gebhart/patrepeval huggingface dataset:
Compressed Sensing With Nonlinear Observations and Related Nonlinear Optimization Problems (2013)

Nonconvex constraints are valuable regularizers in many optimization problems. In particular, sparsity constraints have had a significant impact on sampling theory, where they are used in compressed sensing and allow structured signals to be sampled far below the rate traditionally prescribed. Nearly, all of the theory developed for compressed sensing signal recovery assumes that samples are taken using linear measurements. In this paper, we instead address the compressed sensing recovery problem in a setting where the observations are nonlinear. We show that, under conditions similar to those required in the linear setting, the iterative hard thresholding algorithm can be used to accurately recover sparse or structured signals from few nonlinear observations. Similar ideas can also be developed in a more general nonlinear optimization framework. In the second part of this paper, we therefore present related result that shows how this can be done under sparsity and union of subspaces constraints, whenever a generalization of the restricted isometry property traditionally imposed on the compressed sensing system holds.
Range and contour fused environment recognition for mobile robot (2002)

A sensor fusion scheme for mobile robot environment recognition that incorporates range data and contour data is proposed. An ultrasonic sensor provides coarse spatial description but guarantees open space (with no obstacle) within a sonic cone with relatively high belief. A laser structured light system provides a detailed contour description of the environment but is prone to light noise and is easily affected by surface reflectivity. We present a sensor fusion scheme that can compensate the disadvantages of both sensors. Line models from the laser structured light system play a key role in environment description. The overall fusion process is composed of two stages: noise elimination and belief updates. Dempster-Shafer's evidential reasoning is applied at each stage. Open space estimation from sonar range measurements brings elimination of noisy lines from the laser sensor. Comparing actual sonar data to the simulated sonar data enables data of two disparate sensors to be fused in the unified feature space. Experimental results demonstrate the effectiveness of the proposed method.
Photochemical approaches to T‐cell activation (2010)

Despite decades of intensive research, T-cell activation has remained mysterious because of both the dizzying diversity of antigen recognition and the speed and comprehensiveness of the T-cell-receptor signalling network. Further progress will require new approaches and reagents that provide added levels of control. Photochemistry allows specific biochemical processes to be controlled with light and is well suited to mechanistic studies in complex cellular environments. In recent years, several laboratories have adopted approaches based on photoreactive peptide-major histocompatibility complex reagents in order to study T-cell activation and function with high precision. Here, I review these efforts and outline future directions for this exciting area of research.
A lab-on-a-chip system integrating tissue sample preparation and multiplex RT-qPCR for gene expression analysis in point-of-care hepatotoxicity assessment (2015)

A truly practical lab-on-a-chip (LOC) system for point-of-care testing (POCT) hepatotoxicity assessment necessitates the embodiment of full-automation, ease-of-use and "sample-in-answer-out" diagnostic capabilities. To date, the reported microfluidic devices for POCT hepatotoxicity assessment remain rudimentary as they largely embody only semi-quantitative or single sample/gene detection capabilities. In this paper, we describe, for the first time, an integrated LOC system that is somewhat close to a practical POCT hepatotoxicity assessment device - it embodies both tissue sample preparation and multiplex real-time RT-PCR. It features semi-automation, is relatively easy to use, and has "sample-in-answer-out" capabilities for multiplex gene expression analysis. Our tissue sample preparation module incorporating both a microhomogenizer and surface-treated paramagnetic microbeads yielded high purity mRNA extracts, considerably better than manual means of extraction. A primer preloading surface treatment procedure and the single-loading inlet on our multiplex real-time RT-PCR module simplify off-chip handling procedures for ease-of-use. To demonstrate the efficacy of our LOC system for POCT hepatotoxicity assessment, we perform a preclinical animal study with the administration of cyclophosphamide, followed by gene expression analysis of two critical protein biomarkers for liver function tests, aspartate transaminase (AST) and alanine transaminase (ALT). Our experimental results depict normalized fold changes of 1.62 and 1.31 for AST and ALT, respectively, illustrating up-regulations in their expression levels and hence validating their selection as critical genes of interest. In short, we illustrate the feasibility of multiplex gene expression analysis in an integrated LOC system as a viable POCT means for hepatotoxicity assessment.
Influence of a Lipid-Lowering Therapy on Calcified and Noncalcified Coronary Plaques Monitored by Multislice Detector Computed Tomography (2007)

