gebhart/patrepeval huggingface dataset:
Complete Sequencing and Diversity Analysis of the Enterotoxin-Encoding Plasmids inClostridium perfringensType A Non-Food-Borne Human Gastrointestinal Disease Isolates (2006)

Enterotoxin-producing Clostridium perfringens type A isolates are an important cause of food poisoning and non-food-borne human gastrointestinal diseases, e.g., sporadic diarrhea (SPOR) and antibiotic-associated diarrhea (AAD). The enterotoxin gene (cpe) is usually chromosomal in food poisoning isolates but plasmid-borne in AAD/SPOR isolates. Previous studies determined that type A SPOR isolate F5603 has a plasmid (pCPF5603) carrying cpe, IS1151, and the beta2 toxin gene (cpb2), while type A SPOR isolate F4969 has a plasmid (pCPF4969) lacking cpb2 and IS1151 but carrying cpe and IS1470-like sequences. By completely sequencing these two cpe plasmids, the current study identified pCPF5603 as a 75.3-kb plasmid carrying 73 open reading frames (ORFs) and pCPF4969 as a 70.5-kb plasmid carrying 62 ORFs. These plasmids share an approximately 35-kb conserved region that potentially encodes virulence factors and carries ORFs found on the conjugative transposon Tn916. The 34.5-kb pCPF4969 variable region contains ORFs that putatively encode two bacteriocins and a two-component regulator similar to VirR/VirS, while the approximately 43.6-kb pCPF5603 variable region contains a functional cpb2 gene and several metabolic genes. Diversity studies indicated that other type A plasmid cpe+/IS1151 SPOR/AAD isolates carry a pCPF5603-like plasmid, while other type A plasmid cpe+/IS1470-like SPOR/AAD isolates carry a pCPF4969-like plasmid. Tn916-related ORFs similar to those in pCPF4969 (known to transfer conjugatively) were detected in the cpe plasmids of other type A SPOR/AAD isolates, as well as in representative C. perfringens type B to D isolates carrying other virulence plasmids, possibly suggesting that most or all C. perfringens virulence plasmids transfer conjugatively.
Effect of antibodies to sperm‐specific recombinant contraceptive vaccinogen (rCV) on murine fertilization: search for an animal model to examine its contraceptive potential (2001)

Recently, we cloned and sequenced a sperm-specific antigen, designated as Contraceptive Vaccinogen (rCV), from human testis (Naz et al., 2001). The present study was conducted to examine its proteomic homologue and function in murine sperm, in order to find out whether or not the mouse can provide a suitable model for examining its immunocontraceptive effects. This was examined by using purified antibodies (Ab) raised against the recombinant (r) human CV antigen of approximately 44 kD. In the Western blot procedure, rCV antibodies recognized a specific protein band of approximately 64 +/- 5 kD in murine testis and murine sperm extracts, the band similar to that found in human testis and human sperm. In the immunoprecipitation procedure, rCV Ab immunoprecipitated a protein band of similar size from murine sperm and murine testis extracts. The immunocytochemical (ICT), immunoscanning electronmicroscopic (ISEM) and the immunobead binding technique (IBT) revealed the subcellular localization of CV antigen on the surface of acrosome and tail regions of the noncapacitated and capacitated murine sperm cell. In functional bioassays, rCV Ab inhibited the acrosome reaction as well as sperm-egg binding in vitro. These data indicate that the CV antigen is expressed in murine sperm and has a biological role in sperm function and sperm-egg binding. In vitro inhibition of capacitation/acrosome reaction and sperm-zona binding suggest that the mouse can provide a suitable model to examine the immunocontraceptive effects of CV antigen in actively-immunized animals.
Using Real-Time Data to Warn Nurses of Medication Administration Errors Using a Nurse Situational Awareness Dashboard (2018)

