gebhart/patrepeval huggingface dataset:
The Helicase from Hepatitis C Virus Is Active as an Oligomer (1999)

The helicase from hepatitis C virus (HCV NS3h) residing on the C-terminal domain of nonstructural protein 3 was considered to be monomeric by several researchers. Here we demonstrate, based on biochemical kinetic data, that the HCV helicase acts as an oligomer. The increase in the ATPase k(cat) of the NS3h protein with increasing protein concentration provided evidence for oligomerization. A sharp decrease in the unwinding rate was observed when the wild type NS3h was mixed with the ATPase deficient mutants of NS3h protein. This provided strong support for both mixed oligomer formation and subunit interactions for the HCV helicase. Chemical cross-linking of NS3h protein was an inefficient process, but yielded cross-linked protein oligomers of various sizes. The information currently available for HCV helicase is consistent with the hypothesis that oligomers of NS3h are not stable and the helicase subunits exchange during unwinding. Nevertheless, oligomerization of HCV helicase stimulates the ATPase activity, and it is required for the helicase activity.
A rapid-prototyping environment for digital-signal processors (1991)

A description is given of the Diodes system, a complete rapid prototyping, debugging, and test environment including both hardware and software, for the design of digital-signal-processing chips. The test circuitry in Diodes differs from that in many systems, including those based on boundary scan, by offering full-speed circuit testing and the observation of internal nodes during real time. Diodes also achieves nearly 100% fault coverage because chips are composed of numerous chunks, each of which is tested exhaustively. The discussion covers the high-density interconnection technology and the concepts on which Diodes is based, two types of chips that have been designed, fabricated, and tested for Diodes: module assembly and fabrication; synthesis software; on-chip testing; Diodes test circuitry; test modes; and hardware and software debugging. Diodes is compared with other testing approaches and other rapid prototyping systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Identification of the promoter region for the colanic acid polysaccharide biosynthetic genes in Escherichia coli K-12 (1996)

The colanic acid polysaccharide capsule biosynthetic genes (cps genes) are primarily clustered at one site located at about 45 min on the Escherichia coli chromosome. The network of proteins involved in regulating the expression of these genes includes the two positive regulators RcsA and RcsB. This work describes the site of action of these two activator proteins and the promoter of the cps genes. It is likely that the cps genes are arranged in a single long operon that is at least 13.5 kb. The promoter region was identified with fusions to lacZ that resulted in regulated expression by the Rcs network of regulatory proteins, and the start site of transcription was identified by primer extension. The operator region was cloned from Kohara phage to multicopy plasmids and identified by titrating RcsA or RcsB. Sequence analysis of the promoter and operator region revealed homology to the JUMPstart element found in the untranslated region of many exopolysaccharide biosynthetic operons. In addition, the deduced amino acid sequence of the amino terminus of the first open reading frame of the cps operon was found to be homologous to proteins encoded by the exopolysaccharide biosynthetic operons of Klebsiella pneumoniae and Erwinia amylovora.
Integrated Synthesis of Assembly and Fixture Scheme for Properly Constrained Assembly (2005)

This paper presents an integrated approach to design an assembly, fixture schemes, and an assembly sequence, such that the dimensional integrity of the assembly is insensitive to the dimensional variations of individual parts. The adjustability of critical dimensions and the proper constraining of parts during assembly process are the keys in achieving the dimensional integrity of the final assembly. A top-down design method is developed which recursively decomposes a lump of initial product geometry and fixture elements matching critical dimensions into parts and fixtures. At each recursion, joints are assigned to the interfaces between two subassemblies to ensure that parts and fixtures are properly constrained at every assembly step. A case study on a simple frame structure is presented to demonstrate the method. Note to Practitioners-Achieving dimensional integrity of complex assemblies is a very demanding task due to the dimensional variations of parts and their propagation. Keys to achieving the goal are to adjust critical dimensions using proper fixtures and joint configurations and to minimize unpredictable deformations caused by overconstrained parts, such that assembled products can be robust to dimensional variations of parts. Equally important are arranging fixtures and sequencing assembly steps as these are what really define which critical dimension is adjusted and which subassemblies are put together on what fixture at each assembly step. In this paper, we propose a top-down decomposition-based approach that generates assembly design, assembly sequence, and fixture plan ensuring adjustability for critical dimensions and properly constrained subassemblies at every assembly step. The method does not only prevent costly trial and error following bottom-up approaches, but also enumerates all feasible solutions for a given product geometry and critical dimensions. As the number of solutions can be fairly large, for real-word application, it is crucial to incorporate practical constraints and to identify other important criteria to search optimal designs.
Simple, Cost-Effective 3D Printed Microfluidic Components for Disposable, Point-of-Care Colorimetric Analysis (2015)

