gebhart/patrepeval huggingface dataset:
Easy-DHPSF open-source software for three-dimensional localization of single molecules with precision beyond the optical diffraction limit (2013)

Automated processing of double-helix (DH) microscope images of single molecules (SMs) streamlines the protocol required to obtain super-resolved three-dimensional (3D) reconstructions of ultrastructures in biological samples by single-molecule active control microscopy. Here, we present a suite of MATLAB subroutines, bundled with an easy-to-use graphical user interface (GUI), that facilitates 3D localization of single emitters (e.g. SMs, fluorescent beads, or quantum dots) with precisions of tens of nanometers in multi-frame movies acquired using a wide-field DH epifluorescence microscope. The algorithmic approach is based upon template matching for SM recognition and least-squares fitting for 3D position measurement, both of which are computationally expedient and precise. Overlapping images of SMs are ignored, and the precision of least-squares fitting is not as high as maximum likelihood-based methods. However, once calibrated, the algorithm can fit 15â30 molecules per second on a 3 GHz Intel Core 2 Duo workstation, thereby producing a 3D super-resolution reconstruction of 100,000 molecules over a 20Ã20Ã2 Î¼m field of view (processing 128Ã128 pixels Ã 20000 frames) in 75 min.
Chester Township Community Questionnaire Summary Report (2020)

The Center for Community Planning and Development at CSU’s Maxine Goodman Levin College of Urban Affairs was engaged by Chester Township to assist with conducting a Community Questionnaire. CSU’s role was to work with the Township in developing the questionnaire; and then receiving and analyzing the responses. The questionnaire was mailed to all resident addresses in the Township in May of 2020; responses were received and analyzed during June, July and August. To keep the cost low, the questionnaire was not designed to be a statistically calibrated survey, but rather a questionnaire which would enable the community to get a sense of residents’ interests and desires with regard to the Township’s future. Of 4,724 questionnaires mailed, 1,654 were returned and deemed valid, a 35% response rate. This is a very solid response rate indicative of residents’ high level of interest in participating in Township affairs and expressing their opinion. Questionnaires included both quantitative (multiple choice) questions and open-ended questions. All responses were analyzed by CSU and summarized in this report.
Using Generalized Annotated Programs to Solve Social Network Diffusion Optimization Problems (2013)

There has been extensive work in many different fields on how phenomena of interest (e.g., diseases, innovation, product adoption) “diffuse” through a social network. As social networks increasingly become a fabric of society, there is a need to make “optimal” decisions with respect to an observed model of diffusion. For example, in epidemiology, officials want to find a set of k individuals in a social network which, if treated, would minimize spread of a disease. In marketing, campaign managers try to identify a set of k customers that, if given a free sample, would generate maximal “buzz” about the product. In this article, we first show that the well-known Generalized Annotated Program (GAP) paradigm can be used to express many existing diffusion models. We then define a class of problems called Social Network Diffusion Optimization Problems (SNDOPs). SNDOPs have four parts: (i) a diffusion model expressed as a GAP, (ii) an objective function we want to optimize with respect to a given diffusion model, (iii) an integer k &gt; 0 describing resources (e.g., medication) that can be placed at nodes, (iv) a logical condition VC that governs which nodes can have a resource (e.g., only children above the age of 5 can be treated with a given medication). We study the computational complexity of SNDOPs and show both NP-completeness results as well as results on complexity of approximation. We then develop an exact and a heuristic algorithm to solve a large class of SNDOPproblems and show that our GREEDY-SNDOPs algorithm achieves the best possible approximation ratio that a polynomial algorithm can achieve (unless P = NP ). We conclude with a prototype experimental implementation to solve SNDOPs that looks at a real-world Wikipedia dataset consisting of over 103,000 edges.
Bacillus Probiotics: Spore Germination in the Gastrointestinal Tract (2002)

