gebhart/patrepeval huggingface dataset:
Circadian Rhythms (1998)

1997 marks the 25th anniversary of the discovery of the master circadian pacemaker in mammals in the hypothalamic suprachiasmatic nucleus. Remarkable progress has been made over the last 25 years in elucidating the physiological mechanisms involved in the entrainment, generation and expression of circadian rhythms at the cellular and systems levels. The recent discovery and cloning of the first mammalian clock gene is expected to lead to rapid advances in the understanding of the genetic and molecular mechanisms underlying circadian rhythmicity in mammals. Indeed, the impressive and extensive database on circadian rhythms in mammals obtained over the past 25 years provides a foundation for making rapid progress in utilizing future genetic and molecular findings for discovering the fundamental mechanisms controlling 24-hour temporal organization.
Starch Hydrolysate, an Optimal and Economical Source of Carbon for the Secretion of Citric Acid by <i>Yarrowia lipolytica</i> (DS‐1) (1993)

Abstract Using Yarrowia lipolytica (DS‐1), secretion of citric acid is studied as a function of carbon sources such as glucose, fructose, hydrol, sucrose, cane sugar molasses, kerosene (all available commercially) and tapioca starch hydrolysate, invert sucrose and invert cane sugar molasses (all prepared in laboratory). On the basis of their acceptability by DS‐1 for citric and isocitric acid secretion, it is concluded that (a) sucrose and cane sugar molasses (with/without inversion) served as poor carbon sources, (b) fructose, hydrol, impure tapioca starch hydrolysate (96 DE w/w) and invert sucrose served as relatively better carbon sources and (c) purified tapioca starch hydrolysate (96 DE w/w) was the best carbon source to substitute glucose by giving comparable (75%) efficiency of conversion and economical advantage.
Dynamic configuration of application-specific implicit instructions for embedded pipelined processors (2008)

In this paper, we propose the dynamic configuration of application specific implicit instructions for pipelined processors to better exploit the available parallelism at instruction level. Given the target application, the compiler selects a set of candidate instructions to be implicitly executed - i.e. their execution is controlled through a data-driven model, which avoids explicit instruction fetch. Consequently, the clock cycles usually required for the explicit issues are saved, thus improving the performance and reducing the code size. The compiler generates the reconfiguration operations to properly setup the data-path. The processor pipeline has been optimized to support the parallel execution of implicitly issued instructions, requiring a limited hardware overhead. The proposed technique has a negligible impact on the processor ISA - only reconfiguration instructions are added - which also benefits the compiler development times, since the optimization can be almost seamlessly added to an existing compilation tool-chain. The proposed approach has been applied to DSP and multimedia kernel loops, comparing its performance with those of two different baseline architectures: a scalar MIPS processor and a 4-issue VLIW processor of the LX family provided by STMicroelectronics [5]. Experimental results show a speedup ranging from 10 to 35%, and an average code size reduction of 19%.
Effects of drain to gate stress on NMOSFET with polysilicon/Hf-silicate gate stack (2005)

Negative bias stress on the gate of an nMOSFET causes more damage than positive bias stress in terms of interface states density and accordingly, subthreshold swing degradation. A similar situation to negative bias stress on the gate occurs at the edge of the drain when the gate is off and the drain bias is on. This drain to gate stress causes asymmetric degradation of the channel and subthreshold swing increase. It is more prominent in MOSFETs with small gate length. It is believed to be due to the high geometric ratio of the stressed region to channel. Therefore, it must become a serious challenge to further device scaling.
A comparative study of CMOS LNAs (2007)

Three CMOS RF low noise amplifier circuits have been designed and simulated. These LNAs are intended for use in 402-405 MHz medical implant communication service transceivers. The inductively degenerated common source LNA (CS-LNA) topology is currently popular because it achieves high gain, low noise figure, and high linearity. In this paper cascode LNA with inductive source degeneration, LC folded cascode LNA topology and current reuse technique are used in a CMOS CS-LNA with inductive source degeneration. The performance target is to achieve a moderate gain and moderate noise figure without overly degrading the linearity.
Cast Thin Film Biosensor Design Based on a Nafion Backbone, a Multiwalled Carbon Nanotube Conduit, and a Glucose Oxidase Function (2005)

