gebhart/patrepeval huggingface dataset:
Long-Term Immune Responses to Coxiella burnetii after Vaccination (2012)

Q fever is a zoonotic disease caused by infection with the bacterium Coxiella burnetii. Infection with C. burnetii results in humoral and cellular immune responses, both of which are thought to contribute to protection against subsequent infection. Whole-cell formalin-inactivated vaccines have also been shown to induce both humoral and cellular immunity and provide protection. Whether measurement of cellular or humoral immunity is a better indicator of immune protection is not known, and the duration of immunity induced by natural infection or vaccination is also poorly understood. To better understand the measurement and duration of C. burnetii immunity, 16 people vaccinated against Q fever (0.2 to 10.3 years before analysis) and 29 controls with a low risk of Q fever exposure were tested for immune responses to C. burnetii by an indirect fluorescent-antibody test (IFA) to measure circulating antibody and by a gamma interferon release assay (IGRA) to measure cellular immunity. Among vaccinated subjects, the IFA detected antibodies in 13/16, and the IGRA also detected positive responses in 13/16. All of the vaccinated subjects had a positive response in at least one of the assays, whereas 8/29 control subjects were positive in at least one assay. There was not a correlation between time since vaccination and responses in these assays. These results show that IFA and IGRA perform similarly in detection of C. burnetii immune responses and that Q fever vaccination establishes long-lived immune responses to C. burnetii.
Realization of high performance dual gate DRAMs without boron penetration by application of tetrachlorosilane silicon nitride films (2002)

It is well known that conventional SiN films accelerate boron penetration due to hydrogen desorption during a high temperature annealing process after SiN deposition (Pfiester et al, 1990). The boron penetration causes depletion of the gate electrodes and threshold voltage deviations, and degrades the PMOSFETs. In the case of next generation DRAMs, thick SiN films are necessary as a hard mask for a self-aligned contact (SAC) process to increase the density. Simultaneously, dual gate CMOS systems should be applied to realize high performance. Therefore, SiN films without boron penetration must be developed for realization of dual gate CMOS systems with a SAC process. Conventional silicon nitride (SiN) films accelerate boron penetration, which causes the degradation of PMOSFETs. It was found that boron penetration becomes worse in proportion to SiH content incorporated in SiN LPCVD films. Applications of SiH-less SiN films, formed from tetrachlorosilane (TCS) and ammonia, have successfully realized the high performance of PMOSFETs in dual gate system DRAMs.
MAP-1 and MAP-2 binding sites at the C-terminus of .beta.-tubulin. Studies with synthetic tubulin peptides (1991)

The interaction of microtubule-associated proteins MAP-1 and MAP-2 with different peptides containing sequences covering the C-terminal region of beta-tubulin isoforms has been analyzed. Our results indicate that MAP-1 and MAP-2 bind to a common sequence within the variable C-terminal region of the different beta-tubulin isoforms, while MAP-2 also interacts with the subdomain beta (422-434) of the constant region, in agreement with previous results (Maccioni, R.B., Rivas, C., & Vera, J.C. (1988) EMBO J. 7, 1957-1963). The productive interaction of MAP-2 with the latter domain appears to be involved in the assembly of microtubules.
Shifting goals and mounting challenges for statistical methodology (2002)

Modern interdisciplinary research in statistical science encompasses a wide field: agriculture, biology, biomedical sciences along with bioinformatics, clinical sciences, education, environmental and public health disciplines, genomic science, industry, molecular genetics, socio-behavior, socio-economics, toxicology, and a variety of other disciplines. Statistical science has historically had mathematical perspectives dominating theoretical and methodological developments. Yet, the advent of modern information technology has opened the doors for highly computation intensive statistical tools (i.e., software), wherein mathematical aspects are often de-emphasized. Knowledge discovery and data mining (KDDM) is now becoming a dominating force, with bioinformatics as a notable example. In view of this apparent discordance between mathematical (frequentist as well as Bayesian) and computational approaches to statistical resolutions, and a genuine need to formulate training as well as research curricula to meet growing demands, a critical appraisal of statistical innovations is made with due respect to its mathematical heritage, as well as scope of application. Some of the challenging statistical tasks are illustrated.
Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas (2014)