Spores of Bacillus species are being used commercially as probiotics and competitive exclusion agents. Unlike the more commonly used Lactobacillus-type probiotics, spores are dormant life forms. To address how spore probiotics might function we have investigated whether spores can germinate in the gastrointestinal tract by using a murine model. Using a genetically engineered chimeric gene, ftsH-lacZ, which is strongly expressed only in vegetative cells, we have developed a sensitive competitive reverse transcription-PCR assay which has enabled detection of as few as 10(2) vegetative bacteria in the mouse gut. Using this method we have administered doses of ftsH-lacZ spores to groups of mice and shown that spores can germinate in significant numbers in the jejunum and ileum. The levels of detection we obtained suggest that spores may colonize the small intestine, albeit briefly.
High-resolution photoacoustic tomography (2004)

Optical contrast is sensitive to physiological parameters, such as the oxygen saturation and total concentration of hemoglobin, in biological tissues. Photoacoustic tomography is based on the high optical contrast yet utilizing the high ultrasonic resolution. Our work in this emerging area of research will be summarized in this invited talk. In this technology, a diffraction-based inverse-source problem is solved in the image reconstruction, for which we developed the rigorous reconstruction theory. We implemented a prototype and accomplished non-invasive transdermal and transcranial functional imaging of small-animal brains in vivo. Changes in the cerebral blood oxygenation and blood volume of a rat, as a result of the alternation from hyperoxia to hypoxia, were imaged successfully.
Molecular cloning and sequence analysis of a cDNA encoding a porcine kidney renin-binding protein. (1990)

A complementary DNA encoding a renin-binding protein (RnBP) has been isolated from a porcine kidney cDNA library by immunological screening of in vitro translation products from the cDNAs. Analysis of the nucleotide sequence of the clone revealed a 1,342-nucleotide sequence with a 5'-terminal untranslated region of 52 nucleotides, an open reading frame of 1,206 nucleotides that encodes 402 amino acids, and a 3'-terminal untranslated region of 84 nucleotides that contains the polyadenylation signal sequence, AATAAA. The predicted amino acid sequence contains no hydrophobic amino-terminal sequence and does not show significant homology to those of other identified proteins. The in vitro translated RnBP was found to have the same molecular weight, 42,000, as that of the purified RnBP from porcine kidney on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and it formed a complex with renin purified from porcine kidney, which indicates that the cDNA encodes a functional RnBP without a propeptide sequence. The RnBP cDNA probe hybridized to a 1.5-kilobase mRNA in kidney, liver, adrenal, and pituitary glands, the amount being much greater in kidney than in the other tissues. Southern blot analysis showed the presence of a unique gene for RnBP in the porcine genome.
Sudden Cardiac Death in the United States, 1989 to 1998 (2001)

SCD remains an important public health problem in the US. The increase in death rates for SCD among younger women warrants additional investigation.
Real-Time Creased Approximate Subdivision Surfaces with Displacements (2010)

We present an extension of Loop and Schaefer's approximation of Catmull-Clark surfaces (ACC) for surfaces with creases and corners. We discuss the integration of ACC into Valve's Source game engine and analyze performance of our implementation.
Design of an Axial-Flux Interior Permanent-Magnet Synchronous Motor for Automotive Application: Performance Comparison with Electric Motors Used in EVs and HEVs (2014)

The use of permanent-magnet (PM) machines for electric vehicles (EVs) and hybrid electric vehicles (HEVs) has grown substantially in recent decades. This is due to their high torque/power performances, especially when rare-earth PMs are used. Furthermore, high efficiency and, with adequate control, large speed operation range can be reached. In this paper, an axial-flux (AF) machine type interior PM (IPM) is designed to be used in HEV application. Machine performances will be described and compared to those of conventional IPM motors used in current commercialized EVs and HEVs.
The Strategy of Infection as a Criterion for Phylogenetic Relationships of Non-Coli Phages Morphologically Similar to Phage T7 (1979)

