gebhart/patrepeval huggingface dataset:
Do ImageNet Classifiers Generalize to ImageNet? (2019)

We build new test sets for the CIFAR-10 and ImageNet datasets. Both benchmarks have been the focus of intense research for almost a decade, raising the danger of overfitting to excessively re-used test sets. By closely following the original dataset creation processes, we test to what extent current classification models generalize to new data. We evaluate a broad range of models and find accuracy drops of 3% - 15% on CIFAR-10 and 11% - 14% on ImageNet. However, accuracy gains on the original test sets translate to larger gains on the new test sets. Our results suggest that the accuracy drops are not caused by adaptivity, but by the models' inability to generalize to slightly "harder" images than those found in the original test sets.
Segmentation and leaf sequencing for intensity modulated arc therapy (2007)

A common method in generating intensity modulated radiation therapy (IMRT) plans consists of a three step process: an optimized fluence intensity map (IM) for each beam is generated via inverse planning, this IM is then segmented into discrete levels, and finally, the segmented map is translated into a set of MLC apertures via a leaf sequencing algorithm. To date, limited work has been done on this approach as it pertains to intensity modulated arc therapy (IMAT), specifically in regards to the latter two steps. There are two determining factors that separate IMAT segmentation and leaf sequencing from their IMRT equivalents: (1) the intrinsic 3D nature of the intensity maps (standard 2D maps plus the angular component), and (2) that the dynamic multileaf collimator (MLC) constraints be met using a minimum number of arcs. In this work, we illustrate a technique to create an IMAT plan that replicates Tomotherapy deliveries by applying IMAT specific segmentation and leaf‐sequencing algorithms to Tomotherapy output sinograms. We propose and compare two alternative segmentation techniques, a clustering method, and a bottom‐up segmentation method (BUS). We also introduce a novel IMAT leaf‐sequencing algorithm that explicitly takes leaf movement constraints into consideration. These algorithms were tested with 51 angular projections of the output leaf‐open sinograms generated on the Hi‐ART II treatment planning system (Tomotherapy Inc.). We present two geometric phantoms and 2 clinical scenarios as sample test cases. In each case 12 IMAT plans were created, ranging from 2 to 7 intensity levels. Half were generated using the BUS segmentation and half with the clustering method. We report on the number of arcs produced as well as differences between Tomotherapy output sinograms and segmented IMAT intensity maps. For each case one plan for each segmentation method is chosen for full Monte Carlo dose calculation (NumeriX LLC) and dose volume histograms (DVH) are calculated. In all cases, the BUS method outperformed the clustering, method. We recommend using the BUS algorithm and discuss potential improvements to the clustering algorithms.
Pharmacokinetics and biodistribution of technetium 99m labelled standard heparin and a low molecular weight heparin (enoxaparin) after intravenous injection in normal volunteers (1991)

For a better understanding of low molecular weight heparin pharmacokinetics, 99m technetium labelled heparin and enoxaparin were injected intravenously to four normal volunteers, after approval by the Ethics Committee and preliminary animals studies. In vitro and in vivo, the labelled products proved to be stable and identical to the non-labelled drugs. Radioactivity curves in blood, organs and urines were similar for both products. Anti Xa plasma half-life was 3 times longer for enoxaparin than for heparin. Anti IIa plasma half-lives were similar. However, radioactivity persisted much longer than biological activities for both products. After chromatography, most of the radioactivity was bound to AT III, where an anti Xa activity peak was also detected. The anti Xa activity peak seen after adding AT III to plasma was much higher with heparin than with enoxaparin. In urine, biological activities, measured with AT III supplementation, were higher with enoxaparin than with heparin. These results suggest that phenomena other than biodistribution are responsible for the differences in pharmacokinetics observed between these two products. The two most likely explanations are differences in metabolism and/or a release of an endogenous factor.
Determining nuclear morphology using an improved angle-resolved low coherence interferometry system (2003)

