gebhart/patrepeval huggingface dataset:
Epidemiology of Infection by Nontuberculous Mycobacteria (1987)

Using the fluorochrome auramine-O, direct microscopic counts of log phase cells of Mycobacterium avium, M. intracellulare, and M. scrofulaceum (MAIS) group showed excellent correlations with viable spread-plate counts. Accordingly, an enumeration of total acid-fast and MAIS cells by stain and culture (respectively) in groundwaters from three United States regions that differ in their incidence of human infection by MAIS was undertaken. Of 30 state-monitored, undisinfected wells, 11 were in Georgia coastal plain (high incidence), 10 were in the Virginia coastal plain (intermediate incidence), and 9 were in Montgomery County, Virginia (low incidence). Total acid-fast cells ranged widely between 280 to 5,367 per ml among the groundwaters, and with one exception showed no correlations or trends between regions of different incidence of human infection, or to total bacterial cell counts or colony-forming units. The exception was that the proportions of acid-fast cells relative to total cells were higher in the Georgia groundwaters. However, despite the relatively high auramine-O counts, few mycobacteria were recovered by culture. Of 12 wells yielding mycobacteria, 9 yielded rapidly growing and 4 slowly growing mycobacteria. Only one well in Montgomery County, Virginia (region of low incidence) yielded a MAIS isolate, albeit at low density. This research supports the conclusion that clean groundwaters are unlikely sources of MAIS infection in humans in the southeastern United States.
Immunological Enhancement as Studied by Cell Culture Techniques (1970)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
A Guide to Counseling in Early Recovery from Alcohol Dependence (1991)

This article examines four factors involved in early recovery: neuro-psychological reactions, social attention and support, sense of physical well-being, and emergence of numbed and repressed feelings. In addition, three stages of early recovery-acute pain, euphoric promise, and reality adjustment-are identified in their interactions with the four recovery factors. The counseling methods and goals appropriate to each stage are considered.
The Crystal Structure of Phosphinothricin in the Active Site of Glutamine Synthetase Illuminates the Mechanism of Enzymatic Inhibition (2001)

Phosphinothricin is a potent inhibitor of the enzyme glutamine synthetase (GS). The resolution of the native structure of GS from Salmonella typhimurium has been extended to 2.5 A resolution, and the improved model is used to determine the structure of phosphinothricin complexed to GS by difference Fourier methods. The structure suggests a noncovalent, dead-end mechanism of inhibition. Phosphinothricin occupies the glutamate substrate pocket and stabilizes the Glu327 flap in a position which blocks the glutamate entrance to the active site, trapping the inhibitor on the enzyme. One oxygen of the phosphinyl group of phosphinothricin appears to be protonated, because of its proximity to the carboxylate group of Glu327. The other phosphinyl oxygen protrudes into the negatively charged binding pocket for the substrate ammonium, disrupting that pocket. The distribution of charges in the glutamate binding pocket is complementary to those of phosphinothricin. The presence of a second ammonium binding site within the active site is confirmed by its analogue thallous ion, marking the ammonium site and its protein ligands. The inhibition of GS by methionine sulfoximine can be explained by the same mechanism. These models of inhibited GS further illuminate its catalytic mechanism.
Effects of rewards, peer-modelling and pedometer targets on children's physical activity: A school-based intervention study (2010)

This study evaluated a physical activity intervention for children that comprised peer-modelling, pedometer step goals and tangible rewards. A version of the intervention without the reward component was also tested. Participants (n = 386) were from three primary schools, which were randomly assigned to one of three conditions: (i) full intervention, where children received "Fit 'n' Fun Dude" peer-modelling materials and were given daily pedometer goals to receive rewards, (ii) no-rewards intervention, where children received peer-modelling materials and pedometer goals but rewards were not used and (iii) control, where children wore pedometers with no further intervention. Physical activity was measured at baseline, intervention and at the end of a 14-week 'taper' phase. During the intervention, the full intervention school showed the largest increase in physical activity relative to baseline (+2456 steps per day, p < 0.001). There was a smaller increase in the no-rewards school (+1033 steps per day, p < 0.03), and no significant change in the control. At the end of the taper phase, physical activity in the no-rewards school continued to increase (+2030 steps per day, p < 0.001) but had returned to baseline in the full intervention school. The intervention that used only peer-modelling and pedometer goals produced better effects over time.
Localized reversible frameshift mutation in an adhesin gene confers a phase‐variable adherence phenotype in mycoplasma (1997)

