gebhart/patrepeval huggingface dataset:
The Importance of Assay Imprecision near the Screen Cutoff for Newborn Screening of Lysosomal Storage Diseases (2019)

For newborn screening (NBS) of lysosomal storage diseases, programs measure enzymatic activities in dried blood spots (DBS) and, in most cases, act on samples where the measurement is below a specific cutoff value. The rate of false positives and negatives in any NBS program is of critical importance. The measured values across a population of newborns are governed by many factors, and in this article we focus on assay imprecision. Assay parameters including the Analytical Range and the Z-Factor have been discussed as a way to compare assay performance for NBS of lysosomal storage diseases. Here we show that these parameters are not rigorously connected to the rate of false positives and negatives. Rather, it is the assay imprecision near the screen cutoff that is the most important parameter that determines the rate of false positives and negatives. We develop the theoretical treatment of assay imprecision and how it is linked to screen performance. What emerges is a useful type of parametric plot that allows for rigorous assessment of the effect of assay imprecision on the rate of false positives and false negatives that is independent of the choice of screen cutoff value. Such plots are useful in choosing cutoff values. They also show that a high assay imprecision cannot be overcome by changing the cutoff value or by use of postanalysis, statistical tools. Given the importance of assay imprecision near the cutoff, we propose that quality control DBS are most useful if they span a range of analyte values near the cutoff. Our treatment is also appropriate for comparing the performance of multiple assay platforms that each measure the same quantity (i.e., the enzymatic activity in DBS). The analysis shows that it is always best to use the assay platform that gives the lowest imprecision near the cutoff.
Exosome in ascites can be a potential therapeutic target for gastric cancer with malignant ascites. (2022)

e15008 Background: Recently, exosomes widely distributed in body fluids, including blood, urine, saliva, and ascites, serve as an essential biomarker in cancers. Exosomes are considered as a cargo of potential oncogenic protein such as MET during cancer progression. Methods: Exosomes from the malignant ascites (exo Ascites ) of four patients with stage IV gastric cancers (GCs) were isolated by different serial centrifugation steps (300 g, 2000 g, 10,000 g, and 110,000 g at 4). After ultracentrifugation, nanoparticle tracking analysis, western blotting, and immunocytochemistry were performed for characterization of the exo Ascites . Results: In this study, we enrolled 4 patients with malignant ascites which needed to be drained for symptom control. In all 4 patients, we successfully isolated highly concentrated exosomes in 50 ml of ascites (range, 5510 8 – 260 10 8 exosomes/ml). (pt#1, 14010 8 particles/ml; pt#2, 138 10 8 , pt#3, 55.6 10 8 ; pt#4, 260 10 8 exosomes/ml). In twopatients with MET amplification (MET amp ) in tumor specimens, exo Ascites retrieved from the ascites harbored cMET protein in exosomes. In addition, the in-vitro cancer microenvironment model showed that tropism of exo Ascites harboring cMET oncogenic protein had the potential to induce cancer progression (EpCAM immunofluorescent intensity value; a 2.4-fold increase compared to control). In this model, the cancer invasiveness and angiogenesis were significantly enhanced by treatment with exo Ascites with over time. (2.4-(EpCAM immunofluorescent intensity) and 3.6-(CD31 immunofluorescent intensity) fold increase, respectively). Furthermore, the cancer invasiveness was substantially increased as the exosome concentration increased from 0, 10 1 , 10 3 , 10 5 , 10 7 exosome particles/ml. Cancer invasiveness measured by EpCAM immunofluorescent intensity was significantly decreased upon exo siMET treatment in MET amplified GC cells when compared to the control. Conclusions: For the first time, we demonstrated that exosomes from malignant ascites carry MET protein in their exosomes. Exosomes may be early mediators of cancer spread in GC.
Seeking Time-Composable Partitions of Tasks for COTS Multicore Processors (2015)

