gebhart/patrepeval huggingface dataset:
A method to test the reproducibility and to improve performance of computer‐aided detection schemes for digitized mammograms (2004)

The purpose of this study is to develop a new method for assessment of the reproducibility of computer-aided detection (CAD) schemes for digitized mammograms and to evaluate the possibility of using the implemented approach for improving CAD performance. Two thousand digitized mammograms (representing 500 cases) with 300 depicted verified masses were selected in the study. Series of images were generated for each digitized image by resampling after a series of slight image rotations. A CAD scheme developed in our laboratory was applied to all images to detect suspicious mass regions. We evaluated the reproducibility of the scheme using the detection sensitivity and false-positive rates for the original and resampled images. We also explored the possibility of improving CAD performance using three methods of combining results from the original and resampled images, including simple grouping, averaging output scores, and averaging output scores after grouping. The CAD scheme generated a detection score (from 0 to 1) for each identified suspicious region. A region with a detection score >0.5 was considered as positive. The CAD scheme detected 238 masses (79.3% case-based sensitivity) and identified 1093 false-positive regions (average 0.55 per image) in the original image dataset. In eleven repeated tests using original and ten sets of rotated and resampled images, the scheme detected a maximum of 271 masses and identified as many as 2359 false-positive regions. Two hundred and eighteen masses (80.4%) and 618 false-positive regions (26.2%) were detected in all 11 sets of images. Combining detection results improved reproducibility and the overall CAD performance. In the range of an average false-positive detection rate between 0.5 and 1 per image, the sensitivity of the scheme could be increased approximately 5% after averaging the scores of the regions detected in at least four images. At low false-positive rate (e.g., < or =average 0.3 per image), the grouping method alone could increase CAD sensitivity by 7%. The study demonstrated that reproducibility of a CAD scheme can be tested using a set of slightly rotated and resampled images. Because the reproducibility of true-positive detections is generally higher than that of false-positive detections, combining detection results generated from subsets of rotated and resampled images could improve both reproducibility and overall performance of CAD schemes.
In Vivo Serial MRI-Based Models and Statistical Methods to Quantify Sensitivity and Specificity of Mechanical Predictors for Carotid Plaque Rupture: Location and Beyond (2011)

It has been hypothesized that mechanical risk factors may be used to predict future atherosclerotic plaque rupture. Truly predictive methods for plaque rupture and methods to identify the best predictor(s) from all the candidates are lacking in the literature. A novel combination of computational and statistical models based on serial magnetic resonance imaging (MRI) was introduced to quantify sensitivity and specificity of mechanical predictors to identify the best candidate for plaque rupture site prediction. Serial in vivo MRI data of carotid plaque from one patient was acquired with follow-up scan showing ulceration. 3D computational fluid-structure interaction (FSI) models using both baseline and follow-up data were constructed and plaque wall stress (PWS) and strain (PWSn) and flow maximum shear stress (FSS) were extracted from all 600 matched nodal points (100 points per matched slice, baseline matching follow-up) on the lumen surface for analysis. Each of the 600 points was marked "ulcer" or "nonulcer" using follow-up scan. Predictive statistical models for each of the seven combinations of PWS, PWSn, and FSS were trained using the follow-up data and applied to the baseline data to assess their sensitivity and specificity using the 600 data points for ulcer predictions. Sensitivity of prediction is defined as the proportion of the true positive outcomes that are predicted to be positive. Specificity of prediction is defined as the proportion of the true negative outcomes that are correctly predicted to be negative. Using probability 0.3 as a threshold to infer ulcer occurrence at the prediction stage, the combination of PWS and PWSn provided the best predictive accuracy with (sensitivity, specificity) = (0.97, 0.958). Sensitivity and specificity given by PWS, PWSn, and FSS individually were (0.788, 0.968), (0.515, 0.968), and (0.758, 0.928), respectively. The proposed computational-statistical process provides a novel method and a framework to assess the sensitivity and specificity of various risk indicators and offers the potential to identify the optimized predictor for plaque rupture using serial MRI with follow-up scan showing ulceration as the gold standard for method validation. While serial MRI data with actual rupture are hard to acquire, this single-case study suggests that combination of multiple predictors may provide potential improvement to existing plaque assessment schemes. With large-scale patient studies, this predictive modeling process may provide more solid ground for rupture predictor selection strategies and methods for image-based plaque vulnerability assessment.
Past, present, and future perspectives of heparins in clinical settings and the role of impaired renal function (2016)

