gebhart/patrepeval huggingface dataset:
BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm (2010)

Using our newly developed BLV-CoCoMo-qPCR assay, we were able to detect a wide range of mutated BLV viruses. CoCoMo algorithm may be a useful tool to design degenerate primers for quantification of proviral load for other retroviruses including HTLV and human immunodeficiency virus type 1.
Differential transactivation by the androgen receptor in prostate cancer cells (1998)

Our results indicate that the relative utilization of transactivating functions in N-terminal and ligand binding domains of the AR is promoter and cell specific.
A New, Full-Color, Direct Thermal Imaging System (2005)

A direct thermal printing medium is described that incorporates two color-forming layers separated by a thermally-insulating layer. Any combination of the two colors may be obtained by heating with a conventional thermal print head. Independent addressing of each color is achieved by controlling the time of heating and the power supplied to the heating elements of the print head. In combination with a third color-forming layer that is printed from the reverse side of the medium, full-color imaging with photographic quality is possible using two passes with a single thermal print head or a single pass with two print heads. A novel thermal color-forming process based upon phase change of colorless crystals provides images of excellent quality and stability.
An adaptive close-talking microphone array (2002)

Close-talking differential microphone arrays (CTMAs) are useful in situations where the background noise level is very high because they inherently suppress farfield noise while emphasizing desired nearfield signals. One problem, however, is that the array has to be placed as close to the desired source (talker's mouth) as possible since the frequency response and level of a differential nearfield array depend heavily on its position and orientation relative to the source signal. In order to be able to utilize the advantages of CTMAs for an extended range of microphone positions, this contribution examines the possibility of tracking the desired signal source by estimating its distance and orientation angle. Having this information, appropriate correction filters can be applied adaptively which equalize unwanted frequency response and level deviations within a reasonable range of operation without significantly degrading the noise canceling properties of differential arrays. A PC-based real-time implementation with transducer calibration capabilities of this adaptive CTMA is presented.
ChronoFab (2016)

We present ChronoFab, a 3D modeling tool to craft motion sculptures, tangible representations of 3D animated models, visualizing an object's motion with static, transient, ephemeral visuals that are left behind. Our tool casts 3D modeling as a dynamic art-form by employing 3D animation and dynamic simulation for the modeling of motion sculptures. Our work is inspired by the rich history of stylized motion depiction techniques in existing 3D motion sculptures and 2D comic art. Based on a survey of such techniques, we present an interface that enables users to rapidly explore and craft a variety of static 3D motion depiction techniques, including motion lines, multiple stroboscopic stamps, sweeps and particle systems, using a 3D animated object as input. In a set of professional and non-professional usage sessions, ChronoFab was found to be a superior tool for the authoring of motion sculptures, compared to traditional 3D modeling workflows, reducing task completion times by 79%.
Superconducting a-WxSi1−x nanowire single-photon detector with saturated internal quantum efficiency from visible to 1850 nm (2011)

We have developed a single-photon detector based on superconducting amorphous tungsten–silicon alloy (a-WxSi1−x) nanowire. Our device made from a uniform a-WxSi1−x nanowire covers a practical detection area (16 μm×16 μm) and shows high sensitivity featuring a plateau of the internal quantum efficiencies, i.e., efficiencies of generating an electrical pulse per absorbed photon, over a broad wavelength and bias range. This material system for superconducting nanowire detector technology could overcome the limitations of the prevalent nanowire devices based on NbN and lead to more practical, ideal single-photon detectors having high efficiency, low noise, and high count rates.
Circuit Theory for SPICE of Spintronic Integrated Circuits (2011)

We present a theoretical and a numerical formalism for analysis and design of spintronic integrated circuits (SPINICs). The formalism encompasses a generalized circuit theory for spintronic integrated circuits based on nanomagnetic dynamics and spin transport. We propose an extension to the Modified Nodal Analysis technique for the analysis of spin circuits based on the recently developed spin conduction matrices. We demonstrate the applicability of the framework using an example spin logic circuit described using spin Netlists.
Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations (2019)