The timing verification of real-time single core systems involves a timing analysis step that yields an Execution Time Bound (ETB) for each task, followed by a schedulability analysis step, where the scheduling attributes of the individual tasks, including the ETB, are studied from the system level perspective. The transition between those two steps involves accounting for the interference effects that arise when tasks contend for access to shared resource. The advent of multicore processors challenges the viability of this two-step approach because several complex contention effects at the processor level arise that cause tasks to be unable to make progress while actually holding the CPU, which are very difficult to tightly capture by simply inflating the tasks' ETB. In this paper we show how contention on access to hardware shared resources creates a circular dependence between the determination of tasks' ETB and their scheduling at runtime. To help loosen this knot we present an approach that acknowledges different flavors of time compos ability, examining in detail the variant intended for partitioned scheduling, which we evaluate on two real processor boards used in the space domain.
Lantibiotic Nisin and Its Detection Methods (2007)

The type A lantibiotic nisin produced by several Lactococcus lactis strains, and one Streptococcus uberis strainis a small antimicrobial peptide that inhibits the growth of a wide range of gram-positive bacteria, such as Bacillus, Clostridium, Listeria and Staphylococcus species. It is nontoxic to humans and used as a food preservative (E234) in more than 50 countries including the EU, the USA, and China. National legislations concerning maximum addition levels of nisin in different foods vary greatly. Therefore, there is a demand for non-laborious and sensitive methods to identify and quantify nisin reliably from different food matrices. The horizontal inhibition assay, based on the inhibitory effect of nisin to Micrococcus luteus is the base for most quantification methods developed so far. However, the sensitivity and accuracy of the agar diffusion method is affected by several parameters. Immunological tests have also been described. Taken into account the sensitivity of immunological methods to interfering substances within sample matrices, and possible cross-reactivities with lantibiotics structurally close to nisin, their usefulness for nisin detection from food samples remains limited. \n\nThe proteins responsible for nisin biosynthesis, and producer self-immunity are encoded by genes arranged into two inducible operons, nisA/Z/QBTCIPRK and nisFEG, which also contain internal, constitutive promoters PnisI and PnisR. The transmembrane histidine kinase NisK and the response regulator NisR form a two-component signal transduction system, in which NisK autophosphorylates after exposure to extra cellular nisin, and subsequently transfers the phosphate to NisR. The phosphorylated NisR then relays the signal downstream by binding to two regulated promoters in the nisin gene cluster, i.e the nisA/Z/Qand the nisF promoters, thus activating transcription of the structural gene nisA/Z/Q and the downstream genes nisBTCIPRK from the nisA/Z/Q promoter, and the genes nisFEG from the nisF promoter. \n\nIn this work two novel and highly sensitive nisin bioassays were developed. Both of these quantiﬁcation methods were based on NisRK mediated, nisin induced Green Fluorescent Protein (GFP) ﬂuorescence. The suitabilities of these assays for quantiﬁca¬tion of nisin from food samples were evaluated in several food matrices. These bioassays had nisin sensitivities in the nanogram or picogram levels. In addition, shelf life of nisin in cooked sausages and retainment of the induction activity of nisin in intestinal chyme (intestinal content) was assessed.
Human Cancer Viruses (2008)

The first identification of a tumor-causing virus, Rous sarcoma virus, occurred almost 100 years ago, but it was not until the 1970s that the genetic basis for oncogenesis by this and other acutely transforming retroviruses was appreciated. Since then, numerous viral oncogenes and their corresponding cellular proto-oncogene counterparts have been i
Effect of insulin fragments on biological activity of insulin and desoctapeptide insulin. I. Potentiation of biological activities. (1981)