Statin therapy led to a significant reduction of noncalcified plaque burden that was not reflected in calcium scoring or total plaque burden. This finding might explain the risk reduction after the initiation of statin therapy. Using multislice detector computed tomography, physicians have the potential to monitor medical treatment in patients with coronary atherosclerosis.
Cardiotoxic effects of anthracycline–taxane combinations (2003)

The association of doxorubicin (DOX) and paclitaxel (PTX) is very active in breast cancer. Unfortunately, PTX may potentiate the cardiotoxic effects of anthracyclines: it causes nonlinear disposition of DOX and its metabolites, leading to persistant of elevated plasma concentrations of the anthracyclines. However, this pharmacokinetic interference is not sufficient to explain the enhanced cardiotoxicity of the combination. Recent data suggest that PTX stimulates the conversion of DOX to cardiotoxic metabolites (namely doxorubicinol) inside cardiomyocytes. Docetaxel (DTX) does not have a major influence on DOX plasma concentration because it does not interfere with its elimination. Clinical data suggest that DTX may not enhance anthracycline cardiotoxicity, but patients seldom received a total anthracycline dose compatible with increased risk. Furthermore, there are experimental data indicating that DTX can also stimulate the metabolism of DOX to toxic species in human heart.
Pediatric testicular tumors: evaluation with gray-scale and color Doppler US. (1994)

Color Doppler US is more helpful than gray-scale US in identification of testicular tumor.
Lattice-based computation of Boolean functions (2010)

This paper studies the implementation of Boolean functions with lattices of two-dimensional switches. Each switch is controlled by a Boolean literal. If the literal is 1, the switch is connected to its four neighbours; else it is not connected. Boolean functions are implemented in terms of connectivity across the lattice: a Boolean function evaluates to 1 iff there exists a top-to-bottom path. The paper addresses the following synthesis problem: how should we map literals to switches in a lattice in order to implement a given target Boolean function? We seek to minimize the number of switches. Also, we aim for an efficient algorithm -- one that does not exhaustively enumerate paths. We exploit the concept of lattice and Boolean function duality. We demonstrate a synthesis method that produces lattices with a number of switches that grows linearly with the number of product terms in the function. Our algorithm runs in time that grows polynomially.
Intelligibility Estimation in Law Enforcement Speech Processing (2010)

Speech recordings obtained in the context of law enforce-ment are often degraded in terms of quality and intelligib-ility. Several techniques for assessing the impact of speech enhancement algorithms on quality are available, both in-trusive and nonintrusive, but the assessment of intelligibil-ity is usually reliant on expensive and time consuming sub-jective listening scores. To address this issue, we describe some recent scoring experiments and an adaptive Bayesian procedure which efficiently estimates properties of the psy-chometric function from a small number of listening tests. A data-driven nonintrusive objective intelligibility estima-tion method is also described and tested on car and babble noise. It is shown to give intelligibility estimates that are well correlated with subjective scores. We aim to im-prove our understanding of the quality/intelligibility trade-off and to study speech processing tools in the critical con-text of law enforcement. 1
Comparable survival after HLA-well-matched unrelated or matched sibling donor transplantation for acute myeloid leukemia in first remission with unfavorable cytogenetics at diagnosis (2010)