The HIV-1 envelope (Env) is the target for neutralizing antibodies and exists on the surface of virions in open or closed conformations. Difficult-to-neutralize viruses (tier 2) express Env in a closed conformation antigenic for broadly neutralizing antibodies (bnAbs) but not for third variable region (V3) antibodies. Here we show that select V3 macaque antibodies elicited by Env vaccination can neutralize 26% of otherwise tier 2 HIV-1 isolates in standardized virus panels. The V3 antibodies only bound to Env in its open conformation. Thus, Envs on tier 2 viruses sample a state where the V3 loop is not in its closed conformation position. Envelope second variable region length, glycosylation sites and V3 amino acids were signatures of neutralization sensitivity. This study determined that open conformations of Env with V3 exposed are present on a subset of otherwise neutralization-resistant virions, therefore neutralization of tier 2 HIV-1 does not always indicate bnAb induction.
Digital image subtraction of temporally sequential chest images for detection of interval change (1994)

An automated digital image subtraction technique for temporally sequential chest images has been developed in order to aid radiologists in the detection of interval changes. A number of small regions of interest (ROIs) are selected automatically in the lung areas of two temporally sequential chest images. A local matching, based on a cross‐correlation method, is performed on each pair of corresponding ROIs in order to determine shift values for the coordinates of two images. A proper warping of x , y coordinates is obtained by fitting two‐dimensional polynomials to the distributions of shift values. One of the images is warped and then subtracted from the other. Forty six pairs of chest images (42 with interval changes and 4 without interval change) were processed using this method. The subtraction images were able to enhance various important interval changes, such as differences in the size of tumor masses, changes in heart size, and changes in pulmonary infiltrates or pleural effusions. Approximately 70% of the pairs showed reasonably good registration.
Direct measurement of T cell receptor affinity and sequence from naïve antiviral T cells (2016)

T cells recognize and kill a myriad of pathogen-infected or cancer cells using a diverse set of T cell receptors (TCRs). The affinity of TCR to cognate antigen is of high interest in adoptive T cell transfer immunotherapy and antigen-specific T cell repertoire immune profiling because it is widely known to correlate with downstream T cell responses. We introduce the in situ TCR affinity and sequence test (iTAST) for simultaneous measurement of TCR affinity and sequence from single primary CD8(+) T cells in human blood. We demonstrate that the repertoire of primary antigen-specific T cells from pathogen-inexperienced individuals has a surprisingly broad affinity range of 1000-fold composed of diverse TCR sequences. Within this range, samples from older individuals contained a reduced frequency of high-affinity T cells compared to young individuals, demonstrating an age-related effect of T cell attrition that could cause holes in the repertoire. iTAST should enable the rapid selection of high-affinity TCRs ex vivo for adoptive immunotherapy and measurement of T cell response for immune monitoring applications.
The autoimmune pathogenesis of multiple sclerosis. (2015)

One of the major goals of biomedical research is to reveal the pathomechanisms that lead to a disease on a level on which diagnostic criteria and causal therapies can be designed. The understanding and treatment of multiple sclerosis (MS) is still far from this goal, but exciting developments are on the way. MS is thought to be an autoimmune disease that is mediated by brain tissue-reactive lymphocytes, T cells and B cells, but so far these lymphocytes could not be reliably detected. This article highlights recent developments that permit the detection of autoreactive B cells in MS, the implications of this finding for early diagnosis of the disease, monitoring its activity, and eventually for gaining insight into the specific immune pathology that drives MS.
Nano-immunoassay profiling of ERK and MEK isoforms in fine-needle aspirates of solid tumors. (2010)