We outline the process for determining the morphology of subsurface epithelial cell nuclei using depth-resolved light scattering measurements. The measurements are accomplished using a second generation angle-resolved low coherence interferometry system. The new system greatly improves data acquisition and analysis times compared to the initial prototype system. The calibration of the new system is demonstrated in scattering studies to determine the size distribution of polystyrene microspheres in a turbid sample. The process for determining the size of cell nuclei is discussed by analyzing measurements of basal cells in a sub-surface layer of intact, unstained epithelial tissue.
The Impact of Medication Resistance and Continuation Pharmacotherapy on Relapse following Response to Electroconvulsive Therapy in Major Depression (1990)

After clinical response to electroconvulsive therapy (ECT), 58 patients with major depressive disorder were followed for 1 year or until relapse. The rate of relapse was substantially higher in patients who had failed adequate antidepressant medication trials prior to ECT than in patients not determined to be medication resistant. Adequacy of post-ECT pharmacotherapy was only marginally related to likelihood of relapse. The subgroup of patients who appeared to benefit from adequate post-ECT pharmacotherapy were those who did not receive an adequate medication trial prior to ECT. The findings call into question the common practice of administering as continuation pharmacotherapy following ECT the same class of medications that patients had failed with during the acute episode prior to ECT. The findings also indicate that resistance to antidepressant medication is a strong predictor of relapse following response to ECT.
Stress resistance in Saccharomyces cerevisiae is strongly correlated with assembly of a novel type of multiubiquitin chain. (1994)

The covalent attachment of ubiquitin (Ub) to short-lived or damaged proteins is believed to be the signal that initiates their selective degradation. In several cases, it has been shown that the proteolytic signal takes the form of a multi-Ub chain in which successive Ub molecules are linked tandemly at lysine 48 (K-48). Here we show that Ub molecules can be linked together in vivo at two other lysine positions, lysine 29 (K-29) and lysine 63 (K-63). The formation of these alternative linkages is strongly dependent on the presence of the stress-related Ub conjugating enzymes UBC4 and UBC5. Furthermore, expression of Ub carrying a K-63 to arginine 63 substitution in a strain of Saccharomyces cerevisiae that is missing the poly-Ub gene, UBI4, fails to compensate for the stress defects associated with these cells. Taken together, these results suggest that the formation of multi-Ub chains involving K-63 linkages plays an important role in the yeast stress response. In broader terms, these results also suggest that Ub is a versatile signal in which different Ub chain configurations are used for different functions.
Isolation and characterization of the cDNA encoding the spiny dogfish shark (Squalus acanthias) form of cytochrome P450c17 (1995)

Abstract Cytochrome P450c17 is a key steroidogenic enzyme for the production of sex steroids in gonadal tissue and for cortisol production in adrenal tissue. This protein possesses two enzymatic activities. The 17α‐hydroxylase activity results in the introduction of a hydroxyl group at the 17α‐position. The resultant 17α‐hydroxylated, C21 pregnene is converted to a C19 andro‐gen by the C17,20‐lyase activity. A cDNA library was constructed from poly(A)‐enriched mRNA isolated from spiny dogfish shark ( Squalus acanthias ) testis and ligated into Eco RI‐cut lambda arms. The amplified library was screened using a bovine P450c17 cDNA probe and five positive clones were isolated. The described cDNA encompasses 23 bp of the 5′‐untranslated region, a 1,527 bp open reading frame, and 414 bp of the 3′‐untranslated region. A putative polyadenylation signal (AATAAA) is 18 bp from the poly(A) tail. Northern blot analysis showed a single transcript of 1.9 kb, thus indicating the isolated clone is a full‐length cDNA. The deduced amino acid sequence of the shark form of P450c17 is 59% and 57% identical to the rainbow trout and chicken forms, respectively. The shark form is 43% to 46% identical to mammalian forms (rat, human, mouse, bovine, and porcine). There are large regions of extremely high identity shared among all the forms. The deduced shark 17α‐hydroxylase protein is 509 residues in length with a predicted weight of 57.2 kDa. Non‐steroidogenic COS cells, transfected with the shark P450c17 cDNA, was capable of 17α‐hydroxylase and C17,20‐lyase activities using both pregnenolone and progesterone as initial substrates. © 1995 Wiley‐Liss, Inc.
Comparison of Channel Estimation Methods for Pilot Aided OFDM Systems (2007)

