gebhart/patrepeval huggingface dataset:
The Differentiation of Streptococcus faecalis and S. faecium (1965)

SUMMARY: Enterococci mainly from laboratory collections were separated by established and new or modified tests into two distinct species, Streptococcus faecalis and S. faecium. Of the established tests only reducing activity and potassium tellurite tolerance completely differentiated the organisms. Of the additional tests the most useful were fermentation of glycerol in a soft agar medium containing fumarate, H2O2 formation from polyhydroxy alcohols and the ability to ferment them, H2O2 formation on a basal medium containing no added specific energy source, citrate fermentation and dissimilation of malate in the presence of glucose. Catalase activity and the ability to use malate as an energy source were also useful tests but did not completely differentiate the organisms.
Operations research supports container handling (2001)

textabstractIn this paper we will give an overview of the use of operations research models and methods in the design and operation of container terminals. \nWe will describe the activities that take place at a container terminal and give an overview of the relevant decision problems, both at a\nstrategic, tactical and operational level. For each of these problems the appropriate operations research contributions are discussed.
DETECTING OF SCUFFING USING ACOUSTIC EMISSION (2002)

The sculling failure is a critical problem in modern machine components, especially tor the requirement of high efficiency and small size. In this study, scuffing experiments are conducted using Acoustic Emission(AE) measurement by an indirect sensing approach to detect scuffing failure. Using AE signals we con get and indication about the state of the friction processes, about the quality of solid and liquid layers on the contacting, surfaces in real time. The FFT(Fast Fourier Transform)analyses of the AE signal are used to understand the interfacial interaction and the relationship between the AE signal and the state of contact is presented.
Fiber scintillator/streak camera detector for burn history measurement in inertial confinement fusion experiment (1997)

To measure the burn history in an inertial confinement fusion experiment, we have developed a new neutron detector based on plastic scintillation fibers. Twenty-five fiber scintillators were arranged in a geometry compensation configuration by which the time-of-flight difference of the neutrons is compensated by the transit time difference of light passing through the fibers. Each fiber scintillator is spliced individually to an ultraviolet optical fiber that is coupled to a streak camera. We have demonstrated a significant improvement of sensitivity compared with the usual bulk scintillator coupled to a bundle of the same ultraviolet fibers.
CMOS sensor for dual fluorescence intensity and lifetime sensing using multicycle charge modulation (2017)

This paper proposes a novel CMOS sensor chip that can realize both fast and accurate intensity and lifetime sensing for fluorescence. To enable high sensitivity, we propose parasitic insensitive multi-cycle charge modulation scheme for low-light lifetime extraction benefiting from simplicity, accuracy and compatibility with CMOS process. The designed in-pixel CTIA-based structure is able to capture the weak fluorescence-induced voltage signal by accumulating photon-generated charges in 25 discrete gated time windows within 10ms, in which each time window has 10us pulse width. A pinned photodiode on chip with 1.04pA dark current is utilized for fluorescence detection. The proposed CTIA-based circuitry can achieve 2.1mV/(nW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) responsivity and 4.38nW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> resolution at 630nm for intensity measurement and 45ns resolution for lifetime measurement. We demonstrate functionality by measuring dissolved oxygen concentration with sensitivity of 7.5%/ppm and 6%/ppm in both intensity and lifetime domain.
A Formal Enantioselective Acetate Mannich Reaction: The Nitro Functional Group as a Traceless Agent for Activation and Enantiocontrol in the Synthesis of β-Amino Acids (2008)

A two-step procedure involving the enantioselective addition of alpha-nitro esters to imines, followed by reductive denitration, provides a convenient new enantioselective synthesis of beta-amino acids. Specifically, beta-phenyl alanine derivatives with up to 98% ee are formed in good yield (64-88%) over two steps. The utility of the approach is demonstrated through the first enantioselective synthesis of the key beta-amino acid of (+)-chaenorhine.
AIRA: A Framework for Flexible Compute Kernel Execution in Heterogeneous Platforms (2017)