2564 Background: We have developed the use of a highly sensitive microfluidic nano-immunoassay system (NIA) to analyze proteins in as little as 4 nanoliters of lysate from clinical specimens. We previously reported use of NIA to measure proteins in hematopoietic clinical specimens (Fan et al, Nature Medicine 2009). Now, we present results that NIA can be used to obtain reproducible and distinct signatures of phosphorylated and unphosphorylated ERK and MEK isoforms in fine-needle aspirates (FNAs) of solid tumor and nontumor clinical specimens. Methods: NIA uses isoelectric focusing to separate proteins so that multiple isoforms of a protein can be measured simultaneously and relative abundance of the isoforms can be calculated. We first developed protocols to process FNA specimens for reproducible NIA analysis of solid tumors, then performed NIA analysis of ERK1/2 and MEK1 profiles in 200 specimens of paired tumor and nontumor FNAs. Over 20 proteomic parameters were measured, including unphosphorylated, single- and multiple- phosphorylated isoforms, and calculated percentages of each isoform for each protein. Samples were run in triplicate. ANOVA was used for biostatistical analysis. Results: Across all tumor types, the mean coefficient of variance for technical replicates was less than 5%. We found that transport time up to 60 minutes on ice did not significantly alter the ERK and MEK profiles (p values for each parameter= NS for 0 minutes vs. 60 minutes). Preliminary analysis of the squamous cell tumor and nontumor profiles suggests that different ratios of phosphorylated and unphosphorylated ERK1/2 and MEK1 isoforms can distinguish FNAs from tumor or nontumor specimens. Notably, measurements of single isoforms alone can not resolve the two groups. Conclusions: Our studies demonstrate that NIA can be used to precisely and reliably measure differences in total and relative abundance of ERK and MEK isoforms in solid tumors. We are currently incorporating NIA proteomic analysis in correlative studies for prospective clinical trials. NIA may be a promising novel technology for new diagnostic and biomarker studies. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Cell Biosciences Cell Biosciences
A Method for Selecting Peer Deals in IT Service Contracts (2017)

To respond to requests for proposals from clients requiring complex Information technology (IT) services, IT service providers have to prepare a solution composed of the multiple services requested by the clients and price that solution. Then, each provider competes in a tender-kind of process trying to convince the client with their solution. Pricing these solutions/deals, using historical and market data, is a complex task that we studied in our previous works. In our prior pricing approaches, we used a simple algorithm for selecting similar historical and market deals to the one we are trying to price, before we mine the data of these deals to estimate the costs of that latter deal. However, there are multiple limitations to that algorithm that we overcome in the novel approach that we present in this paper. These limitations include missing on some similar deals due to the way we chose them. Our new approach involves an iterative algorithm that selects peer deals at different levels until a pre-specified number of deals is determined. We present a proof-of-concept implementation of our approach, using real-world data, to illustrate its efficiency.
Enhanced NMR Logging Methods for Accurately Measuring Volumes of Gas and Light Oil in Hydrocarbon Reservoirs (1999)

Abstract Using nuclear magnetic resonance (NMR) logging to determine reservoir porosity occupied by gas or light oil currently requires data simultaneously acquired from at least two Carr-Purcell-Meiboom-Gill (CPMG) sequences having different wait-times. This dual-wait-time and dual-frequency method has been successfully applied to determine gas volumes in both clean and shaley sand formations. The success of the method relies on two factors. First, adequate signal-to-noise levels in an echo train difference must be maintained so that the gas-filled porosity and its transverse relaxation time (T2) can be accurately characterized. Second, methods must be available to reliably estimate the longitudinal relaxation time (T1) of the hydrocarbon phase needed to apply a necessary amplitude correction to the apparent hydrocarbon-filled porosity. A new triple-wait-time and multifrequency method has been developed for determining gas and light-oil-filled porosity over a broader range of reservoir conditions. When compared with the dual-wait-time, dual-frequency logging technique, the new method offers two advantages. First, it improves the signal-to-noise ratio of the echo train difference. Second, it significantly improves the determination of T1 values for the hydrocarbons, especially when the reservoir contains oil, gas, and water. The new method thus enables a more accurate determination of the pore volumes occupied by each hydrocarbon phase as well as the pore volume occupied by water. Results from laboratory experiments, performed on bulk fluids and a sandstone core, are presented to demonstrate the new method. In addition, a set of charts is provided as an aid in the selection of optimum acquisition parameters for logging applications.
Detection of hydrogen sulfide in biological samples: current and future (2010)

