gebhart/patrepeval huggingface dataset:
Generation of stable orthogonal gradients of chemical concentration and substrate stiffness in a microfluidic device (2015)

Cellular responses to chemical cues are at the core of a myriad of fundamental biological processes ranging from embryonic development to cancer metastasis. Most of these biological processes are also influenced by mechanical cues such as the stiffness of the extracellular matrix. How a biological function is influenced by a synergy between chemical concentration and extracellular matrix stiffness is largely unknown, however, because no current strategy enables the integration of both types of cues in a single experiment. Here we present a robust microfluidic device that generates a stable, linear and diffusive chemical gradient over a biocompatible hydrogel with a well-defined stiffness gradient. Device fabrication relies on patterned PSA (Pressure Sensitive Adhesive) stacks that can be implemented with minimal cost and lab equipment. This technique is suitable for long-term observation of cell migration and application of traction force microscopy. We validate our device by testing MDCK cell scattering in response to perpendicular gradients of hepatocyte growth factor (HGF) and substrate stiffness.
Killing of Neisseria meningitidis by Human Neutrophils: Implications for Normal and Complement-Deficient Individuals (1987)

The contributions of complement-dependent phagocytosis and serum bactericidal activity (SBA) to the killing of 62 strains of meningococci were examined by using C8-depleted or pooled human serum (PHS). The complement-dependent nature of killing by neutrophils was confirmed by restoring survival to control values by using heated serum. Serogroups B and 29E, but not A, C, Y, and W135, were ingested and killed by neutrophils in C8-depleted PHS (PHS-C8Dep; 41.7% +/- 7.3% and 60.5% +/- 17.8% vs. greater than or equal to 100% survival, respectively, at 30 min). Group B meningococci were resistant to complement-mediated SBA, whereas group Y were susceptible. Deposition of C3 on serogroups B and Y was similar (28.5 +/- 2.9 vs. 23.5 +/- 2.7 C3 fluorescence units; P greater than .05); however, susceptibility to complement-dependent phagocytosis and complement-mediated SBA of serogroups B and Y did not correlate. We also examined meningococcal phagocytosis by using serum from a C8-deficient patient. In contrast to PHS-C8Dep, this serum supported rapid phagocytic killing of serogroups A, C, Y, and W135 meningococci. This finding suggests that vaccinating individuals deficient in late-complement components may shift the burden of host defense from SBA to phagocytosis.
On the Pulse Extension Loss in Digital Beamforming SAR (2015)

One of the benefits of synthetic aperture radar (SAR) systems utilizing digital beamforming is the ability to increase the receive power. The relevant SAR technique is known as SCan-On-REceive (SCORE), which steers the receive antenna beam such that it follows the radar pulse echo traversing the ground. This allows the use of a narrow receive beam in elevation, and therefore, the height of the receive antenna can be increased, resulting in a higher gain, which explains the higher receive power. Although advantageous, this technique has some pitfalls, which impose an upper limit on the antenna size and constrain the selection of SAR operation parameters. These limitations (which are often neglected in the system conception) are caused by the pulse extent on the ground and the way it is modulated by the receive antenna pattern. This letter addresses and quantifies the effects caused by the transmit pulse length (here denoted as pulse extension loss) through a rigorous analysis, with the purpose of introducing an important SAR performance figure. Closed expressions are derived for the simplified case of a uniform linear antenna array.
Cholesterol as a Bioregulator in the Development and Inhibition of Leukemia (1974)

Leukemia in mice and humans is accompanied by a marked deficiency of unesterified cholesterol in the surface membrane of leukemic cells as compared to normal leukocytes. This deficiency induces a significant reduction in their membrane microviscosity. Since cholesterol in the cell surface membrane is exchangeable with cholesterol in the serum lipoproteins, concomitant to the cellular deficiency of cholesterol, the average level of cholesterol in the blood serum of leukemic patients is substantially below the average normal level. Based on these observations and the effect of membrane microviscosity on biological functions, a working hypothesis that describes the role of cholesterol in the development and inhibition of leukemia is suggested. This hypothesis can also account for the effect of cholesterol and membrane microviscosity on various other cellular activities of leukocytes.
Immunolocalization and Possible Functional Role of PSP‐I/PSP‐II Heterodimer in Highly Extended Boar Spermatozoa (2006)