Electronic Health Records (EHR) are constantly gathering an exponential amount healthcare data. Historical data is often studied to identify trends and determine the effectiveness of interventions, but rarely is Real-time data utilized to positively influence the nurse at the Point of Care. A dashboard allowing nurses to visualize their individual Near-Miss (MN) medication error risk as the needs and subsequent workload of the patients they served changed was created and piloted for 30- days. Implementation of the dashboard resulted in a 15.6% reduction of NMs.
Index Properties and Compaction Characteristics of Kerosene Contaminated Clayey Soil (2008)

In order to excavate and transport kerosene contaminated soils from construction sites, it is critical to understand the changes in geotechnical proportions of the soil when it is contaminated with kerosene. In this study, soils consisting of 80% sand and 20% clay with and without organic matter (5%) were synthetically contaminated up to 7.5% of kerosene (based on dry soil weight). Effect of organic matter and kerosene content on the index properties and compaction characteristics (Harvard miniature) of the clay soils was quantified. Addition of kerosene increased the liquid limit and reduced the maximum dry density of the soil. The liquid limit of the soil was increased by 75 % and the maximum density was reduced by 6 % due to the addition of 7.5% of kerosene.
Improved Classification Robustness for Noisy Cell Images Represented as Principal-Component Projections in a Hybrid Recognition System (1998)

Different types of cells are recognized from their noisy images by use of a hybrid recognition system that consists of a learning principal-component analyzer and an image-classifier network. The inputs to the feed-forward backpropagation classifier are the first 15 principal components of the 10 x 10 pixel image to be classified. The classifier was trained with clear images of cells in metaphase, unburst cells, and other erroneous patterns. Experimental results show that the recognition system is robust to image scaling and rotation, as well as to image noise. Cell recognition is demonstrated for images that are corrupted with additive Gaussian noise, impulse noise, and quantization errors. We compare the performance of the hybrid recognition system with that of a conventional three-layer feed-forward backpropagation network that uses the raw image directly as input.
Epidemiology, treatment and outcome of patients with lower respiratory tract infection presenting to emergency departments with dyspnoea (AANZDEM and EuroDEM studies) (2020)

More patients with LRTI in Europe presented with cardio-respiratory comorbidities, they received more adjunct therapies and had a higher intensive care unit admission rate than patients from Oceania/SEA, although mortality was similar between the two cohorts.
The role of indoleamine 2, 3 dioxygenase in regulating host immunity to leishmania infection (2012)

Pathogen persistence in immune-competent hosts represents an immunological paradox. Increasing evidence suggests that some pathogens, such as, Leishmania major (L. major) have evolved strategies and mechanisms that actively suppress host adaptive immunity. If this notion is correct conventional vaccination therapies may be ineffective in enhancing host immunity, unless natural processes that suppress host immunity are also targeted therapeutically. The key problem is that the basis of pathogen persistence in immune-competent individuals is unknown, despite decades of intense research. This fact, coupled with poor health care and a dearth of effective treatments means that these diseases will remain a scourge on humans unless a better understanding of why the immune system tolerates such infections emerges from research. Indoleamine 2,3-dioxygenase (IDO) has been shown to act as a molecular switch regulating host responses, and IDO inhibitor drugs shown to possess potential in enhancing host immunity to established leishmania infections. It is hoped that this review will help stimulate and help generate critical new knowledge pertaining to the IDO mechanism and how to exploit it to suppress T cell mediated immunity, thus offer an innovative approach to studying the basis of chronic leishmania infection in mice.
Syntheses, characterizations, and crystal and molecular structures of (pentamethylcyclopentadienyl)gallium chlorine compounds Ga(C5Me5)2Cl and Ga(C5Me5)Cl2 (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses, characterizations, and crystal and molecular structures of (pentamethylcyclopentadienyl)gallium chlorine compounds Ga(C5Me5)2Cl and Ga(C5Me5)Cl2O. T. Beachley, R. B. Hallock, H. M. Zhang, and J. L. AtwoodCite this: Organometallics 1985, 4, 9, 1675–1680Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://doi.org/10.1021/om00128a033RIGHTS & PERMISSIONSArticle Views269Altmetric-Citations43LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (711 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Automatic illustration of 3D geometric models: lines (1990)