Evaluation of: Levitt MD, Abdel-Rehim MS, Furne J. Free and acid-labile hydrogen sulfide concentrations in mouse tissues: anomalously high free hydrogen sulfide in aortic tissue. Antioxid. Redox Signal. DOI: 10.1089/ars.2010.3525 (2010) (Epub ahead of print). Hydrogen sulfide (H(2)S), known as a pungent toxic gas, has recently emerged as a novel critical mediator in the cardiovascular system, the nervous system and various biological signaling functions, as well as a therapeutic agent. However, much less certainty exists regarding biological levels of H(2)S in these systems and during disease. Many papers have reported various methods of measuring the levels of sulfide through different techniques both in vitro and in vivo. Complicating this matter is the fact that sulfide exists in multiple forms - free sulfides such as S(2) (-), HS(-), H(2)S, acid-labile and bound sulfides. These different forms of sulfide make quantitative measurement of bioavailable H(2)S difficult and have led to variable reported levels in the literature. The sensitive detection of sulfide in its multiple forms is needed to establish reliable bioavailable concentrations of sulfide species in order to understand their role in various aspects of physiology and pathology, and to address possible therapeutic approaches. A recent method by Levitt et al. describes a unique gas chromatography chemiluminescence-based technique to measure free and acid-labile H(2)S in multiple tissues from mouse.
A Feasible Solvent Separation System for Immunoassays (1981)

Feasibility is demonstrated for a new solvent extraction method to separate free and bound fractions in hapten immunoassays, without the need to centrifuge. A novel mixer-separator device used in conjunction with solvent extraction makes the new separation method simple and rapid, avoids the need for decantation, and has applications for all mass transfer operations involving solvent extraction.
A High‐Throughput, Controllable, and Environmentally Benign Fabrication Process of Thermoplastic Nanofibers (2007)

Abstract Continuous and uniform yarns of thermoplastic nanofibers were prepared via direct melt extrusion of immiscible blends of thermoplastic polymers with CAB and subsequent extraction removal of CAB. Ratios of thermoplastic/sacrificial polymers, melt viscosity, and interfacial tensions affect the formation of nanofibers. Dominating sacrificing polymer content in the blends and low interfacial tensions between thermoplastic polymer and CAB are two key factors. This fabrication process possesses features of high productivity, versatility of thermoplastics, controllability, and environment friendliness in manufacturing thermoplastic nanofibers. magnified image
Fine structure of A and M antigens from Brucella biovars (1989)

Brucella A and M epitopes were found on single O-polysaccharide chains of all biotype strains of this species. Lipopolysaccharides from the type and reference strains of five of the six Brucella species, B. abortus, B. melitensis, B. suis, B. canis, and B. neotomae, were extracted and purified. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, in conjunction with silver staining and immunoblotting developed by monoclonal antibodies, showed bands characteristic of A, M, or mixed A and M antigens. The A antigen previously described as an exclusively alpha 1,2-linked homopolymer of 4,6-dideoxy-4-formamido-D-mannopyranose was shown by 1H and 13C nuclear magnetic resonance spectroscopy to possess a fine structure consistent with the low-frequency occurrence of alpha 1, 3-linked 4,6-dideoxy-4-formamido-D-mannopyranose residues. This feature was previously attributed only to the M antigen, which is also a homopolymer of the same sugar. B. melitensis biotype 3 and B. suis biotype 4 lipopolysaccharides showed characteristics of mixed A and M antigens. Immunoabsorption of these O polysaccharides on a column of immobilized A-antigen-specific monoclonal antibody enriched polymer chains with A-antigen characteristics but did not eliminate M epitopes. Composite A- and M-antigen characteristics resulted from O polysaccharides in which the frequency of alpha 1,3 linkages, and hence, M-antigen characteristics, varied. All biotypes assigned as A+ M- expressed one or two alpha 1,3-linked residues per polysaccharide O chain. M antigens (M+ A-) also possessed a unique M epitope as well as a tetrasaccharide determinant common to A-antigen structures. B. canis and B. abortus 45/20, both rough strains, expressed low-molecular-weight A antigen.
Increased Absorption Rate of Diclofenac from Fast Acting Formulations Containing Its Potassium Salt (2011)