Heparin, whose discovery goes back one hundred years, was first detected as a thromboplastin from liver tissue, and its anticoagulant action was only identified later. The procoagulant action of heparin, which was later characterized as an immunologic reaction by binding to platelet-factor IV, presenting as heparin-induced thrombocytopenia, remains as a side effect. For more than 60 years heparin has been the immediate anticoagulant of choice in many clinical indications. Further development of heparins resulted in the production of low-molecular weight heparins and Fondaparinux, which substituted heparin for many indications and has received many more new indications, including administration for non-anticoagulant purposes. This development is still ongoing and has resulted in more than 300 registered clinical trials at the end of 2015. All types of heparins are still investigated in patients with impairment of renal function to improve the safety of treatment. New therapeutic strategies for the prevention and treatment of thromboembolism, as well as of the non-anticoagulant actions of natural and modified types of heparins, are studied intensively. The clinical study designs include treatment with vitamin-K and non-vitamin K oral anticoagulants. Consequently, heparins, low-molecular weight heparins and Fondaparinux play an important role in the human health care system.
Molecular Cloning of Saccharomyces cerevisiae CDC6 Gene (1989)

The CDC6 gene product is required for entering the S phase of the cell cycle in Saccharomyces cerevisiae. It has been isolated on recombinant plasmids by selection for complementation of temperature-sensitive alleles with a yeast genomic library. The entire complementing activity is carried on a 1.8-kilobase chromosomal DNA fragment, as revealed by deletion mapping. Northern blotting shows that the size of the CDC6 mRNA is about 1.7 kilobases. A Southern blot of yeast chromosomes which were separated by the field inversion gel electrophoresis method indicates that the isolated DNA fragment is derived from chromosome X. The locus from which the clone was derived was marked by integration with a nutritional marker and found by meiotic mapping to cosegregate with CDC6. Thus, we conclude that we have isolated the authentic CDC6 gene. Nucleotide sequence analysis of the CDC6 gene has revealed an open reading frame that encodes a protein with Mr = 57,969. There are five potential Asn-X-(Ser/Thr) glycosylation sites and a highly conserved nucleotide-binding site in the CDC6 sequence. Although computer surveys indicate overall sequence homology between S. cerevisiae CDC6 protein and Saccharomyces pombe CDC10 START protein, they may not be functionally equivalent as evaluated by the complementation assay.
Body Composition and Adiponectin Serum Concentrations in Adult Patients with Cystic Fibrosis (2006)

Central fat accumulation is increased in patients with CF. It is postulated that the energy deficit-induced increase in serum adiponectin could explain the preservation of insulin sensitivity in these patients despite the increase in central fat and in highly sensitive C-reactive protein serum concentrations and could prevent a further deterioration of protein catabolism.
The LG3 Module of Laminin-5 Harbors a Binding Site for Integrin α3β1 That Promotes Cell Adhesion, Spreading, and Migration (2001)

Laminins are a family of extracellular matrix glycoproteins involved in cell adhesion and migration. A major obstacle to understanding their structure-function relationships is the lack of small laminin domains capable of replicating integrin-binding, cell-adhesive, and migratory functions of the intact molecule. Here, we show that the recombinant LG3 (rLG3) module (26 kDa) of laminin-5 (Ln-5) alpha(3) chain replicated key Ln-5 activities. rLG3 but not rLG1 or rLG2 supported cell adhesion and migration of at least two distinct cell lines, in an integrin alpha(3)beta(1)-dependent manner. Cell adhesion to rLG3 was regulated by divalent cations and accompanied by cell spreading and tyrosine phosphorylation of FAK focal adhesion kinase. The integrin binding activity of rLG3 was confirmed by rLG3 affinity chromatography of detergent cell lysates, which resulted in specific purification of integrin alpha(3)beta(1). To our knowledge, this is the first report directly demonstrating that a recombinant laminin LG module is an active domain capable of supporting integrin-dependent cell adhesion and migration.
Vapor Phase Synthesis of Tungsten Nanowires (2003)

