gebhart/patrepeval huggingface dataset:
Decomposition of biospeckle images in temporary spectral bands (2005)

We present a method of analysis of images of dynamic speckle based on the filtering in frequency bands of the temporary history of each pixel. Butterworth filters are applied to the temporary evolution, and different images are constructed showing the energy in each frequency band. Different degrees of activity of the sample in study, presumably attributed to different origins, are found. The method is exemplified with images of bruising damage in fruits and of biological activity in germinating corn seeds. It is found that the activity in the bruised region of an apple differs from the activity of healthy regions in a certain characteristic frequency range. The activity of the embryo can also be distinguished from that of the endosperm in corn seeds during germination.
The Use of Vital Dyes during Vitreoretinal Surgery - Chromovitrectomy (2015)

The aim of this article is to present the current data with regard to the application of vital dyes during vitreoretinal surgery, 'chromovitrectomy', as well as to overview the current literature regarding the properties of dyes, techniques of application, indications and complications in chromovitrectomy. It is well known that indocyanine green is toxic to the retina and consequently not the ideal dye for chromovitrectomy. Different vital dyes has been tested for chromovitrectomy including trypan blue, patent blue, triamcinolone acetonide, infracyanine green, sodium fluorescein and brilliant blue. Brilliant blue seems to be the ideal dye for internal limiting membrane due to its afinity, lower toxic profile and to reduce the appearance of apoptosis. Besides the dye itself, the injection technique is crucial to avoid additional toxicity, slow injection, far from the retina and protection of the macular hole are some tips. More recently the use of dyes has been applied to stain perfluorcarbon liquids that may enhance its visualization during vitrectomy.
A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans (2021)

Deafness, the most frequent sensory deficit in humans, is extremely heterogeneous with hundreds of genes involved. Clinical and genetic analyses of an extended consanguineous family with pre-lingual, moderate-to-profound autosomal recessive sensorineural hearing loss, allowed us to identify CLRN2, encoding a tetraspan protein, as a new deafness gene. Homozygosity mapping followed by exome sequencing identified a 14.96 Mb locus on chromosome 4p15.32p15.1 containing a likely pathogenic missense variant in CLRN2 (c.494C > A, NM_001079827.2) segregating with the disease. Using in vitro RNA splicing analysis, we show that the CLRN2 c.494C > A variant leads to two events: (1) the substitution of a highly conserved threonine (uncharged amino acid) to lysine (charged amino acid) at position 165, p.(Thr165Lys), and (2) aberrant splicing, with the retention of intron 2 resulting in a stop codon after 26 additional amino acids, p.(Gly146Lysfs*26). Expression studies and phenotyping of newly produced zebrafish and mouse models deficient for clarin 2 further confirm that clarin 2, expressed in the inner ear hair cells, is essential for normal organization and maintenance of the auditory hair bundles, and for hearing function. Together, our findings identify CLRN2 as a new deafness gene, which will impact future diagnosis and treatment for deaf patients.
Transcriptional and cell cycle-mediated regulation of myosin heavy chain gene expression during muscle cell differentiation. (1983)

The molecular mechanisms regulating the induction of myosin heavy chain (MHC) gene expression during muscle cell differentiation were studied using a MHC cDNA recombinant plasmid. During in vitro L6E9 cell myogenesis, cytoplasmic MHC mRNA content/cell nucleus increases a minimum of 500-fold during the first 6 days of differentiation. Two independent parameters regulating MHC mRNA accumulation were directly measured. (i) Intrinsic (chemical) MHC mRNA stability (t1/2 = 55-60 h) is the same in both myotubes and when first detected in myoblasts. This suggests that the intrinsic stability of the MHC mRNA molecule does not change during myogenesis. (ii) The rate of MHC gene transcription and MHC mRNA synthesis increases approximately 100-fold during myogenesis but is insufficient to account for the entire MHC mRNA accumulation. An additional independent parameter was found to profoundly affect MHC mRNA accumulation. Withdrawal from the cell cycle, as occurs during terminal myogenic differentiation, increases the final accumulation of stable mRNAs, such as MHC, by increasing mRNA effective stability. During L6E9 myogenesis, the transition from mitotically active myoblasts (doubling time = 16 h) to postmitotic myotubes results in a 4-5-fold increase in the effective stability of cytoplasmic MHC mRNA. This cell cycle-mediated effect, combined with the induction of MHC mRNA synthesis, completely accounts for MHC mRNA accumulation. A parallel effect occurs in the total cytoplasmic poly(A)+ mRNA population. The rates of synthesis of each of the two major stability components (t1/2 = 5 and 50 h, respectively) are equally increased 2-3-fold during myogenesis. However, the composition of the cytoplasmic mRNA population changes due to the preferential accumulation of stable mRNAs. We conclude that both transcriptional and cell cycle-mediated regulation of MHC gene expression is necessary, but either alone is not sufficient to produce the differentiated muscle cell phenotype.
Determining how much software assurance is enough? a value-based approach (2005)