Four derivatives of the insuln B-chain COOH-terminal pentapeptide Arg-Gly-Phe-Phe-Tyr (B22-26) were synthesized and shown to be inactive alone. In the presence of submaximal concentrations of insulin or desoctapeptide insulin, peptides at concentrations of 10(-4) M and higher, markedly stimulated the actions of insulin on rat adipocytes including labeled glucose oxidation, activation of glycogen synthase, and stimulation of 2-deoxyglucose transport. The B-chain COOH-terminal heptapeptide, Gly-Phe-Phe-Tyr-Thr-Pro-Lys (B23-29) was inactive alone or in the presence of submaximal concentrations of insulin or desoctapeptide insulin, suggesting that argnine is required. Dose response curves of insulin, and desoctapeptide insulin for labeled glucose oxidation by rat adipocytes were shifted 1 log concentration unit to the left in the presence of peptide. Peptide shortened the lag time of labeled glucose oxidation and markedly enhanced the rate of 14CO2 production following the lag time. Peptides also enhanced insulin-like activities of concanavalin A and nonsuppressible insulin-like activity P.
Valid and reliable instruments for arm-hand assessment at ICF activity level in persons with hemiplegia: a systematic review (2012)

Although many instruments assess capacity and perceived performance, a dearth exists of instruments assessing actual performance. In addition, instruments appropriate for more than one patient population are sparse. For actual performance, new instruments have to be developed, with specific focus on the usability in different patient populations and the assessment of quality of use as well as amount of use. Also, consensus about the choice and use of instruments within and across populations is needed.
Efficient and Large Scale Pre-training Techniques for Japanese Natural Language Processing (2021)

Pre-training in natural language processing greatly affects the accuracy of downstream tasks. However, pre-training is a bottleneck in the AI system development process because it takes a long time to train the neural network model by using large-scale input data. Our purpose in this paper is to obtain a highly accurate pre-training model in a short time using a large-scale computation environment. Since reducing the time per iteration is difficult even if using large number of computation nodes, it is necessary to reduce the number of iterations. Therefore, we focus on the learning efficiency per iteration and choice a dense Masked Language Model (MLM) task of pretraining in order to utilize a significant power of large-scale cluster. We implemented BERT-xlarge using the dense MLM on Megatron-LM and evaluated the improvement of learning time and learning efficiency for a Japanese language dataset using 768 GPUs on AI Bridging Cloud Infrastructure (ABCI). Our BERT-xlarge improves the learning efficiency per iteration 10 times and completes pre-training in 4.65 hours. This pre-training takes 4.9 months if we use a single GPU. We also evaluated two fine-tunings, JSNLI and Twitter evaluation analysis, to compare the accuracy of downstream tasks with our BERTs and other BERTs. As a result, our BERT-3.9b achieved 94.30% accuracy of JSNLI, and our BERT-xlarge achieved 90.63% accuracy of Twitter evaluation analysis.
Olefin metathesis in aqueous media (2013)

The worldwide undisputable and unattainable chemist is nature, using water as a solvent of choice in biosynthesis. Water as a solvent not only indicates “green chemistry” but is also inevitable in biochemical reactions as well as syntheses of several pharmaceutical products. In the last few decades, several organic reactions were successfully carried out under aqueous conditions, a powerful and attractive tool in organic synthesis metathesis reaction. This review summarises advances made in metathesis reaction in aqueous media. Two main strategies can be distinguished: the design of water soluble catalysts to obtain homogeneous conditions and using commercially available catalysts to utilize the advantages of heterogeneous conditions.
Effet colloide-protecteur d'extraits de parois de levures sur la stabilité tartrique d'une solution hydro-alcoolique modèle (1993)

&lt;p style="text-align: justify;"&gt;L'effet colloïde-protecteur d'extraits mannoprotéiques de parois de levures vis-à-vis de la précipitation tartrique a été étudié en solution hydroalcoolique, en utilisant un IST mètre (Indice de Stabilité Tartrique).&lt;/p&gt;&lt;p style="text-align: justify;"&gt;Nous avons montré que les deux extraits levuriens inhibaient la cristallisation du bitartrate de potassium au même titre que l'acide métatartrique et la carboxyméthylcellulose, mais à un niveau plus faible. Le niveau de stabilité retenu (ISTC-75) est assuré avec des concentrations par litre de 7,5 mg d'acide métatartrique et de 18 mg de carboxyméthylcellulose. Des concentrations en extraits mannoprotéiques inférieures à 100 mg par litre assurent la stabilité tartrique du vin modèle à l'indice retenu. L'efficacité d'inhibition semble dépendre de la quantité de protéines de l'extrait. Ces polymères mannoprotéiques apportés en quantité suffisante éviteraient les risques de précipitation tartrique dans les vins&lt;/p&gt;
The Automated Dictionary (1980)