Diclofenac (CAS 15307-86-5) is a non-steroidal anti-inflammatory drug largely used, mainly to relief pain of various origin. Diclofenac is present on the market as free acid, as sodium salt (CAS 15307-79-6) and as potassium salt (CAS 15307-81-0). The last salification form has shown a prompter absorption rate and a faster onset of analgesic activity than the acid form and sodium salt. This paper extensively reviews three trials carried out on healthy volunteers, where potassium salt of diclofenac present in three fast-acting formulations, namely sachets (Trial 1), tablets (Trial 2) and oral drops (Trial 3), were compared to reference tablet formulations from the market. A very fast absorption rate was encountered with the three test formulations, with the peak reached in one case 5 min and in most cases within 10-15 min after dosing. The quick absorption rate of test formulations was attributed to the special combination of the salt of diclofenac with a dynamic buffering agent, namely bicarbonate, present in the test formulations and covered by an international patent. The prompt absorption of diclofenac from the new fast-acting formulations was accompanied by the presence of only one peak, whereas the reference formulations produced in most cases two peaks, as widely described in literature. This finding suggested the hypothesis that the absorption of test formulations should occur in a shorter tract of the gut. The faster absorption of diclofenac from the three fast-acting formulations is expected to produce a faster onset of analgesic action, which highlights these new formulations as particularly indicated to relief pain of any origin.
In Vitro Models to Study Taste: Can Sweetness Be Modeled in a Dish? (2008)

Primary and immortalized cultures of many cell types have facilitated efforts to understand the signals involved in proliferation, differentiation and senescence, and yielded tools to rapidly assay new molecules targeting specific receptor pathways. Surprisingly, few studies have reported successful primary culture protocols for taste cells, and those reported have had a limited life span and have not purported to generate new cells in vitro. Like other epithelial cells, taste cells are generated throughout life from a basal cell population, although the precise lineage and signaling molecules involved in this process are not well known. We have recently developed a primary taste cell culture method that supports the generation of new cells expressing key molecular and functional features of mature taste cells. These cultures can be maintained for functional assays for over two months. In this chapter we will present insights into the development of this protocol and discuss advantages and disadvantages of the approach. We will also discuss the potential use of these cultures as discovery tools to study the effects of neurotrophic factors on taste cell proliferation and differentiation and as an aid in the development and evaluation of new taste molecules.
A horse identification system using biometrics (2001)

Abstract This paper introduces an application of iris recognition technology, using the iris pattern for horse identification. There are several problems to be solved in horse iris recognition: (1) It is very difficult for horses to remain motionless, which leads to mislocation and loss of focus during image acquisition, so that the images often have poor quality. (2) Pupil size varies significantly between the conditions of dilation (mydriasis) and contraction (miosis). (3) Horse iris patterns are not clear. As a solution for issue (1), we used the reflection of the illumination sources employed for image acquisition and chose adequate images suitable for recognition. For issues (2) and (3), we propose region extraction appropriate to the equine eye structure, a stable coordinate model for pupil variation, and recognition using orthogonal wrinkles in the iris pattern. Recognition experiments based on 100 sets of horse iris data show that highly accurate horse identification is possible. © 2001 Scripta Technica, Syst Comp Jpn, 32(14): 12–23, 2001