Heterogeneous-ISA computing platforms have become ubiquitous, and will be used for diverse workloads which render static mappings of computation to processors inadequate. Dynamic mappings which adjust an application's usage in consideration of platform workload can reduce application latency and increase throughput for heterogeneous platforms. We introduce AIRA, a compiler and runtime for flexible execution of applications in CPU-GPU platforms. Using AIRA, we demonstrate up to a 3.78× speedup in benchmarks from Rodinia and Parboil, run with various workloads on a server-class platform. Additionally, AIRA is able to extract up to an 87 percent increase in platform throughput over a static mapping.
Effect of deviation from the mid‐sagittal plane on the measurement of fetal nuchal translucency (2010)

Fetal NT thickness is greatest in the mid-sagittal plane. Increasing deviation away from the mid-sagittal plane results in progressive underestimation of the fetal NT thickness and so to a corresponding underestimation of the patient-specific risk.
Sex identification by polymerase chain reaction using X‐Y homologous primer (1991)

A method of sex identification using the polymerase chain reaction technique is described. Using a pair of nucleotide primers from an X-Y homologous region, both the X and the Y sequences can be amplified simultaneously, and more importantly, they result in fragments of different lengths. The success of the procedure is therefore monitored by the presence of a X-specific band while sex is identified by the presence or absence of a Y-specific band.
Clinical correlates of low-risk variants in FGFR2, TNRC9, MAP3K1, LSP1 and 8q24 in a Dutch cohort of incident breast cancer cases (2007)

Some recently discovered genomic variants associated with a mildly increased risk of breast cancer are also associated with breast cancer characteristics or family history of breast cancer and ovarian cancer. These findings provide interesting new clues for further research on these low-risk susceptibility alleles.
An Introduction to Biological and Artificial Neural Networks for Pattern Recognition (1991)

Ce cours est destine aussi bien aux specialistes du traitement du signal desireux d'explorer les developpements actuels des reseaux neuronaux, qu'aux chercheurs interesses par l'analyse des formes dans les applications de perception artificielle
Learning Semi-Supervised Anonymized Representations by Mutual Information (2020)

This paper addresses the problem of removing from a set of data (here images) a given private information, while still allowing other utilities on the processed data. This is obtained by training concurrently a GAN-like discriminator and an autoencoder. The optimization of the resulting structure involves a novel surrogate of the misclassification probability of the information to remove. Several examples are given, demonstrating that a good level of privacy can be obtained on images at the cost of the introduction of very small artifacts.
Über Aminosäuren und Peptide, XLVIII Totalsynthese und biomimetische Bildung von Clionamid‐Derivaten (1985)

Abstract Die Totalsynthese von Tetraacetylclionamid ( 9 ) aus dem Schwamm Cliona celata wird beschrieben. Das ( E )‐Enamid wird durch Selenoxid‐Eliminierung gebildet. ‐ Eine biomimetische Bildung von N ‐Boc‐ O,O′,O ′′‐trimethyldesbromclionamid ( 13 ) durch Decarboxylierung der entsprechenden Dehydroaminosäure wird aufgezeigt.
Video Object Segmentation by Salient Segment Chain Composition (2013)

We present a model for video segmentation, applicable to RGB (and if available RGB-D) information that constructs multiple plausible partitions corresponding to the static and the moving objects in the scene: i) we generate multiple figure-ground segmentations, in each frame, parametrically, based on boundary and optical flow cues, then track, link and refine the salient segment chains corresponding to the different objects, over time, using long-range temporal constraints, ii) a video partition is obtained by composing segment chains into consistent tilings, where the different individual object chains explain the video and do not overlap. Saliency metrics based on figural and motion cues, as well as measures learned from human eye movements are exploited, with substantial gain, at the level of segment generation and chain construction, in order to produce compact sets of hypotheses which correctly reflect the qualities of the different configurations. The model makes it possible to compute multiple hypotheses over both individual object segmentations tracked over time, and for complete video partitions. We report quantitative, state of the art results in the SegTrack single object benchmark, and promising qualitative and quantitative results in clips filming multiple static and moving objects collected from Hollywood movies and from the MIT dataset.
A Perylene‐Based Microporous Coordination Polymer Interacts Selectively with Electron‐Poor Aromatics (2016)

