gebhart/patrepeval huggingface dataset:
Increased natural killer cell expression of CD16, augmented binding and ADCC activity to rituximab among individuals expressing the FcγRIIIa-158 V/V and V/F polymorphism (2007)

The presence of valine (V) at position 158 of FcgammaRllla (CD16) is known to improve clinical response to rituximab in indolent non-Hodgkin lymphoma (NHL). Little is known about the basic mechanisms for this observation. We examined natural killer (NK) cells from healthy donors representing the FcgammaRIIIa-158 polymorphic subgroups (V/V, V/F, and F/F) for gene transcript and cell surface CD16 expression, rituximab binding, and rituximab-dependent NK cell-mediated cytotoxicity. We observed higher levels of FcgammaRIIIa transcripts among individuals with the FcgammaRIIIa-158 V/V versus V/F or F/F genotype (P < .001); increased cell surface CD16 expression by quantitative flow cytometry on NK cells from individuals expressing at least one valine at FcgammaRIIIa-158 versus F/F (P = .029); as well as augmented rituximab binding and rituximab-mediated, antibody-dependent cellular cytotoxicity (ADCC). These results suggest that individuals expressing at least one valine at FcgammaRIIIa-158 might, in part, have better clinical outcomes due to increased CD16 expression, rituximab binding, and rituximab-mediated ADCC.
Comparison of transmission loss data with predictions based on inverted seabed parameters from the Yellow Sea ’96 experiment (2006)

Transmission loss is useful in sonar performance prediction. In this paper, the transmission loss data as a function of range, frequency, and propagation direction are obtained from the Yellow Sea ’96 experiment. The experiment was conducted along two radial directions up to 55 km and a quarter of a circle with a radius of 37 km. About 300 broadband explosive sources were detonated above and below the thermocline in the experiment. The seabed acoustic parameters are inverted from the broadband explosive source data. Based on the inverted seabed parameters, the transmission loss is predicted and compared with the experimental data. [Work supported by ONR.]
Minimizing instrumental polarization in the Multiangle SpectroPolarmetric Imager (MSPI) using diattenuation balancing between the three mirror coatings (2008)

Special enhanced silver mirror coatings were designed and fabricated to minimize the polarization introduced by a three-mirror
off-axis high-accuracy telescope. A system diattenuation of approximately 1% in the VIS-NIR was achieved by
both reducing the diattenuation from each mirror individually and by balancing the diattenuations introduced by the
three mirrors over the spectral range. This process of low-polarization engineering involves minimizing system
polarization introduced by surface geometry, thin film coatings and birefringent elements, and measuring the system. In
this report we will outline a methodology to minimize instrumental polarization aberrations, with an emphasis on
achieving low diattenuation in the MSPI camera, given its off-axis geometry and coating design constraints imposed by
the space-based application. This polarization balancing technique for mirror coatings can be applied to astrophysics
applications.
Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome (2002)

We have explored the National Center for Biotechnology Information (NCBI) single nucleotide polymorphisms (SNPs) database for a correlation between the density of putative SNPs, as well as SNPs that map to different chromosomal locations (ambiguously mapped SNPs), and segmental duplications of DNA in chromosome regions involved in genomic disorders. A high density of SNPs (14.4 and 12.4 SNPs per kb) was detected in the low copy repeats (LCRs) responsible for the chromosome 17p12 duplication and deletion that cause peripheral neuropathies. None of the SNPs at the PMP22 gene were ambiguously mapped, but 93% of the SNPs at LCRs mapped on both LCR copies, indicating that they are in fact variants in paralogous sequences. Similarly, a high SNP density was found in the LCR regions flanking the neurofibromatosis type 1 (NF1) gene, with 80% of SNPs mapping on both LCR copies. A high density of SNPs was found within LCR sequences involved in the deletions that mediate contiguous gene syndromes on chromosomes 7q11, 15q11-q13 and 22q11. We have analyzed the whole sequence of chromosome 22, which contains 14% of ambiguously mapped SNPs, and have found a good correlation between these SNPs and segmental duplications detected by BLAST analysis. We have identified several segments of ambiguously mapped SNPs, four corresponding to LCRs involved in the chromosome 22q11 microdeletion syndromes. Our data indicate that most SNPs in LCR segments are in fact paralogous sequence variants (PSVs), and suggest that a significant proportion of the SNPs in the NCBI database correspond to PSVs within segmental duplications of the human genome sequence.
Challenges in Classifying Privacy Policies by Machine Learning with Word-based Features (2018)