Analyses of >1600 GCs suggest that Asian and non-Asian GCs exhibit distinct tumour immunity signatures related to T-cell function. These differences may influence geographical differences in clinical outcome, and the design of future trials particularly in immuno-oncology.
Intraperitoneal P-32 after negative second-look laparotomy in ovarian carcinoma (1989)

Thirty-one patients underwent a negative second-look laparotomy between 1976 and 1986. Fourteen patients received intraperitoneal chromic phosphate (P-32) after a negative second-look laparotomy. There has been no local recurrence (zero of 14) and no deaths attributable to recurrent disease. Local control and disease-free survival are 100%, with a minimum follow-up of 2 years and a mean follow-up of 4 years. Seventeen patients received no further therapy because of patient refusal, poor diffusion, or other contraindications to P-32 installation. Four of 17 patients undergoing negative second-look procedures without the addition of P-32 have subsequently recurred. This difference is highly suggestive (P = .076). There have been no major complications with the addition of P-32. The use of intraperitoneal P-32 after negative second-look laparotomies on ovarian carcinoma is well tolerated and effective in preventing recurrence.
AC Conductivity of Undoped a-Si:H and µc-Si:H in Connection with Morphology and Optical Degradation (1989)

Ac conductivity of a-Si:H and µc-Si:H films is studied experimentally with theoretical consideration. By separating ac conductivity into band, variable range hopping (VRH), band tail multiple hopping and intimate pair hopping conductivities, the effects of the morphology and optical degradation in each type of the conductivities were investigated to elucidate the nature of electronic conduction. Experimental facts on the pair-hopping conductivity seem to be explained in terms of a two-electron correlated barrier hopping (CBH) model between oppositely charged dangling bond pairs located at low-density Si–H alloy regions (voids). Long-range transport (band, multiple hopping, VRH) seems to be related to the percolation through Si clusters and microcrystalline grains, being sensitive to the morphology and Fermi level position.
Measuring Hospital Care from the Patients' Perspective: An Overview of the CAHPS<sup>®</sup> Hospital Survey Development Process (2005)

The CAHPS Hospital Survey is a core set of questions that can be administered as a stand-alone questionnaire or combined with a broader set of hospital specific items.
APU feature integration based on multi-variant flight data analysis (2016)

For aircraft complex systems such as auxiliary power unit (APU), the performance evaluation is currently restricted to observation of several typical parameters. Many other monitoring parameters recorded in Quick Access Recorder (QAR) reflect the APU condition from various aspects yet without enough attention. This study intends to propose integrated performance indicators through feature extraction among many monitoring parameters. Clustering analysis is then conducted to validate the effectiveness of the method by anomaly identification. This method has the potential to easily evaluate performance of some complex aircraft systems for early warning and prevent degradation from early stage.
Improving the Quality of Error-Handling Code in Systems Software using Function-Local Information (2013)

In C, a typical strategy for implementing error handling code is to follow each operation that may encounter an error by a conditional that checks for an error result and, if one is found, performs the appropriate cleanup operations before returning from the function. This basic strategy, however, is itself error-prone, as it is easy to overlook some cleanup operations that are required, and to forget to update some existing error handling code when the function is extended with new operations that need to be undone in an error case. Furthermore, there may be substantial code duplication, as the same error handling code may be needed at many places within a function definition. One style of programming, goto-based strategy, that can somewhat alleviate these difficulties. To improve the structure of error handling code in the system software, we define an algorithm to transform error handling code implemented according to the basic strategy so that it follows the goto-based strategy. Even when error handling code is structured, the management of the releasing of allocated resources remains a continual problem in ensuring the robustness of systems code. In this thesis, we propose a microscopic resource-release omission fault finding algorithm, based on a mostly intraprocedural, flow and path-sensitive analysis, that targets and exploits the properties of error-handling code. Our algorithm is resistant to false positives in the set of resource acquisition and release operations, resulting in a low rate of false positives in the fault reports, and is highly scalable.
Potential use of bioelectrical impedance of the 'whole body' and of body segments for the assessment of body composition: comparison with densitometry and anthropometry. (1989)