Novel electroanalytical sensing nanobiocomposite materials are reported. These materials are prepared by mixing multiwalled carbon nanotubes (MWNTs), a Nafion cation exchanger, and glucose oxidase (GOD) in appropriate amounts. The MWNTs are cylindrical with a diameter in the range 40-60 nm and with a length of up to several micrometers, and they provide electrical conductivity. Nafion acts as a polymer backbone to give stable and homogeneous cast thin films. Both MWNTs and Nafion provide negative functionalities to bind to positively charged redox enzymes such as glucose oxidase. The resulting biosensing composite material is inexpensive, reliable, and easy to use. The homogeneity of the MWNT-Nafion-GOD nanobiocomposite films was characterized by atomic force microscopy (AFM). Amperometric transducers fabricated with these materials were characterized electrochemically using cyclic voltammetry and amperometry in the presence of hydrogen peroxide and in the presence of glucose. Their linear response to hydrogen peroxide was demonstrated. The glucose biosensor sensitivity was strongly influenced by the glucose oxidase concentration within the nanobiocomposite film. The optimized glucose biosensor (2.5 mg/mL GOD) displayed a sensitivity of 330 nA/mM, a linear range of up to 2 mM, a detection limit of 4 microM, and a response time of <3 s.
NMR spectral data: A compilation of aromatic proton chemical shifts in mono- and di-substituted benzenes (1977)

NMR chemical shifts for protons directly attached to mono- and di-substituted benzenes are compiled from the literature. Data for 1053 sets of data are presented. The data have been examined for reliability using criteria which include high spectral quality, rigorous experimental technique, and sufficient description in assure correct interpretation of results. The data, presented in tabular form include compound name and formula, solvent employed, concentration, temperature, chemical shift, and observation frequency. Other NMR-related data are not given. An author index is included. The data and references cover the literature to June 1976.
Lysosomes as Targets for Cancer Therapy (2005)

Tumor invasion and metastasis are associated with altered lysosomal trafficking and increased expression of the lysosomal proteases termed cathepsins. Emerging experimental evidence suggests that such alterations in lysosomes may form an "Achilles heel" for cancer cells by sensitizing them to death pathways involving lysosomal membrane permeabilization and the release of cathepsins into the cytosol. Here, we highlight recent results on cancer-related changes in the composition and function of lysosomes, focusing on possible implications for the development of novel cancer therapeutics that target tumor cell lysosomes.
Joint radar alignment and odometry calibration (2015)

An unsupervised online procedure for the precise alignment of fully integrated Doppler radar sensors is proposed. Alignment is the precise determination of the angle between the principal beam direction of the radar sensor and the thrust axis of the vehicle. The method is based on the accurate determination of the sensor movement through the analysis of the Doppler distribution of stationary targets over the azimuth angle. The precise alignment facilitates estimating the ego motion of the vehicle. The approach is long-term stable and bias free and therefore predestined for the calibration of standard vehicle's odometry (gyroscope and wheel sensors). A hierarchical optimization strategy to obtain the systematic errors is presented and Maximum Likelihood estimators are derived for each step. A Monte-Carlo simulation is used to identify critical impact factors and determine them quantitatively. The performance of all approaches is finally evaluated with promising results using measurements obtained by a pre-series 77 GHz Doppler radar sensor. An alignment precision on the order of 0.01–0.05° is achieved.
Spin Pumping in Ferrimagnet/Normal Metal Bilayers (2015)

Spin pumping is the generation of a pure spin current in a normal metal layer, driven by ferromagnetic resonance in a magnetic layer. In this thesis, spin pumping is performed on both thin film and bulk yttrium iron garnet/platinum bilayers exploring spin pumping in the strong coupling regime. Spin pumping in compensating ferrimagnets and antiferromagnets is investigated using gadolinium iron garnet/platinum and manganese(II) fluoride/platinum bilayers. Furthermore, spin Hall magnetoresistance measurements at microwave frequencies are performed.
Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes (2016)

