modeling for UAS (2014)

Unmanned aircraft systems (UAS) are expected to be used in greatly increasing numbers in the near future. To safely integrate them into the National Airspace System (NAS) [1] requires highly reliable communication links for control and nonpayload communications (CNPC) [2]. Although spectrum allocations for UAS appear to be in place, UAS missions can differ markedly from those of conventional piloted aircraft, and new challenges will appear. One of these challenges is the potential detrimental effects of the air-ground (AG) channel [3]. For past systems that used elevated ground site (GS) antennas in open areas, multipath propagation was minimal. Data rates and bandwidths of past systems were also small, rendering the multipath issue either inconsequential or easily overcome by (sometimes large) transmit power increases or longer latencies. Legacy voice communication systems are also comparatively low rate and forgiving of delay and can usually resort to repetition to improve reliability.
Secreted nuclear protein DEK regulates hematopoiesis through CXCR2 signaling (2019)

The nuclear protein DEK is an endogenous DNA-binding chromatin factor regulating hematopoiesis. DEK is one of only 2 known secreted nuclear chromatin factors, but whether and how extracellular DEK regulates hematopoiesis is not known. We demonstrated that extracellular DEK greatly enhanced ex vivo expansion of cytokine-stimulated human and mouse hematopoietic stem cells (HSCs) and regulated HSC and hematopoietic progenitor cell (HPC) numbers in vivo and in vitro as determined both phenotypically (by flow cytometry) and functionally (through transplantation and colony formation assays). Recombinant DEK increased long-term HSC numbers and decreased HPC numbers through a mechanism mediated by the CXC chemokine receptor CXCR2 and heparan sulfate proteoglycans (HSPGs) (as determined utilizing Cxcr2-/- mice, blocking CXCR2 antibodies, and 3 different HSPG inhibitors) that was associated with enhanced phosphorylation of ERK1/2, AKT, and p38 MAPK. To determine whether extracellular DEK required nuclear function to regulate hematopoiesis, we utilized 2 mutant forms of DEK: one that lacked its nuclear translocation signal and one that lacked DNA-binding ability. Both altered HSC and HPC numbers in vivo or in vitro, suggesting the nuclear function of DEK is not required. Thus, DEK acts as a hematopoietic cytokine, with the potential for clinical applicability.
Theoretical Investigation of Heat Pipes Operating at Low Vapor Pressures (1968)

A one-dimensional analysis of a compressible vapor flowing within the evaporator section of a heat pipe is presented. Comparisons between the theoretical results and existing heat pipe data show that the presence of gasdynamic choking can limit the heat transfer capacity of a heat pipe operating at sufficiently low vapor pressures.
Enzyme-free detection of hydrogen peroxide from cerium oxide nanoparticles immobilized on poly(4-vinylpyridine) self-assembled monolayers (2013)

A simple enzyme-free spectrophotometric detection of hydrogen peroxide is demonstrated based on its colorimetric reaction with oxygen deficient cerium oxide nanoparticles (CNPs). This colorimetric sensitivity of CNPs towards H<sub>2</sub>O<sub>2</sub> increases significantly with decreasing crystallite size due to an increase in the surface area as well as the concentration of Ce<sup>3+</sup> on the surface. The origin of this colorimetric reaction was studied using DFT that suggests the adsorption of peroxide and oxygen molecules on ceria nanoparticles creates new states in the electronic structure leading to transitions absorbing in the visible region of the electromagnetic spectrum. For detection, a single layer of nanoparticles was immobilized on transparent microscopic glass slides using self-assembled monolayers (SAMs) of poly(4-vinylpyridine) (PVP). Cluster-free and uniform immobilization of nanoparticles was confirmed from atomic force microscopy (AFM) and helium ion microscopy (HIM). UV-Visible absorption measurements showed a concentration dependent increase in absorbance from immobilized CNPs that were exposed to increasing concentrations (10-400 μM) of hydrogen peroxide. The immobilized CNPs can be baked at 80 °C after initial use to regenerate the sensor for reuse. The development of a direct, reusable, enzyme-free and dye-free peroxide sensing technology is possible and can be immediately applied in various areas, including biomedicine and national security.
Tyrosine phosphorylation and activation of Bruton tyrosine kinase upon Fc epsilon RI cross-linking. (1994)