In this paper, we discuss challenges when we try to automatically classify privacy policies using machine learning with words as the features. Since it is difficult for general public to understand privacy policies, it is necessary to support them to do that. To this end, the authors believe that machine learning is one of the promising ways because users can grasp the meaning of policies through outputs by a machine learning algorithm. Our final goal is to develop a system which automatically translates privacy policies into privacy labels [1]. Toward this goal, we classify sentences in privacy policies with category labels, using popular machine learning algorithms, such as a naive Bayes classifier.We choose these algorithms because we could use trained classifiers to evaluate keywords appropriate for privacy labels. Therefore, we adopt words as the features of those algorithms. Experimental results show about 85% accuracy. We think that much higher accuracy is necessary to achieve our final goal. By changing learning settings, we identified one reason of low accuracies such that privacy policies include many sentences which are not direct description of information about categories. It seems that such sentences are redundant but maybe they are essential in case of legal documents in order to prevent misinterpreting. Thus, it is important for machine learning algorithms to handle these redundant sentences appropriately.
From handcrafted to deep local features (2018)

This paper presents an overview of the evolution of local features from handcrafted to deep-learning-based methods, followed by a discussion of several benchmarks and papers evaluating such local features. Our investigations are motivated by 3D reconstruction problems, where the precise location of the features is important. As we describe these methods, we highlight and explain the challenges of feature extraction and potential ways to overcome them. We first present handcrafted methods, followed by methods based on classical machine learning and finally we discuss methods based on deep-learning. This largely chronologically-ordered presentation will help the reader to fully understand the topic of image and region description in order to make best use of it in modern computer vision applications. In particular, understanding handcrafted methods and their motivation can help to understand modern approaches and how machine learning is used to improve the results. We also provide references to most of the relevant literature and code.
Detection of retrovirus particles and reverse transcriptase activity in mid-term cultured peripheral blood and lymph node cells from a French woman with Sezary syndrome. (1989)

Retrovirus particles, with an ultrastructure of type C-virus similar to HTLV-I were observed in several mid-term cultures of leukemic cells derived from a woman with a well characterised Sezary syndrome who had always resided in France. Reverse transcriptase activity was detected in supernatant fluids from day 6 to day 40 of culture. However, negative anti HTLV-I serology and the absence of specific molecular hybridization between leukemic cell DNA and two HTLV-I derived probes, argue against a HTLV-I virus.
Microplasma thruster powered by X-band microwaves (2019)