Five phages which are morphologically similar to coliphage T7 but attack other host bacteria have been compared to T7 and to its relative, T3, by the following criteria: (a) cross-reactivity with antisera against T7 and T3, (b) DNA base sequence homologies, as determined by the C0t technique, (c) synthesis of two phage-coded enzymes: RNA polymerase and SAMase, (d) patterns of phage-directed protein synthesis, as determined by SDS-polyacrylamide gel electrophoresis of phage coat subunits. As judged by all these criteria, Pseudomonas phage PX3 is not related to T7; thus, morphological similarity was attributed to convergent evolution. The other phages, i.e. Serratia phage IV, Psuedomonas phage gh-1, Citrobacter phage ViIII and Klebsiella phage No. 11, were considered to be related to T7 on the basis of similarities in the patterns of phage-coded proteins and because, early after infection, these phages induced, as T7 does, an RNA polymerase which specifically transcribes the DNA of thehomologous phage. Phages IV and No. 11 also induced the early synthesis of SAMase (previously only known to occur upon T3 infection). With the exception of phage IV, however, DNA base sequence homologies with T7 or T3 seem to be poor or non-existent. The tested phages, again with the exception of phage IV, did not react with antiserum against T3 or T7. It is concluded that a particular pattern of phage-directed protein synthesis (as characterized by polyacrylamide gel electrophoresis and enzyme tests) may provide evidence for phylogenetic relationships between phages, even in cases where other criteria, such as genetic recombination, serological cross-reaction, and DNA base sequence homologies, fail to indicate relatedness.
Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster (1995)

A fragment of the Salmonella typhimurium ethanolamine utilization operon was cloned and characterized. The 6.3-kb nucleotide sequence encoded six complete open reading frames, termed cchA, cchB, eutE, eutJ, eutG, and eutH. In addition, the nucleotide sequences of two incomplete open reading frames, termed eutX and eutI, were also determined. Comparison of the deduced amino acid sequences and entries in the GenBank database indicated that eutI encodes a phosphate acetyltransferase-like enzyme. The deduced amino acid sequences of the EutE and EutG proteins revealed a significant degree of homology with the Escherichia coli alcohol dehydrogenase AdhE sequence. Mutations in eutE or eutG completely abolished the ability of mutants to utilize ethanolamine as a carbon source and reduced the ability to utilize ethanolamine as a nitrogen source. The product of eutE is most probably an acetaldehyde dehydrogenase catalyzing the conversion of acetaldehyde into acetyl coenzyme A. The product of the eutG gene, an uncommon iron-containing alcohol dehydrogenase, may protect the cell from unconverted acetaldehyde by converting it into an alcohol. The deduced amino acid sequence of cchA resembles that of carboxysome shell proteins from Thiobacillus neapolitanus and Synechococcus sp. as well as that of the PduA product from S. typhimurium. CchA and CchB proteins may be involved in the formation of an intracellular microcompartment responsible for the metabolism of ethanolamine. The hydrophobic protein encoded by the eutH gene possesses some characteristics of bacterial permeases and might therefore be involved in the transport of ethanolamine. Ethanolamine-utilization mutants were slightly attenuated in a mouse model of S. typhimurium infection, indicating that ethanolamine may be an important source of nitrogen and carbon for S. typhimurium in vivo.
Error rate monitoring for digital communications (1982)

The error rate is an important measure of performance in digital communications system, since it gives an indication of the quality of the received information. This paper provides a tutorial overview of methods of error monitoring under four broad classifications, namely, test sequences, parameter measurements, violation detection, and pseudo-error monitoring. A brief discussion of several approaches towards performance monitoring and the definition of error rate parameters is also given. The various methods are described and compared; but, no one monitor is singled out as the "best" since the final choice depends largely on the specific requirements of a given application.
Overview of plasma source ion implantation research at University of Wisconsin–Madison (1994)