The killer cell immunoglobulin-like receptors (KIR) mediate human natural killer (NK) cell cytotoxicity via activating or inhibiting signals. Although informative and functional haplotype patterns have been reported, most genotyping has been performed at resolutions that are structurally ambiguous. In order to leverage structural information given low-resolution genotypes, we performed experiments to quantify the effects of population variations, reference haplotypes, and genotyping resolutions on population-level haplotype frequency estimations as well as predictions of individual haplotypes. We genotyped 10,157 unrelated individuals in 5 populations (518 African American[AFA], 258 Asian or Pacific Islander[API], 8,245 European[EUR], 1,073 Hispanic[HIS], and 63 Native American[NAM]) for KIR gene presence/absence (PA), and additionally half of the AFA samples for KIR gene copy number variation (CNV). A custom EM algorithm was used to estimate haplotype frequencies for each population by interpretation in the context of three sets of reference haplotypes. The algorithm also assigns each individual the haplotype pairs of maximum likelihood. Generally, our haplotype frequency estimates agree with similar previous publications to within <5% difference for all haplotypes. The exception is that estimates for NAM from the U.S. showed higher frequency association of cB02 with tA01 (+14%) instead of tB01 (-8.5%) compared to a previous study of NAM from south of the U.S. The higher-resolution CNV genotyping on the AFA samples allowed unambiguous haplotype-pair assignments for the majority of individuals, resulting in a 22% higher median typing resolution score (TRS), which measures likelihood of self-match in the context of population-specific haplo- and geno-types. The use of TRS to quantify reduced ambiguity with CNV data clearly revealed the few individuals with ambiguous genotypes as outliers. It is observed that typing resolution and reference haplotype set influence haplotype frequency estimates. For example, PA resolution may be used with reference haplotype sets up to the point where certain haplotypes are gene-content subsets of others. At that point, CNV must be used for all genes.
Enumeration and targeted analysis of <i>KRAS</i>, <i>BRAF</i> and <i>PIK3CA</i> mutations in CTCs captured by a label-free platform: Comparison to ctDNA and tissue in metastatic colorectal cancer (2016)

Treatment of advanced colorectal cancer (CRC) requires multimodal therapeutic approaches and need for monitoring tumor plasticity. Liquid biopsy biomarkers, including CTCs and ctDNA, hold promise for evaluating treatment response in real-time and guiding therapeutic modifications. From 15 patients with advanced CRC undergoing liver metastasectomy with curative intent, we collected 41 blood samples at different time points before and after surgery for CTC isolation and quantification using label-free Vortex technology. For mutational profiling, KRAS, BRAF, and PIK3CA hotspot mutations were analyzed in CTCs and ctDNA from 23 samples, nine matched liver metastases and three primary tumor samples. Mutational patterns were compared. 80% of patient blood samples were positive for CTCs, using a healthy baseline value as threshold (0.4 CTCs/mL), and 81.4% of captured cells were EpCAM+ CTCs. At least one mutation was detected in 78% of our blood samples. Among 23 matched CTC and ctDNA samples, we found a concordance of 78.2% for KRAS, 73.9% for BRAF and 91.3% for PIK3CA mutations. In several cases, CTCs exhibited a mutation that was not detected in ctDNA, and vice versa. Complementary assessment of both CTCs and ctDNA appears advantageous to assess dynamic tumor profiles.
Aggregated-Proof Based Hierarchical Authentication Scheme for the Internet of Things (2014)