This paper investigates different channel estimation methods for pilot based OFDM transmission systems. Based on a regular grid of pilot data the channel estimation is separated for time and frequency direction. For time direction linear and spline interpolation are used. In frequency direction also linear and spline interpolation are compared. In addition an estimation based on a DFT method is taken into account. Also the Wiener estimation approach is investigated both for interpolation in time and frequency direction. The methods are compared with respect to performance and implementation complexity. For simulation a DRM (digital radio mondiale) system is used.
Molecular beacon-functionalized gold nanoparticles as probes in dry-reagent strip biosensor for DNA analysis (2009)

The highly specific molecule recognition properties of molecular beacons (MB) are combined with the unique optical properties of gold nanoparticles (Au-NPs) for the development of a dry-reagent strip-type nucleic acid biosensor (DSNAB) that enables sensitive and low-cost detection of nucleic acid samples within 15 min.
Developing fibre optic Raman probes for applications in clinical spectroscopy (2016)

Raman spectroscopy has been shown by various groups over the last two decades to have significant capability in discriminating disease states in bodily fluids, cells and tissues. Recent development in instrumentation, optics and manufacturing approaches has facilitated the design and demonstration of various novel in vivo probes, which have applicability for myriad of applications. This review focusses on key considerations and recommendations for application specific clinical Raman probe design and construction. Raman probes can be utilised as clinical tools able to provide rapid, non-invasive, real-time molecular analysis of disease specific changes in tissues. Clearly the target tissue location, the significance of spectral changes with disease and the possible access routes to the region of interest will vary for each clinical application considered. This review provides insight into design and construction considerations, including suitable probe designs and manufacturing materials compatible with Raman spectroscopy.
CD20: a gene in search of a function. (2000)

CD20 is a signature B-cell differentiation antigen. The function of CD20 is unknown, although it is thought to be involved in B-cell activation, regulation of B-cell growth, and transmembrane calcium flux. This review covers several topics important for understanding CD20 biology. These topics include the expression pattern and transcriptional regulation of the CD20 gene, the structure of the protein and its interaction with other cell surface molecules, as well as CD20 phosphorylation and putative functions. An understanding of CD20 function from signal transduction to biological implications may prove important for the mechanistic understanding of the treatment of certain types of cancer.
Discordance between results for serum troponin T and troponin I in renal disease (1995)

Two patients were investigated for unexplained increases in troponin T. In the first patient, who had rhabdomyolysis and acute renal failure, troponin T reached a peak value of 13.50 micrograms/L (67.5-fold the upper reference limit). The second patient had chronic renal failure and the troponin T peak value was 2.85 micrograms/L (14.3-fold the upper reference limit). Clinical investigations indicated no evidence of myocardial damage. Serum or plasma specimens were analyzed for total creatine kinase (CK), CK-2 mass, CK-2 isoform ratio, myoglobin, troponin T, troponin I, and myosin light chains; all except troponin I were at above-normal concentrations. We also investigated six additional renal patients with above-normal troponin T; troponin I was slightly increased in only one of these six patients. Our findings demonstrate discordance between results for troponin T and troponin I in renal patients.
Sequential Monte Carlo Methods for Dynamic Systems (1998)

Abstract We provide a general framework for using Monte Carlo methods in dynamic systems and discuss its wide applications. Under this framework, several currently available techniques are studied and generalized to accommodate more complex features. All of these methods are partial combinations of three ingredients: importance sampling and resampling, rejection sampling, and Markov chain iterations. We provide guidelines on how they should be used and under what circumstance each method is most suitable. Through the analysis of differences and connections, we consolidate these methods into a generic algorithm by combining desirable features. In addition, we propose a general use of Rao-Blackwellization to improve performance. Examples from econometrics and engineering are presented to demonstrate the importance of Rao–Blackwellization and to compare different Monte Carlo procedures.
Complement and Atherogenesis (1999)