A concept is presented for synthesizing metal nanowires directly from the vapor phase using chemical vapor transport to temperatures higher than the corresponding metal oxide decomposition temperature. Specifically, this concept is demonstrated with the synthesis of tungsten metal nanowires with sizes ranging from 70 to 40 nm by increasing the condensation temperature. The simultaneous condensation and decomposition of the tungsten oxide species during nucleation and growth is suggested for 1-D growth of metallic tungsten nanowires. This synthesis concept could potentially be extended to the vapor phase synthesis of metal nanowires of several other nonvolatile and refractory metals. The tungsten nanowires could find potential applications in gas sensors and as electron sources in electron microscopes.
Some challenges and issues in managing, and preserving access to, long-lived collections of digital scientific and technical data (2004)

The CODATA Data Science Journal is a peer-reviewed, open access, electronic journal, publishing papers on the management, dissemination, use and reuse of research data and databases across all research domains, including science, technology, the humanities and the arts. The scope of the journal includes descriptions of data systems, their implementations and their publication, applications, infrastructures, software, legal, reproducibility and transparency issues, the availability and usability of complex datasets, and with a particular focus on the principles, policies and practices for open data.All data is in scope, whether born digital or converted from other sources.
One-pot synthesis of α,β-epoxy ketones through domino reaction between alkenes and aldehydes catalyzed by proline based chiral organocatalysts (2017)

Proline based metal free organocatalysts were developed by using a new approach for the synthesis of epoxide derivatives through a domino reaction. This domino reaction (oxidative coupling) allows a direct access to epoxides from various alkenes and aldehydes through C-H functionalization and C-C/C-O bond formation. The catalytic efficiencies of the newly synthesized organocatalysts were also determined by domino reaction in the presence of various functional groups containing aldehyde and alkene derivatives with very good yields (up to 95%) and ee's (up to 99%).
Unsupported nickel catalysts for methane catalytic decomposition into pure hydrogen (2014)

Catalytic decomposition of methane to pure hydrogen is a reaction of crucial importance for clean energy, if the problem of catalyst separation is solved and the carbon material has an increased commercial value. Unsupported nickel catalysts were synthesized by fusion method. The catalyst derived from nickel nitrate forms heterogeneous octahedral NiO, whereas the nickel hydroxide precursor results in catalyst containing sponge‐like NiO with folding lamellar structure of high porosity. The catalysts reactivity test was conducted with a fixed bed system at 1073 K. The catalyst subjected to hydrogen prereduction proved to be inactive. However, the methane prereduction was found to produce some coke to disperse the Ni particles and thus activated the catalyst. It was found that the higher concentration of methane resulted in a better methane conversion, but a higher deactivation rate. Carbon growth models were formulated to explain the formation of different types of carbon over Ni catalyst. © 2014 American Institute of Chemical Engineers AIChE J , 60: 2907–2917, 2014
Role of subsite +1 residues in pH dependence and catalytic activity of the glycoside hydrolase family 1 β‐glucosidase BGL1A from the basidiomycete <i>Phanerochaete chrysosporium</i> (2007)

The basidiomycete Phanerochaete chrysosporium produces two glycoside hydrolase family 1 intracellular beta-glucosidases, BGL1A and BGL1B, during the course of cellulose degradation. In order to clarify the catalytic difference between two enzymes, in spite of their high similarity in amino acid sequences (65%), five amino acids around the catalytic site of BGL1A were individually mutated to those of BGL1B (V173C, M177L, D229N, H231D, and K253A), and the effects of the mutations on cellobiose hydrolysis were evaluated. When the kinetic parameters (K(m) and k(cat)) were compared at the optimum pH for the wild-type enzyme, the kinetic efficiency was decreased in the cases of D229N, H231D, and K253A, but not V173C or M177L. The pH dependence of cellobiose hydrolysis showed a significantly more acidic pH profile for the D229N mutant, compared with the wild-type enzyme. Since D229 is located between K253 and the putative acid/base catalyst E170, we prepared the double mutant D229N/K253A, and found that its hydrolytic activity at neutral pH was restored to that of the wild-type enzyme. Our results indicate that the interaction between D229 and K253 is critical for the pH dependence and catalytic activity of BGL1A. Biotechnol. Bioeng.
Whole-breast sonography. (1985)