In the last five years, plasma source ion implantation (PSII) research at the University of Wisconsin–Madison, has encompassed work in the areas of plasma physics, diagnostics, ion-material interactions’ modeling, materials science issues, and a broad spectrum of industrial applications of PSII technology. The third generation PSII system is presently under construction. Three methods of plasma generation, namely, electron impact method, glow discharge, and radio frequency have been successfully employed. In the following article the highlights of the above facets of PSII research activities have been presented.
Differential induction of macrophage-derived cytokines by live and dead intracellular bacteria in vitro (1995)

Marked differences in the abilities of living and heat-killed Brucella abortus and Listeria monocytogenes organisms to induce production of tumor necrosis factor alpha by in vitro-cultured macrophages were observed. Interleukin-1 and interleukin-6 appeared to be under different control. The results are discussed in relation to the induction of gamma interferon-producing Th1 cells and acquired cellular resistance to infection by living vaccines but not killed vaccines.
Use of Ultrasound Imaging to Determine Sex of Shovelnose Sturgeon (2004)

Abstract During November 2002, 51 shovelnose sturgeon Scaphirhynchus platorynchus were sexed by ultrasound imaging using a portable ultrasonograph. We identified males with 96% accuracy (N = 25) and females with 80% accuracy (N = 25); one hermaphroditic individual was misidentified as a male. Overall, ultrasound imaging was 86% accurate. Sex in postspawned females was difficult to determine, 60% being misidentified as males (N = 5). Ultrasonography is an effective noninvasive method for sex determination that can be applied to other species of Acipenseriformes. Modern portable equipment expands its utility to field studies.
Substrate Cleavage Analysis of Furin and Related Proprotein Convertases (2008)

We present the data and the technology, a combination of which allows us to determine the identity of proprotein convertases (PCs) related to the processing of specific protein targets including viral and bacterial pathogens. Our results, which support and extend the data of other laboratories, are required for the design of effective inhibitors of PCs because, in general, an inhibitor design starts with a specific substrate. Seven proteinases of the human PC family cleave the multibasic motifs R-X-(R/K/X)-R downward arrow and, as a result, transform proproteins, including those from pathogens, into biologically active proteins and peptides. The precise cleavage preferences of PCs have not been known in sufficient detail; hence we were unable to determine the relative importance of the individual PCs in infectious diseases, thus making the design of specific inhibitors exceedingly difficult. To determine the cleavage preferences of PCs in more detail, we evaluated the relative efficiency of furin, PC2, PC4, PC5/6, PC7, and PACE4 in cleaving over 100 decapeptide sequences representing the R-X-(R/K/X)-R downward arrow motifs of human, bacterial, and viral proteins. Our computer analysis of the data and the follow-on cleavage analysis of the selected full-length proteins corroborated our initial results thus allowing us to determine the cleavage preferences of the PCs and to suggest which PCs are promising drug targets in infectious diseases. Our results also suggest that pathogens, including anthrax PA83 and the avian influenza A H5N1 (bird flu) hemagglutinin precursor, evolved to be as sensitive to PC proteolysis as the most sensitive normal human proteins.
Osteogenesis in Bone Defects in Rats: The Effects of Hydroxyapatite and Demineralized Bone Matrix (1989)

Hydroxyapatite (HA) and Demineralized Bone Matrix (DBM) are being investigated as potential osteogenic agents with hopes that these substances can be used to induce bone formation in non-union fractures. This study was done to determine the relative effects of HA and DBM implanted as moldable phospholipid composites in bone defects that result in non-unions. We studied 22 ten-month-old Long-Evans male rats with 5.0 mm unilateral radial defects implanted with HA, DBM, and a combination of both substances. Control defects were left unfilled. Eight weeks after implantation, the histological sections demonstrated a decrease in bone formation with HA relative to controls. The HA crystals were encapsulated by connective tissue stroma made up of collagenous elements, fibroblasts, and blood vessels. There were no indications of bone formation within the fibrous stroma. 45Calcium, alkaline phosphatase, and bone gla protein (BGP) assays demonstrated a 16% increase in bone formation in rats implanted with DBM, an 80% decrease in groups implanted with HA (p = 0.01) and an 80% decrease with DBM plus HA (p = 0.01). Radiologic analysis corresponds well with histological and biochemical results. We conclude that osteogenesis in non-union defects is enhanced by the implantation of DBM, while HA interferes with bone formation in the rat model. In the presence of both substances, HA appears to impede new bone growth, negating any positive effects seen with DBM.
Integrated Services in the Internet Architecture: an Overview (1994)