We compared the outcomes of unrelated donor (URD, n = 358) with human leukocyte antigen (HLA)-matched sibling donor (MSD, n = 226) transplantations in patients with acute myeloid leukemia (AML) in first complete remission (CR1) having unfavorable cytogenetics at diagnosis. Unfavorable cytogenetic abnormalities were: complex (≥ 3 abnormalities), 32%; and noncomplex involving chromosome 7, 25%; chromosome 5, 9%; 11q or MLL rearrangements, 18%; t(6;9), 5%; and other noncomplex, 10%. URDs were HLA-well-matched (n = 254; 71%) or partially-matched (n = 104; 29%). Three-year leukemia-free survival (LFS) for MSD was 42% (95% confidence interval [CI], 35%-48%) compared with 34% (95% CI, 28%-41%) for HLA-well-matched URD and 29% (95% CI, 20%-39%) for partially-matched URD (P = .08). In multivariate analysis, HLA-well-matched URD and MSD yielded similar LFS (relative risk [RR] = 1.1, 95% CI, 0.86-1.40, P = .44) and overall survival (OS; RR = 1.06, 95% CI, 0.83-1.37, P = .63). LFS and OS were significantly inferior for HLA-partially-matched URD recipients, those with prior myelodysplastic syndrome, and those older than 50 years. All cytogenetic cohorts had similar outcomes. Patients with chronic graft-versus-host disease had a significantly lower risk of relapse (RR = 0.68, 95% CI, 0.47-0.99, P = .05). Hematopoietic cell transplantation (HCT) using HLA-well-matched URD and MSD resulted in similar LFS and OS in AML patients in CR1 with unfavorable cytogenetics. Outcomes of HCT from HLA-partially- matched URD were inferior.
Bro: An Open Source Network Intrusion Detection System. (2003)

Bro is a powerful, but largely unknown open source network intrusion detection system. Based on a sound design, Bro achieves its main goals -- separating policy from mechanisms, efficient operation in high-volume networks, and withstanding attacks against itself -- by using an event-driven approach. Bro contains several analyzers (e.g. protocol decoders for a variety of network protocols and a signature matching engine), which are by themselves policy-neutral but raise events as an abstraction of the underlying network activity. Based on scripts written in Bro&apos;s own powerful scripting language, the user defines event handlers to specify his environment-specific policy. We give an
A precursor of the neck appendage protein of <i>B. subtilis</i> phage Φ 29 (1974)

The cleavage of precursor proteins to polypeptides \nof smaller molecular weight is a mechanism involved \nin the morphogenesis of the head and DNA encapsulat- \nion in T4 [l-4]. In this paper we present evidence \nwhich indicates the existence of a precursor in the \nsynthesis of the protein which forms the neck appen- \ndages of the Bacillus subtilis phage a29 [S] . Pulse- \nchase experiments indicate that the neck appendage \nprotein (NPl), of molecular weight 80 000, is syn- \nthesized as a precursor (P-NPI) with a molecular \nweight about 90 000, and tryptic peptide analysis \nof both proteins (P-NPl and NPI), show that they \ncontain very similar peptides. These results indicate \na precursor-product relationship of proteins P-NPl \nand NPI. Infection under nonpermissive conditions \nwith temperature-sensitive mutants in cistron B, the \ngene coding for the neck appendage protein precursor \n[6] , which have a clear plaque phenotype, gives place \nto the accumulation of protein P-NPI in higher amount \nthan that present after normal phage infection. Some \nevidence for the existence of a precursor of the @29 \nneck appendage protein has been given by Anderson \nand Reilly [7] .
Endothelial cells secrete a factor that promotes fibroblast contraction of hydrated collagen gels. (1990)

Bovine aortic endothelial cells (BAEC), grown in vitro, are shown to synthesize and secrete factor(s) that stimulate fibroblasts to contract collagen matrices. The amount of contraction-promoting activity in the conditioned media is dependent on conditioning time and the number of cells in the culture. Production of the contraction-promoting activity continues at a high stable level for at least 5 d in serum-free medium but is abolished when the cells are exposed to an inhibitor of protein synthesis. The mechanism of action of the contraction factor(s) derived from endothelial cells was compared with that of unidentified serum factors. The endothelial cell-secreted factor(s) depends on active protein synthesis by the target cell but does not need to be present during the contraction process. The serum factors on the other hand promote collagen contraction in the absence of de novo protein synthesis but need to be continuously present. Preliminary biochemical characterization of the contraction-promoting factors produced by endothelial cells revealed properties similar to those of previously identified growth factors. However, the BAEC-secreted factor was found to be distinct from a previously identified contraction-promoting transforming growth factor beta.
Development and distribution of immunoglobulin-containing cells in the chicken. An immunofluorescent analysis using purified antibodies to mu, gamma and light chains. (1971)