The value of 'whole body' and segmental impedance measurements, and of simple anthropometric methods for predicting body composition was assessed in 24 normal (14m, 10f) subjects (BMI, 18.3-28.6), using densitometry as the reference method. The contribution of segmental impedance was assessed in a separate group of 24 normal (12m, 12f) subjects (BMI, 19.8-28.8) at two frequencies (1 kHz and 50 kHz). Estimates of specific resistivities of certain individual segments (upper arm, forearm, upper leg, and lower leg) were also made in this group, and compared to those obtained from a group of 7 obese female subjects (BMI, 32.6-56.1). The bias and 95 per cent limits of agreement between densitometrically determined body composition (fat and fat-free mass, and total body water) and the alternative methods were found to vary considerably, depending on the technique and/or equations employed. Estimates of whole body composition based on impedance or resistance measurements were found to be associated with only slightly smaller limits of agreement than those made by anthropometry. The upper limb was found to have the greatest influence on whole body impedance measurements. Indeed, the forearm, which accounts for 1.3 per cent of body weight contributes 25.0 per cent to 'whole body' impedance. The estimated specific resistivities of segments were found to be considerably greater in the obese individuals than in normal female subjects (for example, 75 per cent higher for the upper arm, P less than 0.001). The results suggest that: (a) there may be a systematic, population-related, error in predicting densitometric estimates of body composition with the use of standard equations, which incorporate variables such as weight, height, skinfold thicknesses, and impedance/resistance measurements; (b) in this population, impedance or resistance measurements confer only a small advantage over simple anthropometry for predicting body composition; (c) the impedance of the arm or leg may provide a simple alternative method for assessing the composition of the whole body; and (d) the estimated specific resistivity of individual body segments may be useful for assessing the composition of those segments.
An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from <i>Streptomyces</i> sp. strain CL190 (2001)

A gene cluster encoding five enzymes of the mevalonate pathway had been cloned from Streptomyces sp. strain CL190. This gene cluster contained an additional ORF, orfD, encoding an unknown protein that was detected in some archaebacteria and some Gram-positive bacteria including Staphylococcus aureus. The recombinant product of orfD was purified as a soluble protein and characterized. The molecular mass of the enzyme was estimated to be 37 kDa by SDS-polyacrylamide gel electrophoresis and 155 kDa by gel filtration chromatography, suggesting that the enzyme is most likely to be a tetramer. The purified enzyme contained flavin mononucleotide (FMN) with the amount per tetramer being 1.4 to 1.6 mol/mol. The enzyme catalyzed the isomerization of isopentenyl diphosphate (IPP) to produce dimethylallyl diphosphate (DMAPP) in the presence of both FMN and NADPH. The Escherichia coli plasmid expressing orfD could complement the disrupted IPP isomerase gene in E. coli. These results indicate that orfD encodes an unusual IPP isomerase showing no sequence similarity to those of IPP isomerases identified to date. Based on the difference in enzymatic properties, we classify the IPP isomerases into two types: Type 2 for FMN- and NAD(P)H-dependent enzymes, and type 1 for the others. In view of the critical role of this isomerase in S. aureus and of the different enzymatic properties of mammalian (type 1) and S. aureus (type 2) isomerases, this unusual enzyme is considered to be a suitable molecular target for the screening of antibacterial drugs specific to S. aureus.
Posterior Cramér-Rao bounds for Doppler biased multistatic range-only tracking (2011)