Tyrosine phosphorylation of several cellular proteins is one of the earliest signaling events induced by cross-linking of the high-affinity receptor for immunoglobulin E (Fc epsilon RI) on mast cells or basophils. Tyrosine kinases activated during this process include the Src family kinases, Lyn, c-Yes, and c-Src, and members of another subfamily, Syk and PTK72 (identical or highly related to Syk). Recently, some of us described two novel tyrosine kinases, Emb and Emt, whose expression was limited to subsets of hematopoietic cells, including mast cells. Emb turned out to be identical to Btk, a gene product defective in human X-linked agammaglobulinemia and in X-linked immunodeficient (xid) mice. Here we report that Fc epsilon RI cross-linking induced rapid phosphorylation on tyrosine, serine, and threonine residues and activation of Btk in mouse bone marrow-derived mast cells. A small fraction of Btk translocated from the cytosol to the membrane compartment following receptor cross-linking. Tyrosine phosphorylation of Btk was not induced by either a Ca2+ ionophore (A23187), phorbol 12-myristate 13-acetate, or a combination of the two reagents. Co-immunoprecipitation between Btk and receptor subunit beta or gamma was not detected. The data collectively suggest that Btk is not associated with Fc epsilon but that its activation takes place prior to protein kinase C activation and plays a novel role in the Fc epsilon RI signaling pathway.
Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy (2021)

Malignant melanoma is the most serious, life-threatening form of all dermatologic diseases, with a poor prognosis in the presence of metastases and advanced disease. Despite recent advances in targeted therapy and immunotherapy, there is still a critical need for a better understanding of the fundamental mechanisms behind melanoma progression and resistance onset. Recent advances in genome-wide methylation methods have revealed that aberrant changes in the pattern of DNA methylation play an important role in many aspects of cancer progression, including cell proliferation and migration, evasion of cell death, invasion, and metastasization. The purpose of the current review was to gather evidence regarding the usefulness of DNA methylation tracking in liquid biopsy as a potential biomarker in melanoma. We investigated the key genes and signal transduction pathways that have been found to be altered epigenetically in melanoma. We then highlighted the circulating tumor components present in blood, including circulating melanoma cells (CMC), circulating tumor DNA (ctDNA), and tumor-derived extracellular vesicles (EVs), as a valuable source for identifying relevant aberrations in DNA methylation. Finally, we focused on DNA methylation signatures as a marker for tracking response to therapy and resistance, thus facilitating personalized medicine and decision-making in the treatment of melanoma patients.
Sodium-calcium exchanger-3 regulates pain “wind-up”: From human psychophysics to spinal mechanisms (2022)

Repeated application of noxious stimuli leads to a progressively increased pain perception; this temporal summation is enhanced in and predictive of clinical pain disorders. Its electrophysiological correlate is "wind-up," in which dorsal horn spinal neurons increase their response to repeated nociceptor stimulation. To understand the genetic basis of temporal summation, we undertook a GWAS of wind-up in healthy human volunteers and found significant association with SLC8A3 encoding sodium-calcium exchanger type 3 (NCX3). NCX3 was expressed in mouse dorsal horn neurons, and mice lacking NCX3 showed normal, acute pain but hypersensitivity to the second phase of the formalin test and chronic constriction injury. Dorsal horn neurons lacking NCX3 showed increased intracellular calcium following repetitive stimulation, slowed calcium clearance, and increased wind-up. Moreover, virally mediated enhanced spinal expression of NCX3 reduced central sensitization. Our study highlights Ca<sup>2+</sup> efflux as a pathway underlying temporal summation and persistent pain, which may be amenable to therapeutic targeting.
Starved wireless LAN device identifying scheme using beacon signals (2016)