The development and distribution of immunoglobulin-containing cells were studied in chickens using purified antibodies to µ, γ and light chains labeled with fluorochromes. Cells containing µ and light chains were found in lymphoid follicles of the bursa of Fabricius of 14-day embryos. IgG-containing cells were initially observed in bursal follicles at 21 days of incubation. Embryonic infusions of plasma from newly hatched and adult chickens had no effect on the appearance of immunoglobulin-containing cells within the bursa. The developmental sequence of immunoglobulin-containing cells within the bursa was later recapitulated in the spleen, tonsilla caecalis and thymus. Rapid expansion of IgM- and IgG-containing cells began in the spleen on the 3rd and 8th days, respectively, after hatching. The ratio of IgG- to IgM-containing cells was greatest in the intestinal wall of immunologically mature birds. Development of immunoglobulin-containing cells in extra-bursal sites was retarded in chickens hatched under germ-free conditions. In contrast, neither exclusion of exogenous antigens nor antigenic stimulation in ovo affected the time of appearance or proliferation of immunoglobulin-containing cells within the bursa. The medullary regions of individual bursal follicles frequently stained for both IgM and IgG. This pattern was not observed in lymphoid follicles of other tissues. Analysis of single cell suspensions revealed a high proportion of single bursal cells containing heavy chains of both IgM and IgG, wheras spleen cells rarely contained both classes of immunoglobulins. The results suggest that a developmental switch from IgM to IgG synthesis may occur within the bursa.
Nanoscopic templates using self-assembled cylindrical diblock copolymers for patterned media (2004)

We demonstrated a process to create nanoscopic templates for the nanofabrication of patterned media using thin films of diblock copolymers. The self-assembled monolayers (SAMs) technique is used as a means to chemically modify the topographically confined trench surfaces to manipulate the wetting behavior of cylindrical diblock copolymers and perpendicularly oriented cylindrical poly (styrene-block-methyl methacrylate) (PS-b-PMMA) copolymers are obtained. Through optimizing the annealing conditions, long-range ordering in trenches is achieved after annealing at 170°C for about 24h. The ordering is strongly dependent on the line-edge-roughness (LER) of the trenches and the number of defects in the copolymer films inside the trenches. Efforts to decrease the various defects in the copolymer films and improve the trench LER are still in progress. With our approach, a negative phase 20nm nanoporous SiO2 template and a positive phase 20nm Ta nanodot template based on the self-assembled cylindrical PS-b-PMMA block copolymers are feasible for following pattern transfer to make patterned media.
Micro and macro evaluation of classification rules (2008)

Rule evaluation plays an important role in the rule learning and classification process. Many existing rule inductive learning algorithms are based on single rule evaluation measures. However, the overall rule induction system performance and the classification process are involved with the evaluation of a set of rules. This brings the needs for studying the connections between single rule and rule set evaluation measures. The main objective of this paper is to introduce a general framework of classification rule evaluation which connects two types of evaluations, called micro and macro evaluation. Micro evaluation is based on single rules which can be measured by the common empirical measures. Macro evaluation is based on rule sets, depending on the relationships between rules in the set, different resolutions can be applied. By analyzing the relationships between these two types of evaluations, we suggest that under certain conditions, macro evaluation measures can be explicitly expressed by micro evaluation measures.
Rational plasmid design and bioprocess optimization to enhance recombinant adeno‐associated virus (AAV) productivity in mammalian cells (2015)

Viral vectors used for gene and oncolytic therapy belong to the most promising biological products for future therapeutics. Clinical success of recombinant adeno-associated virus (rAAV) based therapies raises considerable demand for viral vectors, which cannot be met by current manufacturing strategies. Addressing existing bottlenecks, we improved a plasmid system termed rep/cap split packaging and designed a minimal plasmid encoding adenoviral helper function. Plasmid modifications led to a 12-fold increase in rAAV vector titers compared to the widely used pDG standard system. Evaluation of different production approaches revealed superiority of processes based on anchorage- and serum-dependent HEK293T cells, exhibiting about 15-fold higher specific and volumetric productivity compared to well-established suspension cells cultivated in serum-free medium. As for most other viral vectors, classical stirred-tank bioreactor production is thus still not capable of providing drug product of sufficient amount. We show that manufacturing strategies employing classical surface-providing culture systems can be successfully transferred to the new fully-controlled, single-use bioreactor system Integrity(TM) iCELLis(TM) . In summary, we demonstrate substantial bioprocess optimizations leading to more efficient and scalable production processes suggesting a promising way for flexible large-scale rAAV manufacturing.
New materials and technologies for micromachined metal oxide gas sensor arrays (2002)