This paper investigates range-only tracking with range-Doppler coupling, where the range measurement of a target of interest is linearly biased by its range-rate (or Doppler). In previous treatments the situation was monostatic, and a simple Riccati analysis sufficed, but here the system is multistatic (notionally, a MIMO radar). Here, the closed form of posterior Cramer-Rao bound (PCRB) is derived for a multistatic system in the tracking of a kinematic target. As the coupling parameter λ can be zero, positive, or negative, a question arises: which kind of λ could result in a lower PCRB for a given system configuration? With the help of numerical analysis, we see that a positive λ may lead to the lowest PCRB, while a negative λ may result in the highest among these three possibilities.
Wastewater biosolids: an overview of processing, treatment, and management (2001)

Treated as a valuable resource, municipal sludge, often today referred to as biosolids, is processed through a variety of novel unit operations leading to a safe, aesthetically pleasing, and sought-after product. The design engineer is concerned first with the ultimate disposal and utilization of the biosolids, providing at least two options for the final disposal. Volume reduction, stabilization or vector attraction reduction, and pathogen inactivation are the key goals; process trains combining them into one unit process are the target technologies. Drying and pelletization are now being applied at much smaller plants because of the introduction of indirect dryers, which have fewer air pollution problems than the direct dryers still used at some larger plants. Stabilization of biosolids in newer plants is more often combined with disinfection at thermophillic temperatures, in anaerobic and particularly in aerobic regimes. For the smallest plants, dewatering is now available in drying bags or vacuum drying beds, and larger plants benefit from an array of new devices offering sludge cakes as dry as 22 to [Formula: see text]40% total solids. The ultimate dryness will depend on the quality of sludge, polymer conditioning program, and machine parameters. Emphasis on cost reduction, with simultaneous demand for an excellent quality end product, calls for innovative and case-specific solutions that go beyond the treatment plant and also address the quality of industrial-commercial discharges to the municipal sewers.Key words: sludge, biosolids, process design, dewatering, digestion.
Integrating Visual and Textual Cues for Query-by-String Word Spotting (2013)

In this paper, we present a word spotting framework that follows the query-by-string paradigm where word images are represented both by textual and visual representations. The textual representation is formulated in terms of character n-grams while the visual one is based on the bag-of-visual-words scheme. These two representations are merged together and projected to a sub-vector space. This transform allows to, given a textual query, retrieve word instances that were only represented by the visual modality. Moreover, this statistical representation can be used together with state-of-the-art indexation structures in order to deal with large-scale scenarios. The proposed method is evaluated using a collection of historical documents outperforming state-of-the-art performances.
Synaptic activity induces input‐specific rearrangements in a targeted synaptic protein interaction network (2018)

Cells utilize dynamic, network-level rearrangements in highly interconnected protein interaction networks to transmit and integrate information from distinct signaling inputs. Despite the importance of protein interaction network dynamics, the organizational logic underlying information flow through these networks is not well understood. Previously, we developed the quantitative multiplex co-immunoprecipitation platform, which allows for the simultaneous and quantitative measurement of the amount of co-association between large numbers of proteins in shared complexes. Here, we adapt quantitative multiplex co-immunoprecipitation to define the activity-dependent dynamics of an 18-member protein interaction network in order to better understand the underlying principles governing glutamatergic signal transduction. We first establish that immunoprecipitation detected by flow cytometry can detect activity-dependent changes in two known protein-protein interactions (Homer1-mGluR5 and PSD-95-SynGAP). We next demonstrate that neuronal stimulation elicits a coordinated change in our targeted protein interaction network, characterized by the initial dissociation of Homer1 and SynGAP-containing complexes followed by increased associations among glutamate receptors and PSD-95. Finally, we show that stimulation of distinct glutamate receptor types results in different modular sets of protein interaction network rearrangements, and that cells activate both modules in order to integrate complex inputs. This analysis demonstrates that cells respond to distinct types of glutamatergic input by modulating different combinations of protein co-associations among a targeted network of proteins. Our data support a model of synaptic plasticity in which synaptic stimulation elicits dissociation of pre-existing multiprotein complexes, opening binding slots in scaffold proteins and allowing for the recruitment of additional glutamatergic receptors. Open Science: This manuscript was awarded with the Open Materials Badge. For more information see: https://cos.io/our-services/open-science-badges/.
Bug report assignee recommendation using activity profiles (2013)