The variable adherence-associated (Vaa) antigen of Mycoplasma hominis is an abundant surface lipoprotein adhesin that may mediate important interactions of this wall-less prokaryotic pathogen with the human host. Extensive mutational variation of Vaa size, as well as sequence and antigenic divergence, has been described previously. Using a series of clonal isolates representing an isogenic lineage of variants oscillating in Vaa expression, Vaa is further shown in this study to undergo high-frequency phase variation in expression, which correlated precisely with the ability of M. hominis to adhere to cultured human cells. Although no DNA rearrangements or sequence differences in the 5' regions flanking vaa alleles were detected between Vaa+ and Vaa variants, intragenic vaa sequences from this lineage revealed an oscillating mutation involving a single nucleotide deletion/insertion in a short tract of adenine residues near the 5' end of the mature Vaa coding sequence, which created a translational frameshift resulting in either a complete Vaa ORF or an in-frame UAG stop codon immediately downstream of the poly-A tract. Evidence for the occurrence of this high-frequency frameshift mutation in vivo was obtained from analysis of PCR-generated vaa sequences amplified from the joint synovial fluid of a patient with M. hominis-associated arthritis, which indicated that Vaa phase variation occurs during M. hominis infection in the natural host. These results identify a distinctive frameshift mutator element in the vaa gene that governs M. hominis adherence and highlight the importance of mutational alteration of primary gene products on the mycoplasma surface as a means of generating and maintaining functional diversity in the host.
A NEW TYPE OF RE‐ENTRANT CANNULA DESIGNED FOR USE IN THE SMALL INTESTINE OF THE PIG (1974)

Summary A new type of intestinal re‐entrant cannula for the small intestine of pigs is described. It consisted of an intestinal tube joined to a stem bearing a flange and two perspex plugs (“maintenance plug” and “collection plug”). The cannula was inserted in the intestine through the incision on the antimesenteric side of the intestine and no transection of the intestine was required. No outside connection was present and the cannula extended only 1 to 2cm beyond the body. Cannulae were inserted in the duodenum and ileum of 5 pigs and these functioned satisfactorily for up to 3 months.
Nonuniform fast Fourier transform (1999)

Abstract The nonuniform discrete Fourier transform (NDFT) can be computed with a fast algorithm, referred to as the nonuniform fast Fourier transform (NFFT). In L dimensions, the NFFT requires O(N(-ln epsilon ) L + (Pi L (sub l = 1) M l ) Sigma L (sub l = 1) log M l ) operations, where M l is the number of Fourier components along dimension l, N is the number of irregularly spaced samples, and epsilon is the required accuracy. This is a dramatic improvement over the O(NPi L (sub l = 1) M l ) operations required for the direct evaluation (NDFT). The performance of the NFFT depends on the lowpass filter used in the algorithm. A truncated Gauss pulse, proposed in the literature, is optimized. A newly proposed filter, a Gauss pulse tapered with a Hanning window, performs better than the truncated Gauss pulse and the B-spline, also proposed in the literature. For small filter length, a numerically optimized filter shows the best results. Numerical experiments for 1-D and 2-D implementations confirm the theoretically predicted accuracy and efficiency properties of the algorithm.
Combined Handwriting and Speech Modalities for User Authentication (2008)