The Internet of Things (IoT) is becoming an attractive system paradigm to realize interconnections through the physical, cyber, and social spaces. During the interactions among the ubiquitous things, security issues become noteworthy, and it is significant to establish enhanced solutions for security protection. In this work, we focus on an existing U2IoT architecture (i.e., unit IoT and ubiquitous IoT), to design an aggregated-proof based hierarchical authentication scheme (APHA) for the layered networks. Concretely, 1) the aggregated-proofs are established for multiple targets to achieve backward and forward anonymous data transmission; 2) the directed path descriptors, homomorphism functions, and Chebyshev chaotic maps are jointly applied for mutual authentication; 3) different access authorities are assigned to achieve hierarchical access control. Meanwhile, the BAN logic formal analysis is performed to prove that the proposed APHA has no obvious security defects, and it is potentially available for the U2IoT architecture and other IoT applications.
Embedded TiNxOy thin-film resistors in a build-up CSP for 10 Gbps optical transmitter and receiver modules (2002)

Integral passive components provide efficient circuit miniaturization while maintaining high performance and reducing assembly costs. The development of practical integral passive components, however, requires advances in the areas of materials, low-cost processes, and structural design. We have developed new TiNxOy thin-film resistors, as well as a termination resistor-embedded CSP, and a process for fabricating integral passive components. Our TiNxOy films exhibit a sheet resistivity in the range of 30-5k /spl Omega//square. To keep costs low, we have made the fabrication process compatible with that for MCM-D/L. Resistors as small as 25 /spl mu/m square have been successfully produced with this process. The chip scale package (CSP) with embedded resistors has been designed for 10 Gbps optical transmitter and receiver modules. A fabricated version shows excellent return loss for its termination resistor, less than -20 dB in the frequency range of 50 MHz-14 GHz, and its resistors showed high reliability in constant voltage stress tests, with less than 5% change in resistance at 800 mW/mm/sup 2/ over 1000 hours.
Plasma Deposition of Inorganic Thin Films (1979)

The possible use of electrical discharges for the preparation of exotic materials has intrigued chemists for nearly as long as the properties of the discharges themselves have been studied by physicists and engineers (1). The use of discharges in chemical reactions now falls under the general subject heading of plasma chemistry. Applications range from extractive metallurgy (2) to investigations of the origins of life itself (3). Polymerization of organic monomers with electric discharges has had periodic popular appeal (4) but has failed to mature into any widespread application. Free radical reactions, which are readily prepared in glow discharges, have been extensively investigated, and their properties are reviewed elsewhere (5). A widespread application of plasma methods for the deposition of dielectrics was developed with the discovery of RF sputtering (6). With the possible exception of reactive RF sputtering, however, this is considered a physical deposition process and is nbt covered in this article. The subject of this review is plasma-enhanced deposition, sometimes referred to as reactive plasma deposition (RPD), of primarily inorganic nonconducting thin films. In this process, gases that normally do not react or decompose at the applied temperature are introduced at moderate pressure (0.1-10.0 torr) into a reaction chamber, and an electric discharge is initiated. The energy coupled into the gas is chosen, along with the other parameters of the system, to produce deposition on exposed surfaces. The development of this process is primarily motivated by the electronics industry, where thin dielectric films are widely used in the manufacture of semiconductor devices. Reactors capable of handling production quantities of material with well-controlled and reproducible results have been developed.
Investigations on Label-Free Identification of Subcellular Tumor Cell Structures by Digital Holographic Phase Contrast Microscopy (2009)

In order to interpret quantitative digital holographic phase contrast images for the analysis of subcellular structures, comparative investigations were performed using fluorescence microscopy with DAPI-staining. Results from statistical studies on adherent pancreas tumor cells with fluorescence microscopy and DHM demonstrate that nucleus components can be identified label-free by digital holographic microscopy.
Preparation of Cells and Reagents for Flow Cytometry (2001)