A system for the automatic generation of line illustrations of three dimensional sculptured objects is described. In particular, an enriched vocabulary of lines are defined which provide a means to impart meaning to visual representations of complex objects. Particular attention is paid to how the end conditions of individual segments effect how they are drawn. A graphical interface is described for creating illustration rules which translate the geometric description into the final drawing. Some algorithmic details are provided for implementation and preliminary results are presented.
Vision Enhancement in Homogeneous and Heterogeneous Fog (2012)

One source of accidents when driving a vehicle is the presence of fog. Fog fades the colors and reduces the contrasts in the scene with respect to their distances from the driver. Various camera-based Advanced Driver Assistance Systems (ADAS) can be improved if efficient algorithms are designed for visibility enhancement in road images. The visibility enhancement algorithm proposed in [1] is not optimized for road images. In this paper, we reformulate the problem as the inference of the local atmospheric veil from constraints. The algorithm in [1] thus becomes a particular case. From this new derivation, we propose to better handle road images by introducing an extra constraint taking into account that a large part of the image can be assumed to be a planar road. The advantages of the proposed local algorithm are the speed, the possibility to handle both color and gray-level images, and the small number of parameters. A new scheme is proposed for rating visibility enhancement algorithms based on the addition of several types of generated fog on synthetic and camera images. A comparative study and quantitative evaluation with other state-of-the-art algorithms is thus proposed. This evaluation demonstrates that the new algorithm produces better results with homogeneous fog and that it is able to deal better with the presence of heterogeneous fog. Finally, we also propose a model allowing to evaluate the potential safety benefit of an ADAS based on the display of defogged images.
Geophysical and geochemical survey of a large marine pockmark on the Malin Shelf, Ireland (2011)

Marine pockmarks are a specific type of seabed geological setting resembling craters or pits and are considered seabed surface expressions of fluid flow in the subsurface. A large composite pockmark on the Malin Shelf, off the northern coast of Ireland was surveyed and ground truthed to assess its activity and investigate fluid related processes in the subsurface. Geophysical (including acoustic and electromagnetic) data confirmed the subsurface presence of signatures typical of fluids within the sediment. Shallow seismic profiling revealed a large shallow gas pocket and typical gas related indicators such as acoustic blanking and enhanced reflectors present underneath and around the large pockmark. Sulphate profiles indicate that gas from the shallow reservoir has been migrating upwards, at least recently. However, there are no chimney structures observed in the sub‐bottom data and the migration pathways are not apparent. Electromagnetic data show slightly elevated electrical conductivity on the edges of the pockmarks and a drop below regional levels within the confines of the pockmark, suggesting changes in physical properties of the sediment. Nuclear Magnetic Resonance (NMR) experiments were employed to characterize the organic component of sediments from selected depths. Very strong microbial signatures were evident in all NMR spectra but microbes outside the pockmark appear to be much more active than inside. These observations coincide with spikes in conductivity and the lateral gas bearing body suggesting that there is an increase in microbial activity and biomass when gas is present.
Measures of Diversity for Populations and Distances Between Individuals with Highly Reorganizable Genomes (2004)

In this paper we address the problem of defining a measure of diversity for a population of individuals whose genome can be subjected to major reorganizations during the evolutionary process. To this end, we introduce a measure of diversity for populations of strings of variable length defined on a finite alphabet, and from this measure we derive a semi-metric distance between pairs of strings. The definitions are based on counting the number of substrings of the strings, considered first separately and then collectively. This approach is related to the concept of linguistic complexity, whose definition we generalize from single strings to populations. Using the substring count approach we also define a new kind of Tanimoto distance between strings. We show how to extend the approach to representations that are not based on strings and, in particular, to the tree-based representations used in the field of genetic programming. We describe how suffix trees can allow these measures and distances to be implemented with a computational cost that is linear in both space and time relative to the length of the strings and the size of the population. The definitions were devised to assess the diversity of populations having genomes of variable length and variable structure during evolutionary computation runs, but applications in quantitative genomics, proteomics, and pattern recognition can be also envisaged.
Rapid Detection and Determination of the Aerodynamic Size Range of Airborne Mycobacteria Associated with Whirlpools (2003)