Throughput starvation, which occurred under well-known exposed/hidden terminal problem in CSMA/CA based channel access mechanisms, will be a critical problem for future wireless LAN systems. This paper describes new schemes that identify starved access points (APs) and user equipments (UEs). One scheme identifies starved APs by observing the delay of beacon signals periodically transmitted by APs. The other identifies starved UEs by observing the miscaptured beacon signals ratio at UEs. Numerous computer simulations verified that the schemes can identify starved APs and UEs having quite low throughput and are superior to graph-based identification schemes.
Room Temperature Phase Transition in Methylammonium Lead Iodide Perovskite Thin Films Induced by Hydrohalic Acid Additives (2016)

Although reactive additives have been employed in perovskite solar cells to enhance film morphology and significantly increase device performance, little is known about the effect of these additives on perovskite structural and optical properties. Here we report a systematic study of how the properties of methylammonium lead iodide perovskite (CH<sub>3</sub> NH<sub>3</sub> PbI<sub>3</sub> ) are influenced by hydrohalic acid additives (HX; X=I, Br, Cl) in the precursor solution. Detailed structural and optical spectroscopic analysis reveals that all three acids affect the optical properties and alter the unit cell lattice parameters. Depending on the identity and concentration of HX, optical bandgaps widen or compress: addition of HBr yields a wider bandgap, whereas HI compresses the gap at high concentrations; HCl, on the other hand, has no significant effect on the bandgap. These changes can be understood by correlating them with the types of defects present in polycrystalline perovskite thin films in combination with the structural strain induced in very small crystallites. The presence of extra halides from HX in the precursor solution enables filling of the lattice vacancies in the perovskite, thereby altering metal-halogen-metal bond connectivity and consequently cell volumes and optical bandgaps. Remarkably, a room temperature tetragonal→cubic phase transition is observed for CH<sub>3</sub> NH<sub>3</sub> PbI<sub>3</sub> films treated with high HX concentrations. Further insights into this anomalous phase transformation are obtained from in situ variable-temperature X-ray diffraction in the 25-55 °C (298-328 K) range, revealing a monotonic fall in transition temperature with increasing precursor solution HX concentration.
Role of T cell-replacing factor (TRF) in the murine B cell differentiation: induction of increased levels of expression of secreted type IgM mRNA. (1987)

T cell-replacing factor (TRF) is known to play a critical role in the regulation of B cell growth and differentiation. In this study, the role of TRF in the expression of mRNA for both IgM and IgG1 class was investigated. The TRF was purified from cellfree supernatants from a T cell hybridoma, B151K12. RNA was isolated from chronic B cell leukemia (BCL1) cells, DNP-KLH-primed B cells, or normal B cells cultured with or without LPS, and LPS plus TRF or LPS plus BSF-1. The steady state level of isotype-specific mRNA was assessed by Northern blot analysis with a mu-specific or a gamma 1-specific probe. It was demonstrated that BCL1 and purified B cells cocultured with TRF expresses increased levels (twofold and fourfold, respectively) of secreted forms of mu mRNA. Purified B cells from DNP-KLH-primed mice also expressed increased levels (twofold to fourfold) of mu as well as gamma 1 mRNA for secreted form by stimulation with TRF. Total expression of mu mRNA, however, was approximately threefold higher than that of gamma 1 mRNA. The stimulation of normal B cells with LPS plus TRF induced an increase in the levels of mu mRNA and gamma 1 mRNA expression, fourfold and threefold, respectively. However, the levels of gamma 1 mRNA expression was one-third of that induced in B cells stimulated with LPS plus BSF-1. These results indicate that TRF preferentially induces increased levels of secreted type of mu mRNA and induces less gamma 1 mRNA than BSF-1. The differential role of TRF from BSF-1 in the expression of Ig mRNA will be discussed.