The fabrication of microfluidic chips can be simplified and accelerated by three-dimensional (3D) printing. However, all of the current designs of 3D printed microchips require off-chip bulky equipment to operate, which hindered their applications in the point-of-care (POC) setting. In this work, we demonstrate a new class of movable 3D printed microfluidic chip components, including torque-actuated pump and valve, rotary valve, and pushing valve, which can be operated manually without any off-chip bulky equipment such as syringe pump and gas pressure source. By integrating these components, we developed a user-friendly 3D printed chip that can perform general colorimetric assays. Protein quantification was performed on artificial urine samples as a proof-of-concept model with a smartphone used as the imaging platform. The protein was quantified linearly and was within the physiologically relevant range for humans. We believe that the demonstrated components and designs can expand the functionalities and potential applications of 3D printed microfluidic chip and thus provoke more investigation on manufacturing lab-on-a-chip devices by 3D printers.
Micro tube insertion into indium, copper and other materials for 3D applications (2010)

The viability of inter-strata low pitch vertical interconnection technologies is mandatory for 3D applications. In order to increase the connection complexity and to reach a 10μm or even smaller interconnection pitch, a new room-temperature insertion technology has been proposed and developed using micro tubes as inserts [1]. In the present work, we study the load required to obtain a full and efficient insertion of a single micro tube into indium, copper or other materials. We use a modified nanoindenter with a very accurate load and displacement control, to qualify the insertion process. The nature of the couple constituted by the insert and the soft metal is of major importance. Our study focuses on two specific parameters: Mechanical properties of the soft metal; Combined geometries of the soft metal and the insert. Thanks to this study, we can give the best conditions to improve insertion load and time for different couple. Finally, some first chips hybridizations are performed and tested mechanically and electrically to validate our work.
Use of Judicial Doctrines in Federal Tax Cases Decided by Trial Courts, 1993-2006: A Quantitative Assessment (2009)

The hypothesis of this Article is that the accepted wisdom--that judicial doctrines are raised exclusively by the government or the courts for the government's benefit--is wrong. Instead, judicial doctrines are used in a much richer manner by courts and by taxpayers, as well as the government, than the “wisdom” would suggest. It is the first paper to question the accepted thought about judicial doctrines and to do so using social science methodology. Starting at the end and working forward, the evidence assembled for this Article from a group of trial decisions about federal tax controversies establishes that, under the language of the judges' opinions, taxpayers frequently raise judicial doctrines. Sometimes arguing that the doctrines should be applied and sometimes arguing that they should not, taxpayers often are able to prevail in their arguments. In other words, the data negate the accepted wisdom. The “sword” wielded by the government has a second edge, perhaps not as sharp as the government's, but nevertheless honed by the taxpayer for its use against the government. Indeed, circumstances can be predictably associated with the litigants prevailing in having judicial doctrines applied for their benefit, most notably the taxpayer prevailing when the business purpose or sham transaction doctrines are used. When a party raises a doctrine and also when the party raising a doctrine wants the court to apply the doctrine on behalf of a litigant, that litigant is likely to prevail in the doctrine's application.
Estimation Techniques for Distributed Parameter Systems (1989)

The research detailed in this monograph was originally motivated by our interest in control problems involving partial and delay differential equations. Our attempts to apply control theory techniques
Resolution improvement in emission optical projection tomography (2007)

A new imaging technique called emission optical projection tomography (eOPT), essentially an optical version of single-photon emission computed tomography (SPECT), provides molecular specificity, resolution on the order of microns to tens of microns, and large specimen coverage ( approximately 1 cubic centimetre). It is ideally suited to gene expression studies in embryos. Reconstructed eOPT images suffer from blurring that worsens as the distance from the axis of rotation increases. This blur is caused in part by the defocusing of the lens' point-spread function, which increases with object distance from the focal plane. In this paper, we describe a frequency space filter based on the frequency-distance relationship of sinograms to deconvolve the distance-dependent point-spread function and exclude highly defocused data from the eOPT sinograms prior to reconstruction. The method is shown to reduce the volume at half-maximum of the reconstructed point-spread function to approximately 20% the original, and the volume at 10% maximum to approximately 6% the original. As an illustration, the visibility of fine details in the vasculature of a 9.5 day old mouse embryo is dramatically improved.
Intrinsic Fluorescence of Metabolite Amyloids Allows Label‐Free Monitoring of Their Formation and Dynamics in Live Cells (2018)