A classical problem facing many software projects is how to determine when to stop testing and release the product for use. On the one hand, we have found that risk analysis helps to address such "how much is enough?" questions, by balancing the risk exposure of doing too little with the risk exposure of doing too much. In some cases, it is difficult to quantify the relative probabilities and sizes of loss in order to provide practical approaches for determining a risk-balanced "sweet spot" operating point. However, we have found some particular project situations in which tradeoff analysis helps to address such questions. In this paper, we provide a quantitative approach based on the COCOMO II cost estimation model and the COQUALMO qualify estimation model. We also provide examples of its use under the differing value profiles characterizing early startups, routine business operations, and high-finance operations in marketplace competition situation. We also show how the model and approach can assess the relative payoff of value-based testing compared to value-neutral testing based on some empirical results. Furthermore, we propose a way to perform cost/schedule/reliability tradeoff analysis using COCOMO II to determine the appropriate software assurance level in order to finish the project on time or within budget.
The Long and Winding Road to FDA Approval of a Novel Prostate Cancer Test: Our Story (2012)

Only a very small fraction of the many tumor biomarkers discovered are successfully translated from the academic research laboratory into clinical practice. The pathway has not always been linear and has involved people with expertise in a wide range of specialties, including basic research, assay development, clinical affairs, regulatory affairs, marketing, business, oncology, and executive-management leadership. The experience with a tumor biomarker, the PCA3 [prostate cancer gene 3 (non-protein coding)] gene, illustrates the long and winding road that must be navigated. Here we reflect, from a historical point of view, on how the interface between academic science, industry, urologists, and clinical laboratories has been essential to advance biomarkers from solid basic science to a validated clinical laboratory test.

PCA3 was first described as DD3 in 1999 by Bussemakers and colleagues (1). Researchers in the Isaacs laboratory at Johns Hopkins University used differential-display analysis to compare patterns of mRNA production in benign and malignant prostate tissue, with the goal of identifying unknown genes involved in prostate tumorigenesis. PCA3 expression was further characterized in the Schalken laboratory at Radboud University, Nijmegen (2), and this research confirmed 2 important properties of PCA3 as a prostate cancer (PCa)6 marker: PCA3 expression is prostate tissue specific, and PCA3 is highly overexpressed in PCa compared with benign tissue. This PCa-specific overexpression led the Nijmegen researchers to assess the feasibility of a PCA3 -based urine test for PCa detection.

In 2001, a license for PCA3 was obtained by DiagnoCure, a company in Quebec City, Canada, to develop the assay and provide a clinical application. Transfer of a cancer biomarker to industry requires both the appropriate technology and a proper cancer strategy. The Nijmegen methodology was converted from PCR to nucleic acid sequence–based amplification (NASBA), a …
Réseaux spontanés et auto-organisants : du codage spatio-temporel au codage de réseaux (2011)