Flow cytometry is widely used for analyzing the expression of cell surface and intracellular molecules (on a per cell basis), characterizing and defining different cell types in heterogeneous populations, assessing the purity of isolated subpopulations, and analyzing cell size and volume. This technique is predominantly used to measure fluorescence intensity produced by fluorescent-labeled antibodies or ligands that bind to specific cell-associated molecules. A procedure for direct and indirect staining of single-cell suspensions of lymphoid tissue or peripheral blood lymphocytes to detect cell surface membrane antigens is presented. In addition, support protocols present methods for fluorescence labeling of purified antibodies. A protocol for flow cytometric analysis of intracellular antigens in single-cell suspensions is also included. Alternate protocols describe intracellular staining of unfixed cells in the presence of a detergent and staining of nonviable cells to facilitate discrimination of dead cells in fixed or permeabilized cell preparations.
Hyaluronan Derivatives and Injectable Gels for Tissue Engineering (2008)

The present work describes the preparation of hyaluronan derivatives and hydrogels with potential use in tissue engineering applications. A potentially injectable hydrogel consisting of hyaluronan and collagen was successfully used to grow neurons in vitro by encapsulation of neural stem and progenitor cells. Attempts were further made to establish a suitable modification strategy which could be used for the preparation of in vivo cross-linkable hyaluronan derivatives. The synthesis of a model substance consisting of a D-glucuronate derivative which could simplify the development of such a modification technique is described, although a new method to prepare hyaluronan derivatives was found without its use. The modification strategy involves the use of a triazine-reagent which enables the covalent attachment of hydrophilic and hydrophobic amines to hyaluronan carboxyl groups in a controlled fashion under mild conditions. Using triazine-activated amidation we synthesized an aldehyde-derivative of hyaluronan which was used to prepare gels by cross-linking with hydrazide-modified polyvinyl-alcohol. Gels were formed in less than 1 minute by mixing equal volumes of the polymer derivatives and they were subsequently used as a carrier for bone morphogenetic protein-2. An in vitro release study showed that approximately 88% of the growth factor is retained in the gel over a 4 week period. The ability to form new bone in vivo was further evaluated in an ectopic rat model by the injection of gels containing 30 µg BMP-2. Radiographic and histological examination 4 and 10 weeks after injection showed the formation of new bone without any signs of inflammation or foreign body response. Hydroxyapatite particles were further added to improve the mechanical properties of the gel, and a comparative study was conducted. This time the induced tissue consisted not only of bone, but also of interconnected cartilage and tendon, as confirmed by histology and immunohistochemistry.
Cross-talk between skeletal muscle and adipose tissue: A link with obesity? (2004)

Since the discovery of leptin, the adipocyte and its products have been the subject of intensive research. Thus, it has been demonstrated that adipose tissue plays a central role in energy homeostasis, behaving as an endocrine organ that expresses molecules involved in regulation of metabolism; alterations in the expression or activity of those molecules have a fundamental role in pathologies such as obesity and insulin resistance. However, little is known about the role played by another tissue, skeletal muscle, which may have similar functions regarding metabolism control. Indeed, some molecules expressed in this tissue have recently been shown to modulate adipose metabolism. The present review considers the metabolic interrelationships and cross-talk of signals derived from both skeletal muscle and adipose tissue. It is suggested that cytokines derived from both tissues may have an important role in maintaining an adequate ratio of skeletal muscle to fat and thus may play an important role in the control of body weight. IL-15 (a cytokine highly-expressed in skeletal muscle), TNF-alpha, and leptin could play a decisive role in the suggested "conversation" between adipose tissue and skeletal muscle.
Automatic Formal Correspondence Checking of ISA and RTL Microprocessor Description (2012)

The paper proposes an automated approach with a formal basis designed for checking correspondence between an RTL implementation of a microprocessor and a description of its instruction set architecture (ISA). The goals of the approach are to find bugs not discovered by functional verification, to minimize user intervention in the verification process, and to provide a developer with practical results within a short period of time. The main idea is to use bounded model checking to check that the output produced by automatically derived RTL and ISA models of a given processor are the same for each instruction and each possible input. Although the approach does not provide full formal verification, experiments with the approach confirm that due to a different way it explores the state space of the design under test, it can find bugs not found by functional verification, and is thus a useful complement to functional verification.