gebhart/patrepeval huggingface dataset:
Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles (2005)

These data demonstrate that the more convenient procedure of macrodissection can be adequately used and yields reliable data regarding the identification of tumor cell-specific gene expression profiles.
Specifying subject-oriented composition (1996)

Subject-oriented programming supports composition of object-oriented programs or program fragments called subjects. This article presents an approach to specifying desired compositions in a convenient and concise manner. We motivate the need for subject composition, and illustrate the key issues. We define a low-level model in which composition is controlled by detailed attributes. We then describe higher-level composition rules as collections of attributes that, together, provide some desired aspect of composition functionality. Compositions are specified by means of composition expressions written as collections of rules, typically a general rule along with rules specifying exceptions. A rule library is thus an open-ended collection of useful abstractions in terms of which to define compositions. We give definitions of a few common rules, Including merge and override, as a first step towards a generally useful composition rule library. We also outline an object-oriented framework for implementing our composition approach, which we are currently building as part of our support for subject-oriented programming in C++. © 1996 John Wiley & Sons, Inc.
Computing variance for interval data is NP-hard (2002)

When we have only interval ranges [ x i , x i ] of sample values x 1 ,…, x n , what is the interval [ V, V ] of possible values for the variance V of these values? We prove that the problem of computing the upper bound V is NP-hard. We provide a feasible (quadratic time) algorithm for computing the lower bound V on the variance of interval data. We also provide a feasible algorithm that computes V under reasonable easily verifiable conditions.
Proangiogenic properties of human myeloma cells: production of angiopoietin-1 and its potential relationship to myeloma-induced angiogenesis (2003)

Patients with multiple myeloma (MM) have increased bone marrow (BM) angiogenesis; however, the proangiogenic properties of myeloma cells and the mechanisms of MM-induced angiogenesis are not completely clarified. The angiopoietin system has been identified as critical in the regulation of vessel formation. In this study we have demonstrated that myeloma cells express several proangiogenic factors, and, in particular, we found that angiopoietin-1 (Ang-1), but not its antagonist Ang-2, was expressed by several human myeloma cell lines (HMCLs) at the mRNA and the protein levels. In a transwell coculture system, we observed that myeloma cells up-regulated the Ang-1 receptor Tie2 in human BM endothelial cells. Moreover, in an experimental model of angiogenesis, the conditioned medium of HMCLs significantly stimulated vessel formation compared with control or vascular endothelial growth factor (VEGF) treatment. The presence of anti-Tie2 blocking antibody completely blunted the proangiogenic effect of XG-6. Finally, our in vitro results were supported by the in vivo finding of Ang-1, but not Ang-2, mRNA and protein expression in purified MM cells obtained from approximately 47% of patients and by high BM angiogenesis in patients with MM positive for Ang-1, suggesting that the angiopoietin system could be involved, at least in part, in MM-induced angiogenesis.
Photo-triggered fluorescent theranostic prodrugs as DNA alkylating agents for mechlorethamine release and spatiotemporal monitoring (2015)

We describe a new theranostic strategy for selective delivery and spatiotemporal monitoring of mechlorethamine, a DNA alkylating agent. A photo-responsive prodrug is designed and composed of a photolabile o-nitrophenylethyl group, a DNA alkylating mechlorethamine drug and a coumarin fluorophore. Masking of the "N" in mechlorethamine in a positively charged state in the prodrug renders it inactive, non-toxic, selective and non-fluorescent. Indeed, the stable prodrug shows negligible cytotoxicity towards normal cells with and without UV activation and is completely non-fluorescent. However, upon photo-irradiation, the active mechlorethamine is released and induces efficient DNA cross-links, accompanied by a strong fluorescence enhancement (152 fold). Furthermore, DNA cross-linking activity from the release can be transformed into anticancer activity observed in in vitro studies of tumor cells. Importantly, the drug release progress and the movement can be conveniently monitored by fluorescence spectroscopy. The mechanistic study proves that the DNA cross-linking activity is mainly due to the release of DNA alkylating mechlorethamine. Altogether, the studies show the power of the theranostic strategy for efficient therapy in cancer treatment.
The elastic moduli of oriented tin oxide nanowires (2009)