We study the rotate-and-forward (RF) cooperative protocol in the two-hop MIMO relay networks. In these networks, the source communicates with the destination via a layer of relays. We consider different network configurations and we study the performance of the RF scheme using a new metric called outage gain. This gain gives us an exact characterization of the outage probability's behavior at moderate and high signal-to-noise ratio. Using this metric, we compare the performance of the RF scheme to the performance of other schemes having the same diversity order. Moreover, we assume that a feedback channel exists between the destination and the relays, and we use the channel knowledge to improve the performance of the RF scheme in terms of outage probability. We consider the physical layer network coding protocol; the compute-and-forward. We consider the transmission rate maximization problem and we relate it to the lattice shortest vector problem. We first implement this protocol for real Gaussian channels and one-dimensional lattices. We derive the maximum likelihood (ML) criterion and we propose a quasi-ML decoding technique and show that it can be implemented by using an Inhomogeneous Diophantine Approximation algorithm. Secondly, we generalize some of these results to the complex Gaussian multi-dimensional lattices, and introduce the flatness factor as a design criterion for lattice codes.
Cholinergic Receptors in the Extraocular Rectus Muscle of the Rabbit (1989)

The cholinergic receptors in rabbit isolated rectus muscle preparations were characterized by means of cholinergic agonists and antagonists. The concentration-dependent contraction induced by acetylcholine, carbachol or oxotremorine remained uninfluenced by atropine (10(-5) M), whereas the nicotinic receptor antagonist hexamethonium caused a parallel shift of the concentration-response curve. The agonists pilocarpine, methacholine and aceclidine, which are selective muscarinic receptor stimulants, did not cause contraction of the muscle preparation. However, the nicotinic receptor stimulant 1,1-dimethyl-4-phenylpiperazine iodide (DMPP) caused contraction similar to that induced by acetylcholine. DMPP-induced contractions were inhibited by hexamethonium, causing a parallel rightward shift of the concentration-response curve. This shift could be quantified by means of a Schild plot, indicating competitive antagonism with a PA2 value of 4.63 for hexamethonium. Atropine when applied together with hexamethonium did not cause a further shift of the concentration-response curve. The present results clearly indicate that the cholinergic receptors which mediate contraction in the rabbit isolated extraocular muscle preparation belong to the nicotinic subtype.
Arginine biosynthesis and regulation in Lactobacillus plantarum: the carA gene and the argCJBDF cluster are divergently transcribed (1997)

A cluster of citrulline biosynthetic genes has been cloned and sequenced from a fragment of Lactobacillus plantarum CCM 1904 (ATCC 8014) DNA isolated as complementing a Bacillus subtilis argF mutation. The gene order was carA-argCJBDF, with carA transcribed divergently from the arg cluster. Although other gram-positive bacteria show similar arg clusters, this arrangement for carA is thus far unprecedented. Downstream from the arg cluster, two open reading frames (ORF7 and ORF8) having unknown functions were found. Sequence analysis of the end of a 10.5-kb cloned DNA fragment showed that argF was 3.5 kb from the ldhL gene coding for L-(+)-lactate dehydrogenase. A tree representation of amino acid sequence clustering relationships of 31 ornithine carbamoyltransferases (OTCases) from various organisms revealed two prokaryotic groups: one with ArgF of L. plantarum and one with ArgF of B. subtilis, which are paralogous. This divergence was not observed in vivo because an L. plantarum argF mutant (AM 1215) harboring no OTCase activity was complemented by the argF genes of L. plantarum and B. subtilis. No OTCase activity was detectable when L. plantarum was grown in the presence of saturating amounts of arginine or citrulline. Arginine may repress the citrulline biosynthetic genes in L. plantarum by using 11 identified DNA motifs which resemble the Escherichia coli ARG box consensus and which are in most cases separated by multiples of 11 bp, corresponding to a DNA helical turn. The carA and argCJBDF genes are divergently transcribed. Their putative promoters are 6 bp apart and are partially overlapped by putative ARG boxes, suggesting concerted transcription regulation.
Correction of Misclassifications Using a Proximity-Based Estimation Method (2004)

An estimation method for correcting misclassifications in signal and image processing is presented. The method is based on the use of context-based (temporal or spatial) information in a sliding-window fashion. The classes can be purely nominal, that is, an ordering of the classes is not required. The method employs nonlinear operations based on class proximities defined by a proximity matrix. Two case studies are presented. In the first, the proposed method is applied to one-dimensional signals for processing data that are obtained by a musical key-finding algorithm. In the second, the estimation method is applied to two-dimensional signals for correction of misclassifications in images. In the first case study, the proximity matrix employed by the estimation method follows directly from music perception studies, whereas in the second case study, the optimal proximity matrix is obtained with genetic algorithms as the learning rule in a training-based optimization framework. Simulation results are presented in both case studies and the degree of improvement in classification accuracy that is obtained by the proposed method is assessed statistically using Kappa analysis.
Calibration of Wideband FMCW Polarimetric Radars Operating at Millimeter-Wave Frequencies (2021)