In this paper, we report on the development of an efficient user authentication system based on a combined acquisition of online pen and speech signals. The novelty of our approach is in the simultaneous recording of these two modalities, simply asking the user to utter what she/he is writing. The main benefit of this multimodal approach is a better accuracy at no extra costs in terms of access time or inconvenience. Another benefit comes from an increased difficulty for forgers willing to perform imitation attacks as two signals need to be reproduced. We are comparing here two potential scenarios of use. The first one is called <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">spoken</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">signatures</i> where the user signs and says the content of the signature. The second scenario is based on <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">spoken</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">handwriting</i> where the user is prompted to write and read the content of sentences randomly extracted from a text. Data according to these two scenarios have been recorded from a set of 70 users. In the first part of this paper, we describe the acquisition procedure, and we comment on the viability and usability of such simultaneous recordings. Our conclusions are supported by a short survey performed with the users. In the second part, we present the authentication systems that we have developed for both scenarios. More specifically, our strategy was to model independently both streams of data and to perform a fusion at the score level. Starting from a state-of-the-art-modeling algorithm based on Gaussian Mixture Models trained with an Expectation-Maximization procedure, we report on several significant improvements that are brought. As a general observation, the use of both modalities outperforms significantly the modalities used alone.
The influence of nitric oxide synthase 2 on cutaneous wound angiogenesis (2011)

NOS 2 is significantly involved in angiogenic signalling in healing skin wounds, particularly within the first 7 days. However, Matrigel plug vascularization suggests that the role of NOS 2 in angiogenesis is related to VEGF-A but not FGF-2 stimulated angiogenesis.
Sidewall Oxidation and Complexation of Carbon Nanotubes by Base-Catalyzed Cycloaddition of Transition Metal Oxide:  A Theoretical Prediction (2002)

By means of a two-layered ONIOM (B3LYP/LANL2DZ:UFF) approach, we predicted the viable oxidation of the sidewalls of single-wall carbon nanotubes by transition metal oxide (OsO4), which gives rise to osmate ester adducts on the nanotube sidewall. We believe that the as-formed osmate ester adducts can be a good starting point for further functionalization, hence, introducing high flexibility to carbon nanotubes for further manipulations for various potential applications.
SERS-based immunoassay using a gold array-embedded gradient microfluidic chip (2012)

Here we report the development of a programmable and fully automatic gold array-embedded gradient microfluidic chip that integrates a gradient microfluidic device with gold-patterned microarray wells. This device provides a convenient and reproducible surface-enhanced Raman scattering (SERS)-based immunoassay platform for cancer biomarkers. We used hollow gold nanospheres (HGNs) as SERS agents because of their highly sensitive and reproducible characteristics. The utility of this platform was demonstrated by the quantitative immunoassay of alpha-fetoprotein (AFP) model protein marker. Our proposed SERS-based immunoassay platform has many advantages over other previously reported SERS immunoassay methods. The tedious manual dilution process of repetitive pipetting and inaccurate dilution is eliminated with this process because various concentrations of biomarker are automatically generated by microfluidic gradient generators with N cascade-mixing stages. The total assay time from serial dilution to SERS detection takes less than 60 min because all of the experimental conditions for the formation and detection of immunocomplexes can be automatically controlled inside the exquisitely designed microfluidic channel. Thus, this novel SERS-based microfluidic assay technique is expected to be a powerful clinical tool for fast and sensitive cancer marker detection.
Dynamics of growth factor production in monolayers of cancer cells and evolution of resistance to anticancer therapies (2013)

Tumor heterogeneity is well documented for many characters, including the production of growth factors, which improve tumor proliferation and promote resistance against apoptosis and against immune reaction. What maintains heterogeneity remains an open question that has implications for diagnosis and treatment. While it has been suggested that therapies targeting growth factors are robust against evolved resistance, current therapies against growth factors, like antiangiogenic drugs, are not effective in the long term, as resistant mutants can evolve and lead to relapse. We use evolutionary game theory to study the dynamics of the production of growth factors by monolayers of cancer cells and to understand the effect of therapies that target growth factors. The dynamics depend on the production cost of the growth factor, on its diffusion range and on the type of benefit it confers to the cells. Stable heterogeneity is a typical outcome of the dynamics, while a pure equilibrium of nonproducer cells is possible under certain conditions. Such pure equilibrium can be the goal of new anticancer therapies. We show that current therapies, instead, can be effective only if growth factors are almost completely eliminated and if the reduction is almost immediate.
Performance weight selection for H-infinity and μ-control methods (1991)