Tin oxide nanowires (NWs) exhibit interesting electronic properties, which can be harnessed for applications in nanoelectronic devices and sensors. Oriented single crystalline tin oxide NWs were grown at 45 degrees from a titanium dioxide substrate. Their elastic properties were investigated in a two-point geometry using an atomic force microscope (AFM) coupled with a scanning electron microscope under ultrahigh vacuum conditions. Young's modulus was calculated by bending individual NWs and measuring the force exerted on the AFM tip during force-displacement measurements. For the NWs investigated, having radial dimensions below 45 nm and length up to 1.2 microm, we found an average value of 100 +/- 20 GPa, which is below the theoretical predictions calculated for different SnO(2) single crystal orientations, yet consistent with the indentation moduli of nanobelts. Finally, we discuss the effects of the nanowire-cantilever configuration on the measured Young's modulus.
A New Haemorrhagic Disorder with Defective Fibrin Stabilization and Cryofibrinogenaemia (1974)

S ummary . An acquired haemorrhagic syndrome is described in which the failure of haemostasis is due to impaired crosslinking of fibrin. This defect, demonstrated by both monochloroacetic acid clot‐solubility test and disc‐gel electrophoretic analysis of individual fibrin chains, existed despite normal fibrin stabilizing factor (factor XIII) levels in the patient's plasma. Activation of the factor by thrombin, measured by amine incorporation into casein, was normal. The unique molecular defect in this patient could be fully accounted for by the presence of an inhibitory IgG antibody against the crosslinking sites in fibrinogen‐fibrin. No alteration could be seen in either the rate or in the extent of the reversible aggregation of fibrin. However, large amounts of cryoprecipitate were found in the patient's plasma. This phenomenon could be reproduced in vitro by incubating the chromatographically purified IgG of the patient with normal fibrinogen at 4°C. It is conceivable that the antibody in the patient could have arisen in response to the modification of normal fibrinogen by isonicotinic acid hydrazide which the patient had ingested for 8 yr.
No Workflow Can Ever Be Enough (2017)

The dominant crowdsourcing infrastructure today is the workflow, which decomposes goals into small independent tasks. However, complex goals such as design and engineering have remained stubbornly difficult to achieve with crowdsourcing workflows. Is this due to a lack of imagination, or a more fundamental limit? This paper explores this question through in-depth case studies of 22 workers across six workflow-based crowd teams, each pursuing a complex and interdependent web development goal. We used an inductive mixed method approach to analyze behavior trace data, chat logs, survey responses and work artifacts to understand how workers enacted and adapted the crowdsourcing workflows. Our results indicate that workflows served as useful coordination artifacts, but in many cases critically inhibited crowd workers from pursuing real-time adaptations to their work plans. However, the CSCW and organizational behavior literature argues that all sufficiently complex goals require open-ended adaptation. If complex work requires adaptation but traditional static crowdsourcing workflows can't support it, our results suggest that complex work may remain a fundamental limitation of workflow-based crowdsourcing infrastructures.
Performance of turbo-codes for WCDMA systems in frequency selective fading channels (2003)

The original parallel concatenated convolutional codes (PCCC) known as turbo codes have been shown to yield very good performance for long block sizes. The performance of turbo codes for short block sizes suitable for real time communication systems has gained a lot of attention. We consider the applicability of such codes to the WCDMA radio link based on the requirements of the wireless third generation (3G). Specifically here, we consider two different structures for the 1/4 rate turbo codes. The first is the conventional structure in which three identical constituent encoders are used. This structure is named equal rate turbo code (ERTC). The second structure is a modified turbo code structure with an encoder consisting of two different constituent encoders (one of rate=1/2 and the other of rate=1/3). This structure is called unequal rate turbo code (URTC). The performance of the proposed URTC, conventional ERTC, and a convolutional code with the same decoding complexity are considered in AWGN as well as frequency selective fading channels.
Entropy data analysis (1986)

Entropy Data Analysis (EDA) is a new approach to the analysis of data. It embodies a framework which encompasses many classical statistical concepts; yet it goes beyond the classical framework both in the generality of its concepts and the correctness of its results. This paper provides an introduction to Entropy Data Analysis. Technical details can be found in the referenced papers.
Polymeric Complexes of Silver(I) with Diphosphine Ligands:  Self-Assembly of a Puckered Sheet Network Structure (2002)