The pocket calculator is now an integral part of math education; a portable language-oriented device could have a similar impact on reading and writing instruction.
Long term stable black phosphorus saturable absorber for mode-locked fiber laser (2017)

We demonstrate a long-term stable fiber laser mode-locked by a solution deposited and encapsulated black phosphorus (BP) saturable absorber. Our work highlights the potential of BP-based devices for photonic applications when operating under ambient conditions.
Gram‐scale carbon nanotubes as semiconducting material for highly versatile route of integration in plastic electronics (2015)

A versatile chemical functionalization of single‐walled carbon nanotubes (SWNT) is developed to eliminate the conductivity of metallic SWNTs in pristine SWNT mixtures, without sorting. Thanks to the high selectivity of the diazoether reagent, metallic SWNTs can be functionalized while preserving the transport properties of semiconducting SWNTs, even in nonindividually dispersed SWNT solutions. In this way, liters of aqueous semiconducting ink for printing or spray can be prepared at the laboratory scale and used for the fabrication of thin‐film transistors (TFT) by spraying. Diazoether grafting also improved SWNT dispersion by preventing rebundling. Consequently, while less conductive than pristine SWNTs, diazoether‐treated SWNTs provided higher TFT transconductance thanks to a more homogeneous percolation in the film. SWNT TFTs made on wafer and plastic with pristine and diazoether‐treated SWNTs were compared. Sprayed films of diazoether treated, unsorted SWNTs provided TFTs with I ON / I OFF around 500, about 2 orders of magnitude higher than pristine SWNT TFTs. Mobilities were similar, up to 1 cm 2 /V s. Interestingly, diazoether‐treated SWNT TFTs kept a high I ON / I OFF in a wide range of SWNT density and channel length, where pristine SWNT films became metallic.
Recurrent invasive lobular carcinoma presenting as a ruptured breast implant (2011)

This may be the first case report of a ruptured breast implant presenting at the same time as the diagnosis of recurrent breast cancer.
An integrated QCM-based narcotics sensing microsystem (2008)

We present the design, fabrication and successful testing of a 14x14x4 mm3 integrated electronic narcotics sensing system which consists of only four parts. The microsystem absorbs airborne narcotics molecules and performs a liquid assay using an integrated quartz crystal microbalance (QCM). A vertically conductive double-sided adhesive foil (VCAF) was used and studied as a novel material for LOC and MEMS applications and provides easy assembly, electrical contacting and liquid containment. The system was tested for measuring cocaine and ecstasy, with successful detection of amounts as small as 100 ng and 200 ng, respectively. These levels are of interest in security activities in customs, prisons and by the police.
Theory and application of induced higher order color aberrations (2020)

Induced aberrations in general are higher-order aberrations caused by ray perturbations of lower order, picked up surface by surface in the preceding optical system. Therefore, induced aberration coefficients are depending on the cumulative preexisting aberrations in the system. In case of color aberrations, induced influences are already observable in the paraxial regime, since even paraxial rays are affected by dispersion. Hence, in every optical system small perturbations in ray heights and ray angles for paraxial rays of different wavelengths are present. These ray perturbations generate induced color aberration effects of higher-order. Here, different orders refer to the paraxial ray dependency on dispersion. The linear or 1st-order terms result in the well-known Seidel contributions of axial and lateral color, where any interaction of dispersion between different lenses is neglected. Starting at 2nd-order terms, induced color effects are present. In this thesis, an introduction on the basic idea of induced color aberrations is given, followed by a surface resolved analytical description for 2nd-order axial and lateral color as well as for the chromatic variations of the five Seidel aberrations. A differentiation between induced and intrinsic parts is derived and discussed. Illustrated by descriptive academic systems as well as by a complex microscopic design example, the importance and the influences of induced color aberrations for optical systems is demonstrated.
Bacterial cultures of the lower respiratory tract in normal volunteers with and without experimental rhinovirus infection using a plugged double catheter system. (1982)