The formation of apoptosis-inducing amyloidal structures by metabolites has significantly extended the "amyloid hypothesis" to include non-proteinaceous, single metabolite building blocks. However, detection of metabolite assemblies is restricted compared to their larger protein-based counterparts owing to the hindrance of external labelling and limited immunohistochemical detection tools. Herein, we present the detection of the formation, dynamics, and cellular distribution of metabolite amyloid-like structures and provide mechanistic insights into the generation of supramolecular chromophores. Moreover, the intrinsic fluorescence properties allow the detection of metabolite assemblies in living cells without the use of external dyes. Altogether, this intrinsic fluorescence of metabolite assemblies further verifies their amyloidal nature, while providing an important tool for further investigation of their pathological role in inborn error of metabolism disorders.
Encounters with consumption during computer-mediated play: the development of digital games as marketing communication media (2003)

This paper explores the use of digital games for marketing communications using two theoretical perspectives. Firstly, the external contexts in which video game play takes place and secondly, internal game processes that are likely to be of interest to marketers and game developers. Findings from exploratory focus groups support the use of brand placement in games. Players feel that it can increase realism and help support the costs of game development. However the repetitive nature of games may cause rapid message wear-out and players' frustrations with aspects of play may lead to negative evaluations of brands. Individuals may also use video games to explore the meaning and benefits of consumption and this raises the question of the degree to which game content supports or opposes existing consumer cultures. An agenda for further research is presented.
MANAGEMENT OF ENDOMETRIOSIS WITH ORAL MEDROXYPROGESTERONE ACETATE (1976)

Efficacy of oral medroxyprogesterone acetate (MPA) was assessed in 35 women with an established diagnosis of endometriosis (33 pelvic and 2 abdominal). MPA was given in a dosage of 30 mg daily for 90 days. Results indicated improvement or remission in all cases, even though breakthrough bleeding occurred in 8. Twenty-six were treated for associated infertility. Twelve of these became pregnant following treatment. Pregnancy rate in those women whose husbands were fertile was 90%. Side effects included spotting and breakthrough bleeding. The patients usually remained amenorrheic and anovulatory while receiving MPA. Posttreatment resumption of ovulation was prompt. The findings indicate that oral MPA is a useful therapeutic agent in the management of minimal to moderate endometriosis, particularly when it is associated with infertility.
Neurovascular unit on a chip: implications for translational applications (2013)

The blood-brain barrier (BBB) dynamically controls exchange between the brain and the body, but this interaction cannot be studied directly in the intact human brain or sufficiently represented by animal models. Most existing in vitro BBB models do not include neurons and glia with other BBB elements and do not adequately predict drug efficacy and toxicity. Under the National Institutes of Health Microtissue Initiative, we are developing a three-dimensional, multicompartment, organotypic microphysiological system representative of a neurovascular unit of the brain. The neurovascular unit system will serve as a model to study interactions between the central nervous system neurons and the cerebral spinal fluid (CSF) compartment, all coupled to a realistic blood-surrogate supply and venous return system that also incorporates circulating immune cells and the choroid plexus. Hence all three critical brain barriers will be recapitulated: blood-brain, brain-CSF, and blood-CSF. Primary and stem cell-derived human cells will interact with a variety of agents to produce critical chemical communications across the BBB and between brain regions. Cytomegalovirus, a common herpesvirus, will be used as an initial model of infections regulated by the BBB. This novel technological platform, which combines innovative microfluidics, cell culture, analytical instruments, bioinformatics, control theory, neuroscience, and drug discovery, will replicate chemical communication, molecular trafficking, and inflammation in the brain. The platform will enable targeted and clinically relevant nutritional and pharmacologic interventions for or prevention of such chronic diseases as obesity and acute injury such as stroke, and will uncover potential adverse effects of drugs. If successful, this project will produce clinically useful technologies and reveal new insights into how the brain receives, modifies, and is affected by drugs, other neurotropic agents, and diseases.
The relationship between capsid protein (VP2) sequence and pathogenicity of Aleutian mink disease parvovirus (ADV): a possible role for raccoons in the transmission of ADV infections (1996)