PSP-I/PSP-II heterodimer is a major protein of boar seminal plasma which is able to preserve, in vitro, the viability, motility, and mitochondrial activity of highly extended boar spermatozoa for at least 5 hours. However, little is known about the binding pattern of the heterodimer to the sperm plasma membrane and its eventual relation with the maintenance of the sperm functionality. The present study investigated the effect of exposing highly extended boar spermatozoa (1 million/mL) to 1.5 mg/mL of PSP-I/PSP-II for 0.5, 5, and 10 hours at 38 degrees C on sperm characteristics and the changes in PSP-I/PSP-II localization as a result of both the addition of PSP-I/PSP-II to the extender and the incubation time. Exposure of the spermatozoa to PSP-I/PSP-II preserved sperm viability, motility, and mitochondrial activity when compared to nonexposed spermatozoa. This protective effect lasted for 10 hours (P < .05). After immunolabeling of highly extended semen with rabbit monospecific polyclonal antibody against PSP-I/PSP-II, the percentage of immunopositive spermatozoa declines over time from 71% (0.5 hours) to 49% (10 hours). However, more than 80% of spermatozoa remained labeled during the 10-hour incubation period if PSP-I/PSP-II was added. Scanning electron microscopy revealed 4 different binding patterns. The heterodimer was mainly localized to the acrosomal area, being redistributed to the postacrosomal area or lost during in vitro incubation. In conclusion, the protective effect of the heterodimer appears to be related to its adhesion to the acrosomal area, and the loss of this protective effect coincides with a stepwise redistribution of PSP-I/PSP-II during incubation.
LIVVIL: Logging Interactive Visualizations and Visualizing Interaction Logs (2016)

International audience
A vector memory system based on wafer-scale integrated memory arrays (2002)

The paper proposes a memory architecture called Wafer-scale Interconnected Memory Array (WIMA), which is intended to replace ultra-high-density monolithic DRAM ICs. This architecture employs the high-performance interconnects provided by multichip module technology, the cache-embedding concept, and prime degree interleaving to expose the DRAM's internal parallelism not exploitable by monolithic DRAMs. Using WIMA modules as the basic building blocks, a high-bandwidth, low latency, and low cost vector memory system is developed that supports parallelism among multiple vector access streams. To mask the long start-up latencies, vector memory accesses are architectured to be split-phased. To alleviate the performance impact of bank conflicts, prime degree memory interleaving is adopted. The major contribution of this work is the development of a novel indexing mechanism for prime degree interleaving, which takes at most two integer divisions for each logical vector memory access.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Gene Expression Profile of Multipotent Mesenchymal Stromal Cells: Identification of Pathways Common to TGF <i>β</i> 3/BMP2-Induced Chondrogenesis (2009)

Multipotent mesenchymal stromal cells (MSC) display a high potential for the development of novel treatment strategies for cartilage repair. However, the pathways involved in their differentiation to functional non hypertrophic chondrocytes remain largely unknown, despite the work on embryologic development and the identification of key growth factors including TGFbeta, Hh, Wnt and FGF. In this study, we asked if we could identify specific biological networks common to the growth factors used (TGFbeta3 or BMP-2). To address this question, we used DNA microarrays and performed large-scale expression profiling of MSC at different time points during their chondrogenic differentiation. By comparing these data with those obtained during the differentiation of MSC into osteoblasts and adipocytes, we identified 318 genes specific for chondrogenesis and developed a new algorithm to classify the genes according to their kinetic profile. We distributed the selected genes in five classes according to their kinetic of expression. We could reconstruct three phases characterized by functional pathways. The first phase corresponds to cell attachment and apoptosis induction; the second phase is characterized by a proliferation/differentiation step, and the third phase is characterized by a differentiation/hypertrophy pathway. Indeed, these data propose new pathways to understand the complexity of MSC differentiation to chondrocytes.
The LLP risk model: an individual risk prediction model for lung cancer (2007)

Using a model-based approach, we estimated the probability that an individual, with a specified combination of risk factors, would develop lung cancer within a 5-year period. Data from 579 lung cancer cases and 1157 age- and sex-matched population-based controls were available for this analysis. Significant risk factors were fitted into multivariate conditional logistic regression models. The final multivariate model was combined with age-standardised lung cancer incidence data to calculate absolute risk estimates. Combinations of lifestyle risk factors were modelled to create risk profiles. For example, a 77-year-old male non-smoker, with a family history of lung cancer (early onset) and occupational exposure to asbestos has an absolute risk of 3.17% (95% CI, 1.67-5.95). Choosing a 2.5% cutoff to trigger increased surveillance, gave a sensitivity of 0.62 and specificity of 0.70, while a 6.0% cutoff gave a sensitivity of 0.34 and specificity of 0.90. A 10-fold cross validation produced an AUC statistic of 0.70, indicating good discrimination.If independent validation studies confirm these results, the LLP risk models' application as the first stage in an early detection strategy is a logical evolution in patient care.
A 13 GHz 3:2 transformer based linear transconductance VCO (2015)