Complement activation occurs in temporal correlation with the subendothelial deposition of LDL during early atherogenesis, and complement also plays a pathogenetic role in promoting lesion progression. Two lesion components have been identified that may be responsible for complement activation. First, enzymatic degradation of LDL generates a derivative that can spontaneously activate complement, and enzymatically degraded LDL (E-LDL) has been detected in the lesions. Second, C-reactive protein (CRP) colocalizes with complement C5b-9, as evidenced by immunohistological studies of early atherosclerotic lesions, so the possibility exists that this acute phase protein also fulfills a complement-activating function. Here, we report that addition of LDL and CRP to human serum did not result in significant C3 turnover. Addition of E-LDL provoked complement activation, which was markedly enhanced by CRP. Binding of CRP to E-LDL was demonstrated by sucrose flotation experiments. Binding was Ca(2+)-dependent and inhibitable by phosphorylcholine, and the complement-activating property of E-LDL was destroyed by treatment with phospholipase C. These results indicated that CRP binds to phosphorylcholine groups that become exposed in enzymatically degraded LDL particles. Immunohistological studies complemented these findings in showing that CRP colocalizes with E-LDL in early human atherosclerotic lesions. Thus enzymatic, nonoxidative modification of tissue-deposited LDL can be expected to confer CRP-binding capacity onto the molecule. The ensuing enhancement of complement activation may be relevant to the development and progression of the atherosclerotic lesion.
Die Wirkung von Propion‐ und Ameisensäure in der Ferkelaufzucht (1988)

Zusammenfassung In einem Versuch an Absetzferkeln wurden Zusätze von 0,3 (P 1) und 1,0% Propionsäure (P 2) sowie 0,35 (A 1) und 1,2% Ameisensäure (A 2) vergleichend zu einer Kontrolle (K) mit einem Ferkelaufzuchtfutter ohne Antibiotika bzw. Ergotropika geprüft. In obiger Reihenfolge lagen die Zunahmen bei 246, 313, 349, 312 und 275 g/Tier und Tag. In der Magendigesta waren 28, 30, 16, 8 und 28 mmol organische Säuren/100 g Trockensubstanz enthalten; die Digesta der Grupen P 2, A 1 und A 2 war frei von E.coli. Eine an Läufern und Sauen durchgeführte Prüfung der Säurenzusätze auf den N‐Ansatz und die ilealen sowie Gesamtverdaulichkeiten ergab keine Wirkungen. Anzeichen von Belastungen gab es nicht. Die A‐Ferkel zeigten eindeutig antibiotische, wachstumsfördernde Effekte vor allem über eine verbesserte Futteraufnahme.
Antibodies to capsular polysaccharides are not protective against experimental Staphylococcus aureus endocarditis (1995)

The protective efficacy of antibodies to the Staphylococcus aureus capsular polysaccharide was examined in a rat model of catheter-induced endocarditis. Capsular antibodies were induced either by active immunization with killed S. aureus or by passive immunization with hyperimmune rabbit antiserum to S. aureus. Control rats were injected with phosphate-buffered saline or passively immunized with normal rabbit serum or rabbit antiserum to a nonencapsulated strain. Animals with indwelling catheters were challenged intravenously with 5 x 10(4) to 4 x 10(6) CFU of the homologous S. aureus strain (capsular serotype 5 strain Reynolds or serotype 1 strain SA1 mucoid). Both immunized and control rats developed S. aureus endocarditis. The numbers of S. aureus cells recovered from the blood and aortic valve vegetations of immunized rats were similar to those of control rats, indicating that capsule-specific antibodies were not protective. To determine whether the presence of an indwelling catheter interfered with antibody-mediated protection against S. aureus endocarditis, catheters were removed 2 h after insertion in additional groups of rats. An inoculum of 10(8) CFU of strain Reynolds was needed to provoke endocarditis in rats catheterized for 2 h, compared with 5 x 10(4) CFU for rats with indwelling catheters. Passively transferred capsular antibodies were not protective since both immunized and nonimmunized animals developed endocarditis, and quantitative cultures of blood and valvular vegetations revealed no differences between immunized and control animals. The findings of this study indicate that antibodies to the capsular polysaccharide are not protective in the rat model of experimental S. aureus endocarditis.
Aerosol and Intravenous Transfection of Human α1-Antitrypsin Gene to Lungs of Rabbits (1994)