This article presents a comprehensive technique for calibrating wideband frequency-modulated continuous-wave (FMCW) fully polarimetric radars employing linear FM (LFM) signal chirps. A detailed system distortion model is developed that accounts for both polarimetric distortions and distortions caused by nonlinearities in the transmitted and received radar chirps over multiple polarization channels. Using the radar responses of two point targets at known distances from the radar, the calibration technique is able to estimate the range-dependent nonlinearities in phase and correct them for all targets at all ranges. This allows the radar to achieve its ideal range resolution. In addition, the calibration technique corrects for channel imbalances in the polarimetric radar using a metallic sphere of known diameter and any depolarizing target. Both numeric simulations and actual polarimetric radar measurements using a wideband FMCW radar operating over 76.5–82 GHz were used to validate the calibration technique.
Judging Heterodox Economics: A Response to Hodgson’s Criticisms (2019)

The renowned institutionalist Geoffrey Hodgson has claimed inter alia that heterodox economics has failed to define its nature and scope, does not take pluralism seriously, and lacks expertise concentration to ensure quality which means it has made limited progress and is held in variable esteem. To address these alleged problems, Hodgson proposes four alternative strategies: the creation of heterodox economics academic departments; for heterodox economists to enter non-economics academic departments; for heterodox economists to 'organise' around a successful approach with future potential; or, to encourage the study of economic institutions by other social science disciplines or by using prominent mainstream techniques and approaches. A response to these criticisms and proposed strategies is warranted for several reasons. These criticisms are not trivial and, as an assemblage the import is much greater than a singular criticism. Hodgson is very influential within the economics discipline and he reiterates, in part, past criticisms from the mainstream as well as presenting his criticisms to a wide range of audiences. These criticisms intersect with longstanding debates within heterodox economics about the role of pluralism, the definition and project of heterodox economics, its relationship to the changing form of mainstream, and the merit of synthesis or convergence of different heterodox schools of economic thought. The suitability of mainstream measures to judge heterodox economics, and the relationship of ideology and economic theory, are also raised by these criticisms as well as the feasibility of proposed strategies to support heterodox economics within the academy. It is argued that several fallacious claims lead Hodgson to misconstrue the nature and evolution of heterodox economics, and inherent flaws in each of his proposed alternative strategies will further marginalise â€“ not advance â€“ the project of heterodox economics.
Mutations induced by glyoxal and methylglyoxal in mammalian cells (2000)

To investigate the mutation spectra of glyoxal and methylglyoxal in mammalian cells, we analyzed mutations in a bacterial suppressor tRNA (supF) gene in the shuttle vector plasmid pMY189. The cytotoxicity and the mutation frequency increased according to the doses of glyoxal and methylglyoxal. The majority of glyoxal-induced mutations (65%) were base-pair substitutions, in which G:C-->C:G transversions were predominant. In the mutants induced by methylglyoxal, multi-base deletions were predominant (50%), followed by base-pair substitutions (35%), in which G:C-->C:G and G:C-->T:A transversions were predominant.
Salmonella infections: immune and non-immune protection with vaccines (2007)