A microplasma thruster of the electrothermal type has been developed with X-band (f = 11 GHz) microwaves and Ar as a propellant. The emphasis was placed on an understanding of distinguished features of the microplasma generation and thrust performance by X-band microwaves, compared with those by S-band (f = 4 GHz) ones. The thruster consisted of a microplasma source 2 mm in the inner diameter and 3–12 mm long with a rod antenna on the axis, followed by a converging-diverging micronozzle. Azimuthally symmetric surface wave-excited plasmas were established by microwaves at powers of ≤6 W, with the source pressure in the range 2–50 kPa at flow rates of 10–70 sccm. The plasma generation, nozzle flow, and thrust performance were numerically analyzed using a two-dimensional fluid model, coupled with an electromagnetic model for microwaves interacting with plasmas in the source region. Simulations indicated that higher frequency f = 11 GHz with the source chamber length Ls ≈ 1/4 of the driving wavelength λ is preferred for the microplasma thruster in terms of efficient plasma generation, gas heating, and thus thrust performance as well as system compactness; moreover, in f = 11 GHz discharges with longer Ls ≈ 3λ/4, standing-wave striation-like plasma structures occur in the axial direction. Experiments were made for f = 11 and 4 GHz microwaves with the respective Ls ≈ λ/4, where the plasma electron density and gas temperature in the microplasma source were measured by optical emission spectroscopy with a small amount of H2 and N2 added. The electron density and gas temperature were in the range of (4–12) × 1019 m−3 and 800–1000 K for f = 11 GHz, being ∼10%–50% higher than those for f = 4 GHz. The thrust performance was also measured by a target-type microthrust stand, giving a thrust, specific impulse, and thrust efficiency in the range 0.2–1.8 mN, 65–90 s, and 2%–14% for f = 11 GHz, which were ∼10%–15% higher than those for f = 4 GHz. These experimental results were consistent with those of simulations, depending on microwave frequency, power, chamber size, and gas flow rate.
ARGUS REFERENCE MANUAL (1987)

Argus is an experimental language/system designed to support the construction and execution of distributed programs. Argus is intended to support only a subset of the applications that could benefit from being implemented by a distributed program. Two properties distinguish these applications: they make use of on-line data that must remain consistent in spite of concurrency and hardware failures, and they provide services under real-time constraints that are not severe. Examples of such applications are office automation systems and banking systems. Argus is based on CLU. It is largely an extension of CLU, but there are number of differences. Like CLU, Argus provides procedures for procedural abstraction, iterators for control abstraction, and clusters for data abstraction. In addition, Argus provides guardians that encapsulate and control access to one or more resources. Argus also provides equate modules as a convenient way to refer to constants. As in CLU, modules may be parameterized, so that a single module can define a class of related abstractions. Keywords: Fault tolerant computing.
Document image retrieval based on 2D density distributions of terms with pseudo relevance feedback (2004)

Document image retrieval is a task to retrieve document images relevant to a user's query. Most existing methods based on word-level indexing rely on the representation called "bag of words" which originated in the field of information retrieval. This paper presents a new representation of documents that utilizes additional information about the location of words in pages so as to improve the retrieval performance. We consider that pages are relevant to a query if they contain its terms densely. This notion is embodied as density distributions of terms calculated in the proposed method. Its performance is improved with the help of "pseudo relevance feedback", i.e., a method of expanding a query by analyzing pages. Experimental results on English document images show that the proposed method is superior to conventional methods of electronic document retrieval at recall levels 0.0-0.6.
Wearable soft robotic device for post-stroke shoulder rehabilitation: Identifying misalignments (2012)

Stroke is the leading cause of long-term disability in the United States, affecting over 795,000 people annually. In order to regain motor function of the upper body, patients are usually treated by regular sessions with a dedicated physical therapist. A cost-effective wearable upper body orthotics system that can be used at home to empower both the patients and physical therapists is described. The system is composed of a thin, compliant, lightweight, cost-effective soft orthotic device with an integrated cable actuation system that is worn over the upper body, an embedded limb position sensing system, an electric actuator package and controller. The proposed device is robust to misalignments that may occur during actuation of the compliant brace or when putting on the system. Through simulations and experimental evaluation, it was demonstrated i) that the soft orthotic cable-driven shoulder brace can be successfully actuated without the production of off-axis torques in the presence of misalignments and ii) that the proposed model can identify linear and angular misalignments online.
Caenorhabditis elegans PIEZO channel coordinates multiple reproductive tissues to govern ovulation (2020)