One question which frequently arises within the context of artifacts stored in a bug tracking repository is: “who should work on this bug report?” A number of approaches exist to semi-automatically identify and recommend developers, e.g. using machine learning techniques and social networking analysis. In this work, we propose a new approach for assignee recommendation leveraging user activities in a bug tracking repository. Within the bug tracking repository, an activity profile is created for each user from the history of all his activities (i.e. review, assign, and resolve). This profile, to some extent, indicates the user's role, expertise, and involvement in this project. These activities influence and contribute to the identification and ranking of suitable assignees. In order to evaluate our work, we apply it to bug reports of three different projects. Our results indicate that the proposed approach is able to achieve an average hit ratio of 88%. Comparing this result to the LDA-SVM - based assignee recommendation technique, it was found that the proposed approach performs better.
Chemically alternating langmuir-blodgett thin films as a model for molecular depth profiling by mass spectrometry (2007)

Langmuir-Blodgett multilayers of alternating barium arachidate and barium dimyristoyl phosphatidate are characterized by secondary ion mass spectrometry employing a 40 keV buckminsterfullerene (C60) ion source. These films exhibit well-defined structures with minimal chemical mixing between layers, making them an intriguing platform to study fundamental issues associated with molecular depth profiling. The experiments were performed using three different substrates of 306 nm, 177 nm, and 90 nm in thickness, each containing six subunits with alternating chemistry. The molecular subunits are successfully resolved for the 306 nm and 177 nm films by cluster ion depth profiling at cryogenic temperatures. In the depth profile, very little degradation was found for the molecular ion signal of the underneath layers compared with that of the top layer, indicating that the formation of chemical damage is removed as rapidly as it is formed. The resolving power decreases as the thickness of the alternating subunits decrease, allowing a depth resolution of 20 to 25 nm to be achieved. The results show the potential of LB films as an experimental model system for studying fundamental features of molecular depth profiling.
Anti-noise-folding regularized subspace pursuit recovery algorithm for noisy sparse signals (2014)

Denoising recovery algorithms are very important for the development of compressed sensing (CS) theory and its applications. Considering the noise present in both the original sparse signal x and the compressive measurements y, we propose a novel denoising recovery algorithm, named Regularized Subspace Pursuit (RSP). Firstly, by introducing a data pre-processing operation, the proposed algorithm alleviates the noise-folding effect caused by the noise added to x. Then, the indices of the nonzero elements in x are identified by regularizing the chosen columns of the measurement matrix. Afterwards, the chosen indices are updated by retaining only the largest entries in the Minimum Mean Square Error (MMSE) estimated signal. Simulation results show that, compared with the traditional orthogonal matching pursuit (OMP) algorithm, the proposed RSP algorithm increases the successful recovery rate (and reduces the reconstruction error) by up to 50% and 86% (35% and 65%) in high noise level scenarios and inadequate measurements scenarios, respectively.
Laboratory Rearing Techniques for the Southern Corn Rootworm12 (1973)

Journal Article Laboratory Rearing Techniques for the Southern Corn Rootworm Get access Robert I. Rose, Robert I. Rose 3 Department of Entomology, The Ohio State University, Columbus 43210 3Present address: Ohio Department of Agriculture, Division of Plant Industry, Reynoldsburg 43068. Search for other works by this author on: Oxford Academic PubMed Google Scholar John M. McCabe John M. McCabe Department of Entomology, The Ohio State University, Columbus 43210 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 66, Issue 2, 16 April 1973, Pages 398–400, https://doi.org/10.1093/jee/66.2.398 Published: 16 April 1973 Article history Received: 27 March 1972 Published: 16 April 1973