The design, synthesis, and properties of the new microporous coordination polymer UMCM-310 are described. The unique electronic character of the perylene-based linker enables selective interaction with electron-poor aromatics leading to efficient separation of nitroaromatics. UMCM-310 possesses high surface area and large pore size and thus permits the separation of large organic molecules based on adsorption rather than size exclusion.
Cloning and expression of human salivary-gland kallikrein in <i>Escherichia coli</i> (1989)

CDNA clones for human kallikrein have been identified in a cDNA library constructed from mRNA of human salivary gland. The entire coding sequence for preprokallikrein and for the 5'- and 3'-untranslated regions were isolated by using a mixture of oligonucleotides corresponding to amino acids 51-56 of human urinary kallikrein and one oligonucleotide corresponding to amino acids 233-238 of human pancreatic kallikrein. The DNA sequence proved that, with the exception of two amino acid exchanges, kallikrein of the human salivary gland is identical with pancreatic kallikrein. Salivary gland and renal kallikrein was expressed in Escherichia coli from plasmid pKK223-3 under the control of the tac promoter. The protein was identified by Western-blot analysis and by demonstration of its specific proteolytic activity.
TempliPhi, φ29 DNA Polymerase Based Rolling Circle Amplification of Templates for DNA Sequencing (2002)

We have developed a novel, isothermal DNA amplification strategy that employs phi29 DNA polymerase and rolling circle amplification to generate high-quality templates for DNA sequencing reactions. The TempliPhi DNA amplification kits take advantage of the fact that cloned DNA is typically obtained in circular vectors, which are readily replicated in vitro using phi29 DNA polymerase by a rolling circle mechanism. This single subunit, proofreading DNA polymerase has excellent processivity and strand displacement properties for generation of multiple, tandem double-stranded copies of the circular DNA, generating as much as 10(7)-fold amplification. Large amounts of product (1-3 microg) can be obtained in as little as 4 hours. Input DNA can be as little as 0.01 ng of purified plasmid DNA, a single bacterial colony, or a 1 microL of a saturated overnight culture. Additionally, the presence of an associated proof reading function within the phi29 DNA polymerase ensures high-fidelity amplification. Once completed, the product DNA can be used directly in sequencing reactions. Additionally, the properties of phi29 DNA polymerase and its use in applications such as amplification ofhuman genomic DNA for genotyping studies is discussed.
Change of a conserved amino acid in the <scp>MYC</scp>2 and <scp>MYC</scp>3 transcription factors leads to release of <scp>JAZ</scp> repression and increased activity (2015)

The bHLH transcription factor MYC2, together with its paralogues MYC3 and MYC4, is a master regulator of the response to the jasmonate (JA) hormone in Arabidopsis (Arabidopsis thaliana). In the absence of JA, JASMONATE ZIM (JAZ) proteins interact with the MYC proteins to block their activity. Understanding of the mechanism and specificity of this interaction is key to unravel JA signalling. We generated mutant MYC proteins and assessed their activity and the specificity of their interaction with the 12 Arabidopsis JAZ proteins. We show that the D94N mutation present in the atr2D allele of MYC3 abolishes the interaction between MYC3 and most JAZ proteins. The same effect is observed when the corresponding conserved Asp (D105) was mutated in MYC2. Accordingly, MYC2(D105N) activated target genes in the presence of JAZ proteins, in contrast to wild-type MYC2. JAZ1 and JAZ10 were the only JAZ proteins still showing interaction with the mutant MYC proteins, due to a second MYC interaction domain, besides the classical Jas domain. Our results visualize the divergence among JAZ proteins in their interaction with MYC proteins. Ultimately, the transferability of the Asp-to-Asn amino acid change might facilitate the design of hyperactive transcription factors for plant engineering.
Embryopathy in Genetically Diabetic Mice, Yellow KK, and Its Prevention by Maternal Therapy (1986)