PIEZO1 and PIEZO2 are newly identified mechanosensitive ion channels that exhibit a preference for calcium in response to mechanical stimuli. In this study, we discovered the vital roles of <i>pezo-1</i>, the sole <i>PIEZO</i> ortholog in <i>Caenorhabditiselegans,</i> in regulating reproduction. A number of deletion alleles, as well as a putative gain-of-function mutant, of PEZO-1 caused a severe reduction in brood size. In vivo observations showed that oocytes undergo a variety of transit defects as they enter and exit the spermatheca during ovulation. Post-ovulation oocytes were frequently damaged during spermathecal contraction. However, the calcium signaling was not dramatically changed in the <i>pezo-1</i> mutants during ovulation. Loss of PEZO-1 also led to an inability of self-sperm to navigate back to the spermatheca properly after being pushed out of the spermatheca during ovulation. These findings suggest that PEZO-1 acts in different reproductive tissues to promote proper ovulation and fertilization in <i>C. elegans</i>.
Anisotropic moment tensor inversion and visualization applied to a dual well monitoring survey (2014)

Summary In this paper we review the workflow used for anisotropic moment tensor inversion and visualization applied to a dual well monitoring survey from the West Pembina field in Alberta. The workflow makes use of an exact, dynamic layered VTI ray-tracer that allows for constant dip. Included are a description of VTI model calibration, moment tensor inversion, moment tensor decomposition and visualization. Interpretation of the results is ongoing.
Enhanced Cu(II) Removal Performance and Mechanisms on Fe(II)-Modified LDH-GO Composites (2020)

This study evaluated the use of Fe(II)-modified layered double hydroxides-graphene oxide [LDHs-GO@Fe(II)] for Cu(II) adsorption. The Fe(II)-modified LDH-GO composites [LDH-GO@Fe(II)x] was synthesized by contacting the powdered LDH-GO with Fe(II)-containing solution. The effect of Fe(II) modification on the surface morphology and adsorption behavior, as well as the Cu(II) adsorption mechanism were investigated. With the modification, noncrystalline iron oxides clusters generated on the surface of the LDH/GO, with a slight decrease of the structure of LDH-GO. Cu(II) removal capacity was enhanced after Fe(II) modification. The kinetics data correlated well with the pseudo-first-order rate law. The adsorption equilibrium data were analyzed by both Freundlich and Langmuir isotherm models and the data well with the Langmuir isotherm model. The maximum Cu(II) adsorption capacity of the unmodified LDH-GO, LDH-GO@Fe(II)10, and LDH-GO@Fe(II)50 were 148.47, 166.16, and 174.87 mg/g, respectively. The X-ray powder diffraction and the X-ray photoelectron spectroscopy analysis manifested the formation of Cu2Cl(OH)3 and isomorphic substitution of Mg(II) for Cu(II) removal by the unmodified LDH-GO. The enhanced removal of Cu(II) by Fe(II)-modified LDH-GO was induced by the enlarged specific surface area and the reaction with Fe ions to form CuFe2O4.
Supplementary Figure 6 from Targeting the MYC and PI3K Pathways Eliminates Leukemia-Initiating Cells in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;Pten null T-ALL blasts show lower levels of phospho-AKT in response to JQ1 in comparison to LICs.&lt;/p&gt;
Molecular Mechanism of Low-Temperature Passive NOx Adsorption (PNA) on Palladium-Loaded FER Zeolite (2023)

Palladium exhibits a complex chemistry in the PNA process, especially in the presence of gas mixtures containing CO and NOx. In this work the mechanism of NOx adsorption in gas mixtures with CO, O2, and H2O on a Pd/FER zeolite is investigated. The redox state of palladium and its clustering during high-temperature pretreatment and NOx adsorption was investigated. Insight into the chemisorption mechanism was gained by detailed monitoring of the evolution of the NOx and COx concentrations. Oxidized palladium is required for achieving NOx adsorption. Clustered zerovalent palladium reduced with H2 did not adsorb NOx in the presence of O2. Evidence is provided for a reaction mechanism departing from oxygen-bridged PdII–O–PdII moieties of PdO nanoclusters. The NO adsorption site on palladium is obtained by reduction of one of the two PdII atoms to the zerovalent state which occurs more readily with CO as compared to NO explaining the beneficial role of CO.
Pros, Cons, and Future Possibilities for Use of Computer Navigation in Hip Arthroscopy (2014)