We present a new silicon micromachined low power heater platform comprising sensor arrays which feature a number of different gas sensitive metal oxides. The sensing elements of the arrays are composed of alternatively n-type SnO/sub 2/, n-type WO/sub 3/, n-type ZnO, p-type Cr/sub 1.8/Ti/sub 0.2/O/sub 3+z/ or n-type V/sub 2/O/sub 5/. Characterisation of the arrays under trace gas exposure is presented.
The rich against the poor: Can global injustice be rectified (2011)

It is a fact that none of the world orders throughout history have satisfied the necessary conditions for existence - to satisfy all the participating countries. Still, it seems that none of the world orders caused controversy and opposite opinions except globalization. Some consider globalization to be a new, contemporary phase of human society development while to others it represents nothing but a great myth. Some consider it to be an objective and spontaneous planetary process, others see it as the domination of developed countries, a process which brings with it a number of divisions and a deeper economic and social gap between parts of the world. For the winners of globalization, it represents the advancement of civilization and a source of the new boon for mankind, but for the losers it is nothing but a destructive power. Both parties are right: globalization provided a new quality dimension of development but at the same time the developing possibilities are not equally allocated and available to all.
ANDP-2, A Novel Acrinol Degradation Product by Light (2007)

To clarify the degradation pathway of acrinol by light, isolation and identification of acrinol degradation products (ANDP) were attempted. ANDP-2, one of the ANDPs, was isolated by extraction with methanol from cloths dampened with acrinol solution, and purified by column chromatography on Diaion HP-10, Sephadex LH-20 and G-25. The structural elucidation of ANDP-2 was examined by infrared, 1H-NMR, 13C-NMR and Fast atom bombardment mass (FAB-MS) spectra studies. From the spectroscopic data, the structure of ANDP-2 was determined to be 4-amino-6-ethoxyl-2,3-dicarboxyquinoline, that was found to be a novel degradation product of acrinol by light. The solution of ANDP-2 has fluorescence with a blue color, though that of acrinol has fluorescence with green. ANDP-2 did not show growth inhibition at a concentration of 100 μg/ml against Gram-positive, -negative bacteria, yeast and fungi.
Measurement of Serum C-Reactive Protein Concentration after Renal Transplantation (1987)

A prospective study of serial serum C-reactive protein (CRP) concentrations was made on 21 patients who had received renal allografts. CRP was raised during 27 of 32 rejection episodes and in all of five episodes of rejection associated with infection. CRP values were persistently elevated in three irreversible rejection episodes. Significantly raised CRP concentrations were documented in 14 of 20 episodes of infection. In some cases CRP was a predictive indicator of rejection or infection. In all cases of infection or rejection associated with a rise in CRP, CRP values fell following successful treatment with appropriate agents. Serial CRP measurement used in conjunction with other clinical and biochemical parameters appears to be valuable clinically following renal transplantation.
Modeling of Heat Transfer and Crystallization in Thermoplastic Composite Tape Placement Process (1997)

The crystallization behavior of thermoplastic composites during the tape placement process has been analyzed. A heat transfer analysis has been carried out using a finite element method. The heat transfer analysis is coupled with a crystallization kinetics model to predict the resulting morphology. In order to determine the heat intensity that could be applied to the laminate, a degradation kinetics model is added. The degradation kinetics model thus provides an upper bound for the heat input. The models relate the process parameters (e.g., roller velocity, roller pressure, heat input) to temperature and crystallinity distributions and degradation weight loss. These models are incorporated into a computer code to generate numerical results. By using this code, process conditions which are favorable to consolidation and also likely to produce optimum crystallinity levels are identified.