The paper discusses, from a process control perspective, different approaches to performance weight selection when using H-infinity objectives. Approach A considers direct bounds on important transfer functions such as sensitivity and complementary sensitivity. Approach B considers the output response to sinusoidal disturbances, setpoints and noise. We also give some insight into the practical use of H-infinity and μ methods. μ is the structured singular value (SSV) introduced by Doyle (1982). μ-synthesis is generally not a convex optimisation problem and is presently not straightforward. We will discuss some of the problems we have encountered.
Scaling laws of microactuators and potential applications of electroactive polymers in MEMS (1999)

Besides the scale factor that distinguishes the various spices fundamentally biological muscles changes little between species indicating a highly optimized system, Electroactive polymer actuators offer the closest resemblance to biological muscles however beside the large actuation displacement these materials are falling short with regards to the actuation force. As improved materials emerging it is becoming necessary to address key issues such as the need for effective electromechanical modeling and guiding parameters in scaling the actuators. In this paper, we will review the scaling laws for three major actuation mechanisms that are of relevance to micro electromechanical systems: electrostatic actuation, magnetic actuation, thermal bimetallic actuation, and piezoelectric actuation. Keywords: MEMS, micro actuators, electroactive polymers, EAP I.
NOISE REDUCTION OF A CROSS-FLOW FAN (1997)

ABSTRACT This study attempts to reduce the aerodynamic sound noise from a cross-flow fan by varying the geometrical parameters of the cross- flow fan as the similar amount of air flow rate is delivered by the cross- flow fan. Two different rotors (fixed-pitch and staggered-pitch) and tongues (wedge- shape and saw-tooth shape), and four different tongue clearances (ε=3mm, 5mm, 7mm, and 10mm) are also tested. At Ω≥ 1200 r/min, a screech tone produced from the peak sound pressure levels at the harmonics of blade passage frequency always occurs for the cross- flow fan with the fixed-pitch rotor, the wedge shape, and ε=3 mm. At Ω≥1200 r/min, the sound pressure level at the first harmonic of blade passage frequency is significantly reduced by either replacing the fixed- pitch rotor with the staggered-pitch one as well as replacing the wedge shape with the saw-tooth tongue or enlarging the tongue clearance. However, the overall sound pressure level from the cross-flow fan to deliver the same air flow rate is slightly changed with geometrical parameters varied in this study.
Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer (2019)

The flexibility and utility of PurIST on low-input samples such as tumor biopsies allows it to be used at the time of diagnosis to facilitate the choice of effective therapies for patients with pancreatic ductal adenocarcinoma and should be considered in the context of future clinical trials.
The amino terminus of the aspartate chemoreceptor is formylmethionine. (1990)

The amino terminus of the Salmonella typhimurium aspartate receptor has been identified as formylmethionine by mass spectral analysis of the amino-terminal tryptic peptide. Purification and analysis of the blocked amino-terminal peptide was facilitated by the use of a mutant aspartate receptor which has a cysteine residue at position 3. The sequence of this peptide confirms the translational start site predicted from the nucleotide sequence of the tar gene. Furthermore, in vivo labeling experiments reveal that the formyl group is present on chemotaxis receptors produced at wild-type levels in Escherichia coli, indicating that the presence of the formyl group is not a consequence of over-production of the receptor. The stability of the amino-terminal formyl group on the receptor may be a consequence of the membrane localization of the receptor and the dependence of this localization on the membrane transport machinery of the cell.
The Concept of Delayed Nucleation in Nanocrystal Growth\nDemonstrated for the Case of Iron Oxide Nanodisks (2016)