The syntheses and structures of polymeric silver(I)-diphosphine complexes are reported, in which the silver(I) center is surrounded by 1, 2, or 3 phosphorus atoms. When rigid diphosphine ligands are used in combination with weakly coordinating anions, linear polymers are obtained that contain both diphosphine and anion bridges. However, with excess of a diphosphine with a long, flexible, spacer group, a remarkable puckered sheet structure, comprised of fused giant 54-membered rings, is obtained that is a coordination polymer analogue of laminated materials such as micas and clays. The polymeric chain and sheet structures may be considered to be formed by ring-opening polymerization of cyclic precursors.
Carbohydrate induced modulation of cell membrane. VI. Binding of exogenous lectin induces susceptibility of erythrocytes to free radical damage: a spin label study (1997)

The oxidation of erythrocyte membrane has been widely used as a model to study the damage of biomembranes by free radicals. Whether binding of lectin to erythrocytes has any effect on peroxidant injury has never been studied. This study reports for the first time that crosslinking of erythrocyte surface glycoprotein by an exogenous lectin significantly enhances the susceptibility to membrane damage by free radicals, as evidenced by the increase in membrane fluidity measured by EPR using spin label and the increase in the amount of oxyhemoglobin liberated due to cell lysis.
Sodium Channel Inactivation Is Altered by Substitution of Voltage Sensor Positive Charges (1997)

The role of the voltage sensor positive charges in fast and slow inactivation of the rat brain IIA sodium channel was investigated by mutating the second and fourth conserved positive charges in the S4 segments of all four homologous domains. Both charge-neutralizing mutations (by glutamine substitution) and charge-conserving mutations were constructed in a cDNA encoding the sodium channel alpha subunit. To determine if fast inactivation altered the effects of the mutations on slow inactivation, the mutations were also constructed in a channel that had fast inactivation removed by the incorporation of the IFMQ3 mutation in the III-IV linker (West, J.W., D.E. Patton, T. Scheuer, Y. Wang, A.L. Goldin, and W.A. Catterall. 1992. 89:10910- 10914). Most of the mutations shifted the vof fast inactivation in the negative direction, with the largest effects resulting from mutations in domains I and II. These shifts were in the opposite direction compared with those observed for activation. The effects of the mutations on slow inactivation depended on whether fast inactivation was intact or not. When fast inactivation was eliminated, most of the mutations resulted in positive shifts in the v of slow inactivation. The largest effects again resulted from mutations in domains I and II. When fast inactivation was intact, the mutations in domains II and III resulted in negative shifts in the v of slow inactivation. Neutralization of the fourth charge in domain I or II resulted in the appearance of a second component in the voltage dependence of slow inactivation that was only observable when fast inactivation was intact. These results suggest the S4 regions of all four domains of the sodium channel are involved in the voltage dependence of inactivation, but to varying extents. Fast inactivation is not strictly coupled to activation, but it derives some independent voltage sensitivity from the charges in the S4 domains. Finally, there is an interaction between the fast and slow inactivation processes.
Controlled Leaky-Wave Radiation From a Planar Configuration of Width-Modulated Microstrip Lines (2013)

Planar leaky-wave antenna (LWA) designs that utilize a printed surface wave (SW) source are presented. Specifically, by the addition of a periodic arrangement of width-modulated microstrip lines on top of a grounded dielectric slab (GDS), a sinusoidally modulated reactance surface (SMRS) can be realized, providing appropriate conditions for leaky wave (LW) radiation. In addition, a transition section near the SW source improves antenna matching, while also, controlling the leakage rate and aperture distribution. A numerically computed dispersion diagram (DD) for the periodic structure is also calculated in terms of Mathieu functions. Full-wave simulations and measurements are in agreement with the developed numerical model and results suggest that these LWAs can offer broadside radiation as well as continuous beam scanning with radiation efficiencies of more than 85%. In addition, the investigated width-modulated microstrip lines offer ease of fabrication and may also be useful in the design of new periodic structures for wave guidance and other low-cost printed circuits and antennas.
Impossible Boomerang Attack for Block Cipher Structures. (2009)