Abstract\n Salmonella enterica in poultry remains a major political issue. S. serovar Enteritidis, particularly, remains a world-wide problem. Control in poultry by immunity, whether acquired or innate, is a possible means of containing the problem. Widespread usage of antibiotics has led to the emergence of multiple antibiotic resistant bacteria. This problem has indicated an increasing requirement for effective vaccines to control this important zoonotic infection.&#13;\n\tAn attempt is made in this review to explain the relatively poor success in immunising food animals against these non-host-specific Salmonella serotypes that usually produce food-poisoning, compared with the success obtained with the small number of serotypes that more typically produce systemic "typhoid-like" diseases. New examinations of old problems such as the carrier state and vertical transmission, observed with S. Pullorum, is generating new information of relevance to immunity. Newer methods of attenuation are being developed. Live vaccines, if administered orally demonstrate non-specific and rapid protection against infection which is of biological and practical interest. However, from the point of view of consumer safety, there is a school of thought that considers inactivated or sub-unit vaccines to be the safest. The benefits of developing effective killed or sub-unit vaccines over the use of live vaccines are enormous. Recently there have been significant advances in the development of adjuvants, for example microspheres, that are capable of potent immuno-stimulation, targeting different arms of the immune system. The exploitation of such technology in conjunction with the ongoing developments in identifying key Salmonella virulence determinants should form the next generation of Salmonella sub-unit vaccines for the control of this important group of pathogens. There are additional areas of concern associated with the use of live vaccines, particularly if these are generated by genetic manipulation.
Severe platelet desialylation in a patient with glycoprotein Ib/IX antibody-mediated immune thrombocytopenia and fatal pulmonary hemorrhage (2014)

Immune thrombocytopenia (ITP) is a common bleeding disorder characterized by autoantibody-mediated platelet destruction. Antibodies predominantly target platelet glycoproteins GPIIb/IIIa (70–80%) and GPIb/IX (20–40%), with some patients having both. In animal models, anti-GPIb/IX but not anti-
Enterobacteriaceae complicate the recovery of Listeria monocytogenes from food product enrichments using buffered Listeria enrichment broth (2016)

Buffered Listeria enrichment broth (BLEB) is the preferred enrichment formulation of the U.S. Food and Drug Administration (FDA) for the recovery of Listeria monocytogenes. BLEB, which relies on sodium nalidixate, cycloheximide and acriflavine-HCl for selectivity, permits the growth of all foodborne species of Listeria and several non-Listeria species including some members of the family Enterobacteriaceae. Five species of Enterobacteriaceae and four strains of non-pathogenic Listeria species were evaluated to determine which ones most suppressed to L. monocytogenes 48 hour populations in BLEB; these were subsequently used in spiked-food enrichment competition studies. L. monocytogenes recovery was complicated by the simultaneous presence of both Listeria innocua and Enterobacteriaceae competitors. The overall mean L. monocytogenes enrichment populations (n=15 per matrix) were 4.2 ± 0.6, 3.1 ± 0.4, and 2.4 ± 0.7 log CFU/mL for guacamole, asadero cheese, and refrigerated crabmeat, respectively. The overall mean L. innocua enrichment populations (n=15 per matrix) were 8.0 ± 0.7, 6.4 ± 0.7, and 6.5 ± 0.3 log CFU/mL for the same three matrices, respectively. L. monocytogenes was not recovered from any spiked-food enrichment when using either Oxford or chromogenic agars. L. innocua was recovered from all enrichments. Matrix-free competition assays using non-pathogenic Listeria species and Citrobacter braakii, simultaneously, indicate the potential for Enterobacteriaceae competitors to contribute considerably to both L. monocytogenes population suppression and to large Listeria inter-species population differentials. In some instances, Enterobacteriaceae competitors suppressed L. monocytogenes populations more than the non-pathogenic Listeria species. The ability to recover L. monocytogenes from food matrices with complex microflora, including multiple species of Listeria, is an important issue for regulatory agencies since detection without recovery is considered a false positive test result.https://doi.org/10.21423/jrs-v04n01p010 (DOI assigned 7/23/2019)
Evaluation of selected approximations used in pressure vessel fluence calculations (1984)

In response to concerns over the issue of Pressurized Thermal Shock (PTS), Brookhaven National Laboratory (BNL), under the direction of the USNRC, has developed and benchmarked a methodology for calculating pressure vessel (PV) (>1-MeV) damage fluence. The methodology is based on the DOT-3.5 discrete ordinates transport code and has been shown to yield fluence results in good agreement with measurements and results from other calculations. This paper describes the basic methodology employed in BNL PV fluence calculations, and the results of a number of studies performed to assess the impact of various special effects on the calculated (>1-MeV) PV fluence.