Abstract Embryopathy in yellow KK mice with non‐insulin dependent diabetes mellitus was examined among the conceptuses of females mated at 7, 11, and 13 weeks of age. The numbers of corpora lutea and implants were comparable in all maternal age groups. Early embryonic deaths were frequently observed in all maternal age groups (37.7 46.4%), but no significant difference was found among the groups. The incidence of late embryonic deaths was significantly higher in 11‐ and 13‐wk‐old dams (25.6% and 28.8%) than in 7‐wk‐old dams (14.4%). Moreover, in 13‐wk‐old dams, but not in 7‐wk‐old dams, a positive correlation existed between maternal plasma glucose levels on day 18 of pregnancy and late embryonic deaths. Fetuses from 13‐wk‐old dams weighed less than those from 7‐wk‐old dams (0.73 g vs 0.86 g). Yellow KK mice mated at 13 weeks of age were treated with an oral‐hypoglycemic agent, 5‐[4‐(l‐methylcyclohexylmethoxy)benzyl] thiazolidine‐2,4‐dione (ciglitazone), as an 0.1% dietary admixture. Plasma glucose on day 18 of pregnancy was lower in all treated groups (159‐170 mg/dl) than in the untreated control (345 mg/dl). A significant decrease of late embryonic deaths (12.7‐15.6%) and a slight increase of fetal weights (0.79‐0.81 g) were noted when compared with the untreated controls (36.8% and 0.74 g).
Ligand and Protein Fishing with Heat Shock Protein 90 Coated Magnetic Beads (2008)

Heat shock protein 90alpha (Hsp90alpha) is a molecular chaperone that has been targeted for the development of new anticancer therapies. To date, co-immunoprecipitation (IP) has been primarily used to identify novel client proteins. We now report an alternative approach in which Hsp90alpha has been immobilized onto the surface of silica-based magnetic beads. The beads were used to isolate known Hsp90alpha ligands from a mixture containing ligands and nonligands. In addition, they were also used to isolated proteins from a mixture of proteins, as well as a cellular extract. The results indicate that the Hsp90alpha coated magnetic beads can be used to "fish" from complex chemical and biological mixtures for new lead drug candidates and client proteins.
Stable Organic Field-Effect Transistors for Continuous and Nondestructive Sensing of Chemical and Biologically Relevant Molecules in Aqueous Environment (2014)

The use of organic field-effect transistors (OFETs) as sensors in aqueous media has gained increased attention for environmental monitoring and medical diagnostics. However, stable operation of OFETs in aqueous media is particularly challenging because of electrolytic hydrolysis of water, high ionic conduction through the analyte, and irreversible damage of organic semiconductors when exposed to water. To date, OFET sensors have shown the capability of label-free sensing of various chemical/biological species, but they could only be used once because their operational stability and lifetime while operating in aqueous environments has been poor, and their response times typically slow. Here, we report on OFETs with unprecedented water stability. These OFETs are suitable for the implementation of reusable chemical/biological sensors because they primarily respond to charged species diluted in an aqueous media by rapidly shifting their threshold voltage. These OFET sensors present stable current baselines and saturated signals which are ideal for detection of low concentration of small or large molecules that alter the pH of an aqueous environment. The overall response of these OFET sensors paves the way for the development of continuous chemical/biological nondestructive sensor applications in aqueous media.
Separation and identification of structural isomers by quadrupole collision-induced dissociation-hydrogen/deuterium exchange-infrared multiphoton dissociation (QCID-HDX-IRMPD) (2010)

A new approach that uses a hybrid Q-FTICR instrument and combines quadrupole collision-induced dissociation, hydrogen-deuterium exchange, and infrared multiphoton dissociation (QCID-HDX-IRMPD) has been shown to effectively separate and differentiate isomeric fragment ion structures present at the same m/z. This method was used to study protonated YAGFL-OH (free acid), YAGFL-NH(2) (amide), cyclic YAGFL, and YAGFL-OCH(3) (methyl ester). QCID-HDX of m/z 552.28 (C(29)H(38)N(5)O(6)) from YAGFL-OH reveals at least two distributions of ions corresponding to the b(5) ion and a non-C-terminal water loss ion structure. Subsequent IRMPD fragmentation of each population shows distinct fragmentation patterns, reflecting the different structures from which they arise. This contrasts with data for YAGFL-NH(2) and YAGFL-OCH(3), which do not show two distinct H/D exchange populations for the C(29)H(38)N(5)O(6) structure formed by NH(3) and HOCH(3) loss, respectively. Relative extents of exchange for C(29)H(38)N(5)O(6) ions from six sequence isomers (YAGFL, AGFLY, GFLYA, FLYAG, LYAGF, and LFGAY) show a sequence dependence of relative isomer abundance. Supporting action IRMPD spectroscopy data are also presented herein and also show that multiple structures are present for the C(29)H(38)N(5)O(6) species from YAGFL-OH.
A Multi-Year Analysis of Islet Transplantation Compared With Intensive Medical Therapy on Progression of Complications in Type 1 Diabetes (2008)