In vivo gene transfer to the lungs is possible either by an intravenous or an airway route of administration. A plasmid containing the recombinant human alpha 1-antitrypsin (h alpha 1AT) gene and a cytomegalovirus promoter complexed to cationic liposomes was given either intravenously or by aerosol to New Zealand White rabbits. Both routes of administration resulted in successful transfection and expression of the h alpha 1AT gene. h alpha 1AT mRNA and protein were detected for at least 7 days. Immunohistochemical staining showed h alpha 1AT protein in the pulmonary endothelium following intravenous administration, in alveolar epithelial cells following aerosol administration, and in the airway epithelium by either route. After intravenous injection of radiolabeled plasmids, autoradiographs showed localization of plasmid in endothelial cells, especially at arterial bifurcations, and at the alveolar level. A plasmid-liposome delivery system for gene therapy to the lungs may permit targeting of the DNA to subsets of lung cells by selection of the route of delivery and may permit a broad application of gene therapy to acute as well as chronic diseases.
All in the CCN family: essential matricellular signaling modulators emerge from the bunker (2006)

The CCN family is a group of six secreted proteins that specifically associate with the extracellular matrix. Structurally, CCN proteins are modular, containing up to four distinct functional domains. CCN family members are induced by growth factors and cytokines such as TGFbeta and endothelin 1 and cellular stress such as hypoxia, and are overexpressed in pathological conditions that affect connective tissues, including scarring, fibrosis and cancer. Although CCN family members were discovered over a decade ago, the precise biological role, mechanism of action and physiological function of these proteins has remained elusive until recently, when several key mechanistic insights into the CCN family emerged. The CCNs have been shown to have key roles as matricellular proteins, serving as adaptor molecules connecting the cell surface and extracellular matrix (ECM). Although they appear not to have specific high-affinity receptors, they signal through integrins and proteoglycans. Furthermore, in addition to having inherent adhesive abilities that modulate focal adhesions and control cell attachment and migration, they execute their functions by modulating the activity of a variety of different growth factors, such as TGFbeta. CCN proteins not only regulate crucial biological processes including cell differentiation, proliferation, adhesion, migration, apoptosis, ECM production, chondrogenesis and angiogenesis, but also have more sinister roles promoting conditions such as fibrogenesis.
Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding? (1980)

(A) Evolutionary similarities of protein structures Two decades have passed from the time that the three dimensional structure of the first globular protein, sperm whale myoglobin, was decoded (Kendrew et al. 1960). Its structure, which now looks so simple and habitual, then seemed to be unusually complicated. The decoding of the subsequent proteins, lysozyme (Blake et al. 1965), ribonuclease (Kartha, Bello &amp; Harker, 1967), chymotrypsin (Matthews et al. 1967), carboxypeptidase (Lipscomb et al. 1969) redoubled the feeling of amazement and even of some confusion before the extremely complicated, intricate and, above all, absolutely unlike protein structures. Some consolation against this background was the evident and far-reaching similarity between the three-dimensional structures of myoglobin and hemoglobin subunits (Perutz, Kendrew &amp; Watson, 1965) and an analogous similarity between the structures of chymotrypsin and other serine proteases, elastase (Shotton &amp; Watson, 1970) and trypsin (Stroud, Kay &amp; Dickerson, 1972). However this similarity was easily explained by the far-reaching homology between the primary structures of myoglobin and hemoglobin and between the primary structures of serine proteases.