This memo discusses a proposed extension to the Internet architecture and protocols to provide integrated services, i.e., to support real- time as well as the current non-real-time service of IP. This extension is necessary to meet the growing need for real-time service for a variety of new applications, including teleconferencing, remote seminars, telescience, and distributed simulation.
Cloning of mid-G1 serum response genes and identification of a subset regulated by conditional myc expression. (1994)

The emergence of cells from a quiescent G0 arrested state into the cell cycle is a multistep process that begins with the immediate early response to mitogens and extends into a specialized G1 phase. Many immediate early serum response genes including c-fos, c-myc, and c-jun are transcriptional regulators. To understand their roles in regulating cell cycle entry and progression, the identities of their regulatory targets must be determined. In this work we have cloned cDNA copies of messenger RNAs that are either up- or down-regulated at a mid-G1 point in the serum response (midserum-response [mid-SR]). The mid-SR panel is expected to include both direct and indirect targets of immediate early regulators. This expectation was confirmed by the identification of several transcriptional targets of conditional c-myc activity. In terms of cellular function, the mid-SR class is also expected to include execution genes needed for progression through G1 and into S-phase. DNA sequence data showed that the mid-SR panel included several genes already known to be involved in cell cycle progression or growth transformation, suggesting that previously unknown cDNAs in the same group are good candidates for other G1 execution functions. In functional assays of G0-->S-phase progression, c-myc expression can bypass the requirement for serum mitogens and drive a large fraction of G0 arrested cells through G1 into S-phase. However, beyond this general similarity, little is known about the relation of a serum-driven progression to a myc-driven progression. Using the mid-SR collection as molecular reporters, we found that the myc driven G1 differs qualitatively from the serum driven case. Instead of simply activating a subset of serum response genes, as might be expected, myc regulated some genes inversely relative to serum stimulation. This suggests that a myc driven progression from G0 may have novel properties with implications for its action in oncogenesis.
The Mucin Degrader Akkermansia muciniphila Is an Abundant Resident of the Human Intestinal Tract (2007)

A 16S rRNA-targeted probe, MUC-1437, was designed and validated in order to determine the presence and numbers of cells of Akkermansia muciniphila, a mucin degrader, in the human intestinal tract. As determined by fluorescent in situ hybridization, A. muciniphila accounted more than 1% of the total fecal cells and was shown to be a common bacterial component of the human intestinal tract.
Selective Inhibitors of Cyclic AMP-Specific Phosphodiesterase:  Heterocycle-Condensed Purines (1997)

To reverse the adverse reactions of alkylxanthines and to develop novel inhibitors of cyclic AMP-specific phosphodiesterase (PDE IV), a series of heterocycle-condensed purines were designed and synthesized. Some of these new compounds had similar or more potent and selective inhibitory activity against PDE IV than known PDE IV inhibitors. The tracheal-relaxant activity of these compounds was closely correlated with their PDE IV-inhibitory activity. Moreover, these purine analogues did not have any positive-chronotropic action or adenosine-antagonistic action on isolated heart preparations, which are the particular adverse reactions of alkylxanthines. Among them, 3,4-dipropyl-4,5,7,8-tetrahydro-3H-imidazo[1,2-i]-purin-5-one (1c), which was the most selective and potent PDE IV inhibitor, did not cause emesis in Suncus murinus at a dosage range of 10-100 mg/kg (po), while an imidazole analogue of 1c (4c) and known PDE IV inhibitors such as rolipram and denbufylline caused emesis even at 10 or 30 mg/kg.