Islet transplantation yields improved HbA1c and less progression of retinopathy compared with intensive medical therapy during 3 years follow-up.
Broad Functional Correction of Molecular Impairments by Systemic Delivery of scAAVrh74-hSGSH Gene Delivery in MPS IIIA Mice (2015)

Mucopolysaccharidosis (MPS) IIIA is a neuropathic lysosomal storage disease caused by deficiency in N-sulfoglucosamine sulfohydrolase (SGSH). Genome-wide gene expression microarrays in MPS IIIA mice detected broad molecular abnormalities (greater than or equal to twofold, false discovery rate ≤10) in numerous transcripts (314) in the brain and blood (397). Importantly, 22 dysregulated blood transcripts are known to be enriched in the brain and linked to broad neuronal functions. To target the root cause, we used a self-complementary AAVrh74 vector to deliver the human SGSH gene into 4-6 weeks old MPS IIIA mice by an intravenous injection. The treatment resulted in global central nervous system (CNS) and widespread somatic restoration of SGSH activity, clearance of CNS and somatic glycosaminoglycan storage, improved behavior performance, and significantly extended survival. The scAAVrh74-hSGSH treatment also led to the correction of the majority of the transcriptional abnormalities in the brain (95.9%) and blood (97.7%), of which 182 and 290 transcripts were normalized in the brain and blood, respectively. These results demonstrate that a single systemic scAAVrh74-hSGSH delivery mediated efficient restoration of SGSH activity and resulted in a near complete correction of MPS IIIA molecular pathology. This study also demonstrates that blood transcriptional profiles reflect the biopathological status of MPS IIIA, and also respond well to effective treatments.
Channel models for wireless body area networks (2008)

Wireless patient monitoring using wearable sensors is a promising application. This paper provides stochastic channel models for wireless body area network (WBAN) on the human body. Parameters of the channel models are extracted from measured channel transfer functions (CTFs) in a hospital room. Measured frequency bands are selected so as to include permissible bands for WBAN; ultra wideband (UWB), the industry, science and medical (ISM) bands, and wireless medical telemetry system (WMTS) bands. As channel models, both a path loss model and a power delay profile (PDP) model are considered. But, even though path loss models are derived for the all frequency bands, PDP model is only for the UWB band due to the highly frequency selectiveness of UWB channels. The parameters extracted from the measurement results are summarized for each channel model.
A compact tapping mode AFM with sliding mode controller for precision image scanning (2011)

Nowadays, atomic force microscopy is an advanced technique which aims to image a sample through the use of a probe, or tip, with a radius of about 20 nm. Due to requirement of ultra-high resolution of the surface imaging, the appropriate setup of the device is as important as the precision probe scan. In this paper, we present a self-designed tapping mode atomic force microscope (AFM) system. This system has been demonstrated to have the following characteristics and advantages. The first is the detection sensor, and we use the compact disk/digital versatile disk (CD/DVD) pick-up-head (PUH) to measure the deflection of the probe that is more compact and cheap than the traditional sensor. Besides this advantage, the AFM's cantilever is wider than the CD/DVD PUH's laser spot so that the laser energy will not be leaked to the reflective sample to cause sensing errors due to optical interference. The second is the piezoelectric stage, where we apply the voltage compensation to modify the hysteresis phenomenon so as to reduce the imaging distortion. Concerning this point, two AFM images are taken experimentally: One is without voltage compensation whereas the other is with the compensation. At the end, the effectiveness of the compensator has been clearly shown. The last one is the control mechanism, which applies the adaptive sliding mode control technique aiming to gain higher precision positioning in the scanning process. In this control approach, on-line gain-tuning of the controller has been successfully achieved. Finally, the experimental results provided have demonstrated appealing performance of our proposed system.