A comprehensive study of iron oxide nanocrystal growth through non-hydrolitic, surfactant-mediated thermal reaction of iron pentacarbonyl and an oxidizer has been conducted, which includes size\ncontrol, anisotropic shape evolution, and crystallographic phase transition of monodisperse iron oxide\ncolloidal nanocrystals. The reaction was monitored via in situ UV−vis spectroscopy, taking advantage of\nthe color change accompanying the iron oxide colloid formation, allowing measurement of the induction\ntime for nucleation. Features of the synthesis such as the size control and reproducibility are related to the\noccurrence of the observed delayed nucleation process. As a separate source of iron and oxygen is adopted,\nphase control could also be achieved by sequential injections of oxidizer.
On the Xylanase System of Aspergillus batatae (1957)

Journal Article On the Xylanase System of Aspergillus batatae Get access Sakuzo Fukui, Sakuzo Fukui Division of Zymomycology, Institute of Applied Microbiology, University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Masatada Sato Masatada Sato Division of Zymomycology, Institute of Applied Microbiology, University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Bulletin of the Agricultural Chemical Society of Japan, Volume 21, Issue 6, 1 November 1957, Pages 392–393, https://doi.org/10.1080/03758397.1957.10857421 Published: 01 November 1957 Article history Received: 30 September 1957 Published: 01 November 1957
Towards automation of checklist-based code-reviews (2002)

Different types of code-reviews (Fagan-style code-inspections, Parnas-like active design reviews and walkthroughs) have been found to be very useful in improving the quality of software. In many cases reviewers use checklists to guide their analysis during review sessions. However, valuable, checklist-based code-reviews have the principal shortcoming of their high costs due to lack of supporting tools enabling at least partial automation of typical multiple appearing rules. This paper describes an approach towards semi-automation of some steps of individual review processes based on checklists. The method proposed is interactive, i.e. reviewers will be enabled to actualize, extend, and check the consistency and redundancy of their checklists. The basic idea underlying the approach is the usage of a rule-based system, adapting concepts of the compiler theory and knowledge engineering, for acquisition and representation of knowledge about the program. Redundant and conflicting knowledge about the program under study is recognized and solved by means of an embedded truth maintenance system. As a result of fault diagnosis, rules for fault classification are used. Software reliability models are applied to validate the results of each review session. The approach has shown promising preliminary results in analyses of conventional C-programs developed in the automotive industry.
Subtle and atypical cobalamin deficiency states (1990)

Evidence for cobalamin (vitamin B12) deficiency usually involves some combination of low serum cobalamin levels, clinical abnormalities (classically, megaloblastic anemia and neurologic defects), metabolic abnormalities, and response to therapy. However, cobalamin deficiency may often display few of the expected clinical findings. Identification of the underlying cause is also important in the diagnosis of deficiency, and its value may be particularly great when the expression of deficiency is subtle. The cause of cobalamin deficiency is usually malabsorptive, but may sometimes be limited to malabsorption of food cobalamin while free cobalamin is absorbed normally. Nongastroenterologic entities may sometimes also be found. All of these considerations allow the proposal of four patterns of cobalamin deficiency. The first type is classical deficiency; typical megaloblastic anemia with or without neurologic dysfunction occurs because of classical cobalamin malabsorption such as lack of intrinsic factor (pernicious anemia). The second type consists of classical cobalamin malabsorption in which the cobalamin deficiency is expressed subtly rather than in classical fashion. There is no megaloblastic anemia and sometimes the only evidence of deficiency may be metabolic. In the third type, cobalamin deficiency is expressed classically but is attributable to a subtle or atypical cause, such as food-cobalamin malabsorption. In the fourth type, deficiency is both expressed subtly and arises from subtle or atypical causes. Such presentations require further investigation but are a challenging expansion of our understanding and recognition of cobalamin deficiency.