To test a method of obtaining specimens for microbiologic culture from the lower respiratory tract, we bronchoscoped 25 otherwise normal subjects with and without experimental rhinovirus infections and collected specimens for bacterial culture with a brush housed in a plugged double catheter apparatus. Fifty-two specimens of the lower respiratory tract were obtained from the 25 subjects; nasopharyngeal swabs were also obtained from each subject prior to bronchoscopy. Specimens obtained from the lower respiratory tract were positive for bacteria in 21 (84%) of 25 subjects and at 38 (73%) of 52 sites. The frequency of obtaining positive bacterial cultures was similar in volunteers with (69%) or without (90%) rhinovirus infection. Oropharyngeal contamination of bronchial specimens was minimized by administering atropine and by bronchoscoping subjects in the supine or Trendelenburg position. These data indicate that the plugged double catheter brush system does not consistently yield specimens that are free of bacterial contamination from the oropharynx.
Fusion de Détecteurs Locaux par SVM. Application à la Détection de Ratés de Combustion d'un Moteur Thermique (2007)

International audience
Laboratory Performance Evaluation of Recycled Asphalt Binders with Differing Rejuvenators (2015)

PURPOSES: The objective of this study is to investigate the properties of recycled asphalt binders with five different rejuvenators, in order to evaluate the applicability of the recycled asphalt binders compared with the original asphalt binder. METHODS: In order to simulate recycled asphalt binders, fresh asphalt binders are aged by various Superpave aging procedures, such as the rolling thin-film oven (RTFO) and the pressure aging vessel (PAV). Then, selected rejuvenators are added to the aged asphalt binders in the amount of 5%, 10%, and 15%. The asphalt binder properties are evaluated by the dynamic shear rheometer (DSR), the rotational viscometer (RV), and the bending beam rheometer (BBR). In this study, AP-5 (penetration grade 60-80, PG 64-16) asphalt binder is used. A total of five types of rejuvenators are employed. RESULTS AND CONCLUSIONS : When considering aged asphalt without a new asphalt binder, it seems that the percentage of rejuvenator used in Korea is a bit too low, and that it fails to possess the characteristics of the original binder. From the current practice of evaluating the properties of recycled binder based on penetration ratio only, the amount of rejuvenator required is similar for the long-term-aged binder, but is excessive for the longest-term aged binder, causing deterioration of workability and stiffness of the recycled binder.
Fibrous biomaterials: Effect of textile topography on foreign body reaction (2021)

Foreign Body Reaction (FBR) is a critical issue to be addressed when polyethylene terephthalate (PET) textile implants are considered in the medical field to treat pathologies involving hernia repair, revascularization strategies in arterial disease, and aneurysm or heart valve replacement. The natural porosity of textile materials tends to induce exaggerated tissue ingrowth which may prevent the implants from remaining flexible. The purpose of this study is to assess the influence of the textile topography of various woven substrates on the wetting properties of these substrates and on their in vitro interaction with mesenchymal stem cells (MSC) at 24 and 72 hr. The tests were performed both at yarn and fabric level under forced wetting and ingrowth conditions in order to replicate the mechanisms going on in vivo under blood pressure. Results demonstrate that cell proliferation is influenced by the textile wetting properties, which can be tuned at yarn and fabric level. In particular, it is shown that a satin weave obtained from porous spun yarn limits cell proliferation due to the high porosity of the yarn and the limited saturation index of the weave. Yarn and fabric saturation seems to play a predominant role in cell proliferation on textile substrates.