Ultrasound has been found to be useful as an adjunct to mammography and physical examination of the breast. It has detected lesions not identified by any other modality and has allowed more precise diagnosis of palpable and/or radiographically demonstrated lesions. Ultrasound should not be used as the sole breast imaging modality, however, because of its inability to detect microcalcifications and its difficulty in demonstrating small solid lesions, particularly in the fatty breast.
Active mirror: a large-aperture medium-repetition rate Nd:glass amplifier (1981)

Progress in the development of Nd:glass active mirror laser amplifiers is presented. Included is a detailed discussion of hardware design as well as gain and repetition rate performance. Finally, multiunit test results, in a higher power and high energy beam, are presented.
Accuracy evaluation of NIST-F1 (2002)

The evaluation procedure of a new laser-cooled caesium fountain primary frequency standard developed at the National Institute of Standards and Technology (NIST) is described. The new standard, NIST-F1, is described in some detail and typical operational parameters are discussed. Systematic frequency biases for which corrections are made - second-order Zeeman shift, black-body radiation shift, gravitational red shift and spin-exchange shift - are discussed in detail. Numerous other frequency shifts are evaluated, but are so small in this type of standard that corrections are not made for their effects. We also discuss comparisons of this standard both with local frequency standards and with standards at other national laboratories.
Polymers in orthopedic surgery and tissue engineering: From engineering materials to smart biofunctionalization of a surface (2012)

Polymeric materials are important for biomedical applications. Nevertheless, during the last few decades, the requirements on the used polymers have experienced significant changes. In the present review, the data illustrating the history of application of polymers in orthopedic surgery and tissue engineering are systemized and generalized. Special attention is given to the discussion of new problems which could be solved through creation of smart biologically functional polymeric structures able to control the behavior of cells.
Biological Channel Modeling and Implantable UWB Antenna Design for Neural Recording Systems (2014)

Ultrawideband (UWB) short-range communication systems have proved to be valuable in medical technology, particularly for implanted devices, due to their low-power consumption, low cost, small size, and high data rates. Neural activity monitoring in the brain requires high data rate (800 kb/s per neural sensor), and we target a system supporting a large number of sensors, in particular, aggregate transmission above 430 Mb/s (∼512 sensors). Knowledge of channel behavior is required to determine the maximum allowable power to 1) respect ANSI guidelines for avoiding tissue damage, and 2) respect FCC guidelines on unlicensed transmissions. We utilize a realistic model of the biological channel to inform the design of antennas for the implanted transmitter and the external receiver under these requirements. Antennas placement is examined under two scenarios having contrasting power constraints. Performance of the system within the biological tissues is examined via simulation and experiment. Our miniaturized antennas, 12 mm ×12 mm, need worst-case receiver sensitivities of -38 and -30.5 dBm for the first and second scenarios, respectively. These sensitivities allow us to successfully detect signals transmitted through tissues in the 3.1-10.6-GHz UWB band.
Hierarchical Latent Class Models for Cluster Analysis (2004)

Latent class models are used for cluster analysis of categorical data. Underlying such a model is the assumption that the observed variables are mutually independent given the class variable. A serious problem with the use of latent class models, known as local dependence, is that this assumption is often untrue. In this paper we propose hierarchical latent class models as a framework where the local dependence problem can be addressed in a principled manner. We develop a search-based algorithm for learning hierarchical latent class models from data. The algorithm is evaluated using both synthetic and real-world data.
Stereotaxic needle core biopsy of breast lesions using a regular mammographic table with an adaptable stereotaxic device. (1994)