Novel environmental air and water mycobacteria sampling and analytical methods are needed to circumvent difficulties associated with the use of culture-based methodologies. To implement this objective, a commercial, clinical, genus DNA amplification method utilizing the polymerase chain reaction (PCR) was interfaced with novel air sampling strategies in the laboratory. Two types of air samplers, a three-piece plastic, disposable filter cassette and an eight-stage micro-orifice uniform deposit impactor (MOUDI), were used in these studies. In both samplers, 37-mm polytetrafluoroethylene (PTFE) filters were used. Use of the MOUDI sampler permitted the capture of airborne mycobacteria in discrete size ranges, an important parameter for relating the airborne mycobacteria cells to potential respirable particles (aerodynamic diameter <10 microm) capable of causing health effects. Analysis of the samples was rapid, requiring only 1-1.5 days, as no microbial culturing or DNA purification was required. This approach was then used to detect suspected mycobacteria contamination associated with pools at a large public facility. PCR was also used to analyze various water samples from these pools. Again, no culturing or sample purification was required. Water samples taken from all ultraviolet light/hydrogen peroxide-treated whirlpools tested positive for the presence of mycobacteria. No mycobacteria were detected in the chlorine-treated pools and the water main supply facility. All air samples collected in the proximity of the indoor whirlpools and the associated changing rooms were strongly positive for airborne mycobacteria. The airborne mycobacteria particles were predominantly collected on MOUDI stages 1-6 representing an aerodynamic size range of 0.5 to 9.9 microm. In conclusion, using this approach permits the rapid detection of mycobacteria contamination as well as the routine monitoring of suspected pools. The approach circumvents problems associated with culture-based methods such as fungal overgrowth on agar plates, and the presence of nonculturable or difficult to culture mycobacteria strains.
Impact of cover crop on soil carbon accrual in topographically diverse terrain (2017)

Farmers must consider real-world problems and variability to maximize yields and minimize environmental impacts when using cover crops in corn (<i>Zea mays</i> L.)-based cropping systems. Much of the variability encountered by farmers of the Midwest Corn Belt is due to the topographical diversity of the undulating landscape. The objectives of this study are to explore the effects of cover crops on soil organic carbon (C), both total organic C and its labile form, particulate organic C (POC), and on water retention at contrasting topographies (summit, slope, and depression). A cereal rye (<i>Secale cereal</i> L.) cover crop was established in the fall of 2011 at two experimental sites. At each site, the experimental design was a split-split plot with whole plot factor, topographical position, in a randomized complete block design with two replications. Topographical position affected all studied plant and soil characteristics, including aboveground plant biomass, rye residue decomposition, POC, total soil C, and soil water retention. Across all topographical positions, rye residue decomposition was ~5% greater in the treatment with than without cover crop. In slopes and summits, the POC in the treatment with cover crop was significantly (~0.7 mg g<sup>−1</sup> soil [~700 ppm]) greater than in the treatment without the cover crop; however, the difference was not statistically significant in depressions. The cover crop effect on both total organic C and soil water retention levels was not statistically significant. The study points to potential interactions between topography and C sequestration benefits of cover crops; however, longer experimental times are needed to detect significant differences in soil total C and water retention measurements.
Structural Characterization of Soil Organic Matter and Humic Acids in Particle‐Size Fractions of an Agricultural Soil (2002)