This paper describes a 13 GHz 3:2 transformer based linear transconductance (LiT) voltage controlled oscillator (VCO) in 65 nm RF CMOS process. Transconductance linearization technique which is simply realized by a 3:2 transformer is used for good phase noise performance. An injection-locked buffer is designed for high output power. The measured output frequency of the proposed VCO shows 12.25 GHz ~ 12.86 GHz and 12.86 GHz ~ 13.52 GHz. The phase noise of the VCO is -113.94 dBc/Hz at 1 MHz offset frequency. DC power consumption of the VCO core and the buffer is 7.7 mW and 21.6 mW, respectively.
Intravenous topiramate: Comparison of pharmacokinetics and safety with the oral formulation in healthy volunteers (2013)

In healthy adults, oral TPM is bioequivalent to intravenous TPM, and infusion of 50-100 mg over 15 min is safe. Neurologic effects occurred during the infusion, demonstrating that TPM rapidly diffuses into the brain, which supports its evaluation for neonatal seizures. Results from this pilot study will inform the design of subsequent studies in children and newborns, including controlled clinical trials intended to assess the efficacy and safety of intravenous TPM for neonatal seizures. In addition, our results provide support for the further development of intravenous TPM as bridge therapy for older children and adults in whom oral TPM therapy is interrupted.
Inkjet Printing Assisted Synthesis of Multicomponent Mesoporous Metal Oxides for Ultrafast Catalyst Exploration (2012)

We describe an inkjet printing assisted cooperative-assembly method for high-throughput generation of catalyst libraries (multicomponent mesoporous metal oxides) at a rate of 1,000,000-formulations/hour with up to eight-component compositions. The compositions and mesostructures of the libraries can be well-controlled and continuously varied. Fast identification of an inexpensive and efficient quaternary catalyst for photocatalytic hydrogen evolution is achieved via a multidimensional group testing strategy to reduce the number of performance validation experiments (25,000-fold reduction over an exhaustive one-by-one search).
Microprocessors : Principles and Applications (1989)

From the Publisher:
Microprocessors: Principles and Applications, Second Edition is an introductory text on microprocessors, microcomputers, their associated subsystems and software, and related careers in this area of electronics. Although, the subject matter is less than two decades old, the material required to introduce the subject properly grows significantly each year.
Intelligent assistance for software construction: a case study (2002)

An important type of software design task involves constructing software artifacts from existing components. Major user tasks are locating relevant components, reusing existing artifacts, and ensuring that the artifact is complete and consistent. We developed a prototype knowledge-based graphical system that supports these tasks. It delivers information to users by adding and deleting graphical objects and changing their appearance. The system was developed in cooperation with an AT&T product organization. They created a production version of the tool for assembling sets of telecommunications features for customers. The tool lets users work at a high level and eases problems with locating relevant features, reusing feature lists, and maintaining consistency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Exploiting background knowledge to build reference sets for information extraction (2009)

Previous work on information extraction from unstructured, ungrammatical text (e.g. classified ads) showed that exploiting a set of background knowledge, called a “reference set, ” greatly improves the precision and recall of the extractions. However, finding a source for this reference set is often difficult, if not impossible. Further, even if a source is found, it might not overlap well with the text for extraction. In this paper we present an approach to building the reference set directly from the text itself. Our approach eliminates the need to find the source for the reference set, and ensures better overlap between the text and reference set. Starting with a small amount of background knowledge, our technique constructs tuples representing the entities in the text to form a reference set. Our results show that our method outperforms manually constructed reference sets, since hand built reference sets may not overlap with the entities in the unstructured, ungrammatical text. We also ran experiments comparing our method to the supervised approach of Conditional Random Fields (CRFs) using simple, generic features. These results show our method achieves an improvement in F1-measure for 6/9 attributes and is competitive in performance on the others, and this is without training data.
Determination of Chlorinated Hydrocarbons in Water Using Highly Sensitive Mid-Infrared Sensor Technology (2013)

Chlorinated aliphatic hydrocarbons and chlorinated aromatic hydrocarbons (CHCs) are toxic and carcinogenic contaminants commonly found in environmental samples, and efficient online detection of these contaminants is still challenging at the present stage. Here, we report an advanced Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR) sensor for in-situ and simultaneous detection of multiple CHCs, including monochlorobenzene, 1,2-dichlorobenzene, 1,3-dichlorobenzene, trichloroethylene, perchloroethylene, and chloroform. The polycrystalline silver halide sensor fiber had a unique integrated planar-cylindric geometry, and was coated with an ethylene/propylene copolymer membrane to act as a solid phase extractor, which greatly amplified the analytical signal and contributed to a higher detection sensitivity compared to the previously reported sensors. This system exhibited a high detection sensitivity towards the CHCs mixture at a wide concentration range of 5~700 ppb. The FTIR-ATR sensor described in this study has a high potential to be utilized as a trace-sensitive on-line device for water contamination monitoring.
The second-order analysis of stationary point processes (1976)