The recent integration of computer-assisted surgery as a resource for preoperative planning and intraoperative assistance in hip arthroscopy has paved the way for more precise surgical planning and the potential for improved operative results. The aims of computer-assisted surgery are to better define the pathoanatomy underlying patient symptomatology in an effort to refine surgical techniques, decrease human error, and ultimately improve clinical outcomes. Multiple studies have been published describing various technologies. The majority of these systems create 3D dynamized computer models from 2D CT scans to allow for precise preoperative planning, and some offer real-time intraoperative capabilities. Although these technologies have shown potential for increasing surgical precision in treating femoroacetabular impingement, they are not without limitations, including an inability to factor in soft-tissue structures and an incompatibility with dysplastic and arthritic hips. Future studies must be conducted to determine whether these systems result in improved clinical outcomes.
Enhanced chemiluminescent detection scheme for trace vapor sensing in pneumatically-tuned hollow core photonic bandgap fibers (2012)

We demonstrate an in-fiber gas phase chemical detection architecture in which a chemiluminescent (CL) reaction is spatially and spectrally matched to the core modes of hollow photonic bandgap (PBG) fibers in order to enhance detection efficiency. A peroxide-sensitive CL material is annularly shaped and centered within the fiber's hollow core, thereby increasing the overlap between the emission intensity and the intensity distribution of the low-loss fiber modes. This configuration improves the sensitivity by 0.9 dB/cm compared to coating the material directly on the inner fiber surface, where coupling to both higher loss core modes and cladding modes is enhanced. By integrating the former configuration with a custom-built optofluidic system designed for concomitant controlled vapor delivery and emission measurement, we achieve a limit-of-detection of 100 parts per billion (ppb) for hydrogen peroxide vapor. The PBG fibers are produced by a new fabrication method whereby external gas pressure is used as a control knob to actively tune the transmission bandgaps through the entire visible range during the thermal drawing process.
Fluorescence Microscopy of the HIV-1 Envelope (2020)

Human immunodeficiency virus (HIV) infection constitutes a major health and social issue worldwide. HIV infects cells by fusing its envelope with the target cell plasma membrane. This process is mediated by the viral Env glycoprotein and depends on the envelope lipid composition. Fluorescent microscopy has been employed to investigate the envelope properties, and the processes of viral assembly and fusion, but the application of this technique to the study of HIV is still limited by a number of factors, such as the small size of HIV virions or the difficulty to label the envelope components. Here, we review fluorescence imaging studies of the envelope lipids and proteins, focusing on labelling strategies and model systems.
Traction force screening enabled by compliant PDMS elastomers (2017)

Abstract Acto-myosin contractility is an essential element of many aspects of cellular biology, and manifests as traction forces that cells exert on their surroundings. The central role of these forces makes them a novel principal therapeutic target in diverse diseases. This requires accurate and higher capacity measurements of traction forces; however, existing methods are largely low throughput, limiting their utility in broader applications. To address this need, we employ Fourier-transform traction force microscopy in a parallelized 96-well format, which we refer to as contractile force screening (CFS).Critically, rather than the frequently employed hydrogel polyacrylamide (PAA), we fabricate these plates using polydimethylsiloxane (PDMS) rubber. Key to this approach is that the PDMS used is very compliant, with a lower-bound Young’s modulus of approximately 0.7 kPa. We subdivide these monolithic substrates spatially into biochemically independent wells, creating a uniform multiwell platform for traction force screening. We demonstrate the utility and versatility of this platform by quantifying the compound and dose-dependent contractility responses of human airway smooth muscle cells and retinal pigment epithelial cells.