Organic matter (OM) in agricultural soils consists mainly of partially decomposed plant residues, microbial biomass, and humic substances. The advanced analytical techniques of 13 C nuclear magnetic resonance (NMR), tetramethylammonium hydroxide (TMAH) thermochemolysis‐gas chromatography (GC)/mass spectroscopy (MS), and pyrolysis‐GC/MS (Py‐GC/MS) were employed to study the chemical structure of bulk soil organic matter (SOM) and its corresponding humic acid (HA) extracts from different aggregate‐size fractions (&lt;2 and &gt;250 μm) of a dark brown Mediterranean soil. The main products released by TMAH thermochemolysis of the bulk soil and HA samples were: lignin‐derived compounds (LG) and nonlignin‐derived aromatic compounds, heterocyclic N, fatty acid methyl esters (FAMEs), and dicarboxylic acid dimethyl esters (DAMEs). The TMAH chromatogram of the &gt;250‐μm size fraction revealed more LG than that of the &lt;2‐μm fraction. The relative intensity of the long‐chain FAMEs and DAMEs peaks decreased with aggregate size, but their presence highlights the contribution of aliphatic biopolymers to the structure of the SOM. Both Py‐GC/MS and TMAH‐thermochemolysis data suggest that the HAs contain large portions of lignin and cuticular materials in their structure. With decreasing particle size, the HA contained more lignin‐derived units in the final stages of oxidation, more fatty acids originating from microbial activity, and higher contents of aromatic nonlignin‐derived structures. Our data suggest that a steady‐state situation exists for the presence of HA, where fresh OM is being decomposed and humified into the HA‐like structures, but this fraction is subject to further decomposition (mainly through loss of O–alkyl and transformation of O‐substituted aromatic carbons) as humification proceeds.
Polymer Process Optimization for Electrical and Optical I/O Interconnect Pillar Fabrication (2005)

A second cycle of 10 days of MET with tamsulosin in nonresponders to a 10-day first cycle of MET with tamsulosin and deflazacort is safe and effective, and therefore should be considered as an option in the management of uncomplicated distal ureteric stones.
PREPARATION OF POLYMER BRUSHES FROM POLY(VINYLIDENE FLUORIDE) SURFACES BY UV IRRADIATION PRETREATMENT (2007)

Grafting of polymer brushes from the poly(vinylidene fluoride) (PVDF) surfaces was carried out. The active species, such as peroxide and hydroperoxide, on the surface were generated via ultraviolet (UV) irradiation pretreatment in nitrogen, followed by air exposure. Homopolymer brushes of methyl methacrylate (MMA) were prepared by the surface-initiated free radical polymerization from the peroxide initiators on the PVDF surface. The peroxides formed on UV-treated and air-exposed PVDF surfaces were determined quantitatively by the reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) in toluene. The chemical composition and topography of the graft-functionalized PVDF surfaces were characterized by X-ray photoelectron spectroscopy (XPS), attenuated total reflectance (ATR) FT-IR spectroscopy, and atomic force microscopy (AFM). ATR FT-IR revealed an increase in the graft concentration of poly(methyl methacrylate) (PMMA) on PVDF surfaces with an increase of the UV irradiation pretreatment time. Water contact angles on PVDF surfaces were reduced by surface grafting of PMMA.
Supplementary Figure from A Genomically and Clinically Annotated Patient-Derived Xenograft Resource for Preclinical Research in Non–Small Cell Lung Cancer (2023)

Supplementary Figure from A Genomically and Clinically Annotated Patient-Derived Xenograft Resource for Preclinical Research in Non–Small Cell Lung Cancer
EVALUATION OF EMOTION ESTIMATION METHODS BASED ON STATISTIC FEATURES OF EMOTION TAGGED CORPUS (2008)

Development of information technology has been increasing the chance of interaction between human and computer. Computer used to be a tool and its develop- ment had been mainly emphasized on the speed of information processing. However, by understanding not only semantic information but also ambiguous information such as emotion, computer can be a versatile partner for human that can detect emotional state of a person and can response appropriately the emotion. As a primary study of text-based emotion estimation by computer we focused on statistically analyzing the relationship be- tween word emotion and sentence emotion based on the originally created emotion tagged corpus then propose two emotion estimation methods according to the obtained statistic features. The proposed methods are evaluated using a prototype system. Keywords: Corpus analysis, Affective computing, Statistic analysis