This paper provides a rigorous foundation for the second-order analysis of stationary point processes on general spaces. It illuminates the results of Bartlett on spatial point processes, and covers the point processes of stochastic geometry, including the line and hyperplane processes of Davidson and Krickeberg. The main tool is the decomposition of moment measures pioneered by Krickeberg and Vere-Jones. Finally some practical aspects of the analysis of point processes are discussed.
Fast Execution of Loops with IF Statements (1984)

A parallel method of execution for a certain class of loops containing IF statements is described. We replace a given loop by an equivalent set of five loops, four of which are vectorizable; the fifth loop is executed in hardware as a Boolean recurrence. The proposed architecture handles all loops that produce recurrences with order ≤m, a hardware parameter.
Gold-Catalyzed Three-Component Coupling: Oxidative Oxyarylation of Alkenes (2010)

The three-component coupling of terminal alkenes with arylboronic acids and oxygen nucleophiles is described. The reaction employs a binuclear gold(I) bromide as a catalyst and Selectfluor reagent as the stoichiometric oxidant. Alcohols, carboxylic acids, and water can be employed as oxygen nucleophiles, thus providing an efficient entry into beta-aryl ethers, esters, and alcohols from alkenes.
GaAs FET with a degenerate semiconductor gate (1985)

A new GaAs FET structure has been proposed and examined experimentally in which the gate material is degenerate p-Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.3</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.7</inf> As fabricated directly on to a p-type layer of undoped semi-insulating GaAs substrates. Obtained transconductance was 207mS/mm under the gate bias of 2V for the gate length of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2\micro</tex> m and the onset voltage of the gate leakage current was 0.5-0. 6V higher than that of MESFETs. These characteristics were explained by the presence of an n-type inversion layer located at p-AlGaAs/p-GaAs interface. Temperature dependence of the drain current leads to a conclusion that the Fermi level was pinned at the interface states 0.475eV above the valence band.
High Throughput Routing in Hybrid Cellular and Ad-Hoc Networks (2005)

We present DST, a dynamic spanning tree based algorithm, as a routing protocol for hybrid networks. It is scalable with the network size and achieves high throughput by taking advantage of multiple channels. DST maintains a close to optimal spanning tree of the network by using distributed topology trees. DST is fully dynamic and generates only O(log n) messages per update operation. We show experimentally that DST scales well with network size, making it ideal for metropolitan environment hybrid networks.
Dextromethorphan As a Phenotyping Test to Predict Endoxifen Exposure in Patients on Tamoxifen Treatment (2011)

Dextromethorphan exposure after a single administration adequately predicted endoxifen exposure in individual patients with breast cancer taking tamoxifen. This test could contribute to the personalization and optimization of tamoxifen treatment, but it needs additional validation and simplification before being applicable in future dosing strategies.
VE‐cadherin‐CreER <sup>T2</sup> transgenic mouse: A model for inducible recombination in the endothelium (2006)

To introduce temporal control in genetic experiments targeting the endothelium, we established a mouse line expressing tamoxifen-inducible Cre-recombinase (Cre-ERT2) under the regulation of the vascular endothelial cadherin promoter (VECad). Specificity and efficiency of Cre activity was documented by crossing VECad-Cre-ERT2 with the ROSA26R reporter mouse, in which a floxed-stop cassette has been placed upstream of the beta-galactosidase gene. We found that tamoxifen specifically induced widespread recombination in the endothelium of embryonic, neonatal, and adult tissues. Recombination was also documented in tumor-associated vascular beds and in postnatal angiogenesis assays. Furthermore, injection of tamoxifen in adult animals resulted in negligible excision (lower than 0.4%) in the hematopoietic lineage. The VECad-Cre-ERT2 mouse is likely to be a valuable tool to study the function of genes involved in vascular development, homeostasis, and in complex processes involving neoangiogenesis, such as tumor growth.
Automatic parsing of news video (1994)

Video content parsing is possible when one has an a priori model of a video's structure based on domain knowledge. This paper presents work on using domain knowledge to parse content of news video programs. Approaches to locating and identifying frame structure models based on temporal and spatial structure of news video data, along with algorithms to apply these models in parsing news video, have been developed and are presented in detail in this paper. Experimental results are also discussed in detail to evaluate the approaches and algorithms. Finally, proposals for future work are summarized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Electrospun Polymer Nanofibers Decorated with Noble Metal Nanoparticles for Chemical Sensing (2017)

The integration of different noble metal nanostructures, which exhibit desirable plasmonic and/or electrocatalytic properties, with electrospun polymer nanofibers, which display unique mechanical and thermodynamic properties, yields novel hybrid nanoscale systems of synergistic properties and functions. This review summarizes recent advances on how to incorporate noble metal nanoparticles into electrospun polymer nanofibers and illustrates how such integration paves the way towards chemical sensing applications with improved sensitivity, stability, flexibility, compatibility, and selectivity. It is expected that further development of this field will eventually make a wide impact on many areas of research.