Aleutian mink disease parvovirus (ADV) DNA was identified by PCR in samples from mink and raccoons on commercial ranches during an outbreak of Aleutian disease (AD). Comparison of DNA sequences of the hypervariable portion of VP2, the major capsid protein of ADV, indicated that both mink and raccoons were infected by a new isolate of ADV, designated ADV-TR. Because the capsid proteins of other parvoviruses play a prominent role in the determination of viral pathogenicity and host range, we decided to examine the relationship between the capsid protein sequences and pathogenicity of ADV. Comparison of the ADV-TR hypervariable region sequence with sequences of other isolates of ADV revealed that ADV-TR was 94 to 100% related to the nonpathogenic type 1 ADV-G at both the DNA and amino acid levels but less than 90% related to other pathogenic ADVs like the type 2 ADV-Utah, the type 3 ADV-ZK8, or ADV-Pullman. This finding indicated that a virus with a type 1 hypervariable region could be pathogenic. To perform a more comprehensive analysis, the complete VP2 sequence of ADV-TR was obtained and compared with that of the 647-amino-acid VP2 of ADV-G and the corresponding VP2 sequences of the pathogenic ADV-Utah, ADV-Pullman, and ADV-ZK8. Although the hypervariable region amino acid sequence of ADV-TR was identical to that of ADV-G, there were 12 amino acid differences between ADV-G and ADV-TR. Each of these differences was at a position where other pathogenic isolates also differed from ADV-G. Thus, although ADV-TR had the hypervariable sequence of the nonpathogenic type 1 ADV-G, the remainder of the VP2 sequence resembled sequences of other pathogenic ADVs. Under experimental conditions, ADV-TR and ADV-Utah were highly pathogenic and induced typical AD in trios of both Aleutian and non-Aleutian mink, whereas ADV-Pullman was pathogenic only for Aleutian mink and ADV-G was noninfectious. Trios of raccoons experimentally inoculated with ADV-TR and ADV-Utah all became infected with ADV, but only a single ADV-Pullman-inoculated raccoon showed evidence of infection. Furthermore, none of the ADV isolates induced pathological findings of AD in raccoons. Finally, when a preparation of ADV-TR prepared from infected raccoon lymph nodes was inoculated into mink and raccoons, typical AD was induced in Aleutian and non-Aleutian mink, but raccoons failed to show serological or pathological evidence of infection. These results indicated that raccoons can become infected with ADV and may have a role in the transmission of virus to mink but that raccoon-to-raccoon transmission of ADV is unlikely.
Characterization of the highly active fragment of glyceraldehyde-3-phosphate dehydrogenase gene promoter for recombinant protein expression in Pleurotus ostreatus (2015)

Developing efficient native promoters is important for improving recombinant protein expression by fungal genetic engineering. The promoter region of glyceraldehyde-3-phosphate dehydrogenase gene in Pleurotus ostreatus (Pogpd) was isolated and optimized by upstream truncation. The activities of these promoters with different lengths were further confirmed by fluorescence, quantitative real-time PCR and Western blot analysis. A truncated Pogpd-P2 fragment (795 bp) drove enhanced green fluorescence protein (egfp) gene expression in P. ostreatus much more efficiently than full-length Pogpd-P1. Further truncating Pogpd-P2 to 603, 403 and 231 bp reduced the eGFP expression significantly. However, the 403-bp fragment between -356 bp and the start codon was the minimal but sufficient promoter element for eGFP expression. Compact native promoters for genetic engineering of P. ostreatus were successfully developed and validated in this study. This will broaden the preexisting repertoire of fungal promoters for biotechnology application.
CD40 Signaling and Plaque Instability (2001)

Today, multiple lines of evidence support the view of atherosclerosis as a chronic inflammatory disease and implicate components of the immune system in atherogenesis. Recent work has documented overexpression of the potent immune mediator CD40 and its counterpart CD40 ligand (CD40L) in experimental and human atherosclerotic lesions. Notably, interruption of CD40/CD40L interactions not only diminished the formation and progression of mouse atheroma, but also fostered changes in lesion biology and structure, which are associated in humans with "plaque stabilization." In accordance with the hypothesis that CD40 signaling promotes plaque instability, in vitro studies demonstrated that ligation of CD40 on atheroma-associated cell types, namely endothelial cells, smooth muscle cells, and macrophages, mediates functions considered crucial to the process of atherogenesis, such as the expression of cytokines, chemokines, growth factors, matrix metalloproteinases, and procoagulants. The combination of the broad gamut of proatherogenic biological responses triggered by ligation of CD40 on endothelial cells, smooth muscle cells, and macrophages in vitro and the results of in vivo studies of interruption of CD40 signaling suggests a central role for this receptor/ligand dyad during atherogenesis, proposing CD40/CD40L interactions as a novel potential therapeutic target for this prevalent human disease.
Janus Emulsions for the Detection of Bacteria (2017)

Janus emulsion assays that rely on carbohydrate-lectin binding for the detection of <i>Escherichia coli</i> bacteria are described. Surfactants containing mannose are self-assembled at the surface of Janus droplets to produce particles with lectin binding sites. Janus droplets orient in a vertical direction as a result of the difference in densities between the hydrocarbon and fluorocarbon solvents. Binding of lectin to mannose(s) causes agglutination and a tilted geometry. The distinct optical difference between naturally aligned and agglutinated Janus droplets produces signals that can be detected quantitatively. The Janus emulsion assay sensitively and selectively binds to <i>E. coli</i> at 10<sup>4</sup> cfu/mL and can be easily prepared with long-time stability. It provides the basis for the development of inexpensive portable devices for fast, on-site pathogen detection.