The SNCB technique is not limited to use on a dedicated biopsy table but can be readily adapted to a regular mammography unit. It is a safe, reliable and cost-effective procedure that often spares the patient a surgical procedure.
Inhibition of postsurgical adhesions by liposomes containing nonsteroidal antiinflammatory drugs. (1991)

Intraperitoneal administration of liposomes containing the nonsteroidal antiinflammatory drugs (NSAID) ibuprofen or tolmetin was tested for their efficacy in the prevention of adhesion formation. Both NSAIDs were able to reduce adhesions in an animal model for moderate adhesion formation. However, tolmetin-containing liposomes were more efficacious than ibuprofen-containing liposomes in the reduction of adhesion formation following bilateral uterine abrasion and devascularization surgery.
The frequency of CD25+CD4+ and FOXP3+ regulatory T cells in ectopic endometrium and ectopic decidua (2010)

The disturbance in the immunological equilibrium observed in ectopic endometrium and decidua would seem to be related to the alteration in the Treg cell population that occurs in these ectopic tissues.
Improvement in the Turnover Rate of the Stratum Corneum in False Aged Model Rats by the Administration of Geniposidic Acid in Eucommia ulmoides OLIVER Leaf. (1999)

We earlier reported that collagen synthesis in false aged model rats was stimulated by the administration of a methanol extract from the leaves of Eucommia ulmoides OLIVER. When the methanol extract was fractionated to n-hexane, ethyl acetate, acetone and methanol fractions by silica gel chromatography, we discovered that geniposidic acid and aucubin, contained in the acetone fraction, were the active ingredients. In the current study, we set out to examine if active compounds found in the Eucommia ulmoides OLIVER leaf (EUOL) improved the low turnover rate in the stratum corneum of false aged model rats. The turnover rate in the stratum corneum in rats was measured as 50% dansyl chloride clearance day. In the first experiment, administration of a 2.4% water soluble methanol extract (WSME) of EUOL, along with an 11% protein diet, led to a 20% higher turnover rate in the stratum corneum (p<0.05, Mann-Whitney) than the control value. The WSME mainly contained iridoid mono-glycosides such as geniposidic acid. In the second experiment, treatment with geniposidic acid similarly caused a higher turnover rate in the stratum corneum, increasing turnover by 23% (p<0.05, Mann-Whitney) compared to the control value. In this paper we reveal that the WSME contains compounds effective against aging, and one of them is geniposidic acid.
Text mining and ontologies in biomedicine: Making sense of raw text (2005)

The volume of biomedical literature is increasing at such a rate that it is becoming difficult to locate, retrieve and manage the reported information without text mining, which aims to automatically distill information, extract facts, discover implicit links and generate hypotheses relevant to user needs. Ontologies, as conceptual models, provide the necessary framework for semantic representation of textual information. The principal link between text and an ontology is terminology, which maps terms to domain-specific concepts. This paper summarises different approaches in which ontologies have been used for text-mining applications in biomedicine.
Real-Time Bid Prediction using Thompson Sampling-Based Expert Selection (2015)

We study online meta-learners for real-time bid prediction that predict by selecting a single best predictor among several subordinate prediction algorithms, here called "experts". These predictors belong to the family of context-dependent past performance estimators that make a prediction only when the instance to be predicted falls within their areas of expertise. Within the advertising ecosystem, it is very common for the contextual information to be incomplete, hence, it is natural for some of the experts to abstain from making predictions on some of the instances. Experts' areas of expertise can overlap, which makes their predictions less suitable for merging; as such, they lend themselves better to the problem of best expert selection. In addition, their performance varies over time, which gives the expert selection problem a non-stochastic, adversarial flavor. In this paper we propose to use probability sampling (via Thompson Sampling) as a meta-learning algorithm that samples from the pool of experts for the purpose of bid prediction. We show performance results from the comparison of our approach to multiple state-of-the-art algorithms using exploration scavenging on a log file of over 300 million ad impressions, as well as comparison to a baseline rule-based model using production traffic from a leading DSP platform.