Abstract. Impossible boomerang attack [5] (IBA) is a new variant of differential cryptanalysis against block ciphers. Evident from its name, it combines the ideas of both impossible differential cryptanalysis and boomerang attack. Though such an attack might not be the best attack available, its complexity is still less than that of the exhaustive search. In impossible boomerang attack, impossible boomerang distinguishers are used to retrieve some of the subkeys. Thus the security of a block cipher against IBA can be evaluated by impossible boomerang distinguishers. In this paper, we study the impossible boomerang distinguishers for block cipher structures whose round functions are bijective. Inspired by the U-method in [3], we provide an algorithm to compute the maximum length of impossible boomerang distinguishers for general block cipher structures, and apply the algorithm to known block cipher structures such as Nyberg’s generalized Feistel network, a generalized CAST256-like structure, a generalized MARS-like structure, a generalized RC6-like structure, etc.
Ref‐1/Ape is critical for formation of the hypoxia‐inducible transcriptional complex on the hypoxic response element of the rat pulmonary artery endothelial cell VEGF gene (2004)

The co-transcription factor and DNA repair enzyme, Redox effector factor-1/apurinic/apyrimidinic endonuclease (Ref-1/Ape), facilitates DNA binding and transcriptional activity of a number of transactivating factors, including those governing hypoxia-induced gene expression HIF-1. It is not known, however, whether Ref-1/Ape is a component of the hypoxic transcriptional complex. Electrophoretic mobility shift assays failed to detect direct DNA binding of Ref-1/Ape to either the HIF-1 or AP1 DNA recognition sequences present in the hypoxic response element of the VEGF gene. However, immunodepletion of Ref-1/Ape from nuclear extract prevented DNA binding of ATF/CREB and HIF-1 to the HIF-1 DNA recognition sequence. DNA affinity-precipitation analyses showed that Ref-1/Ape was part of the multiprotein transcriptional complex forming on a 64-mer sequence encompassing a minimal hypoxic response element. Immunodepletion of Ref-1/Ape prevented probe association with HIF-1, p300, ATF, and CREB. Co-immunoprecipitation experiments indicated that Ref-1/Ape present in nuclear extract interacted with HIF-1 and p300 but not ATF/CREB. However, when Ref-1/Ape was immunoprecipitated from the oligonucleotide probe, both HIF-1 and p300 remained probe-associated while ATF/CREB co-immunoprecipitated. These findings suggest that Ref-1/Ape is a critical component of the hypoxia-inducible transcriptional complex forming on the VEGF gene's hypoxic response element and that the presence of Ref-1/Ape in the complex is required for the apparent high affinity association between HIF-1 and its DNA recognition sequence.
The Pound Weight and the Pound Sterling: The Relationship Between Weight and Coinage and its Consequences (1988)

In a previous article attention was drawn to the many customary systems of weights and measures used in the past in different parts of the country. Since many of them remained in use until the late nineteenth century, it was suggested that familiarity with the customary measures formerly current in the study area was essential before drawing conclusions from documentary evidence originating in an earlier period. In that context little was said about the fundamental relationship between weight and coinage, and this short note is an attempt to rectify that omission. With a centralized monetary system since before the Conquest the apparent anomalies were not themselves regional, but since different weight and valuation systems were often applied to different commodities, the importance of their correct interpretation may be readily appreciated.
In situ localization of PCR-amplified human and viral cDNAs. (1992)

We describe a technique, called reverse transcriptase (RT) in situ PCR, whereby RNA may be nonisotopically detected in fixed cells when amplified by PCR after cDNA synthesis by RT. RT in situ PCR using primers specific for the measles virus generated an intense signal in most measles-infected HeLa cells, as compared to the weak signal generated in few cells using standard in situ hybridization analysis. The viral RNA that localized to the nucleus spared the nucleoli, was most evident when the RT step used the primer complementary to the negative genomic strand, and was demonstrated in all multinucleated cells and the majority of uninucleate cells. A hybridization signal was evident with standard RNA in situ hybridization using the human megakaryocyte cell line Dami and a probe for glycoprotein IIB (GIIB) mRNA but not a probe for amyloid precursor protein (APP) or gelsolin (GEL) mRNA. After RT in situ PCR, signals were evident for each target localizing to the nucleolus for APP and to perinucleolar and cytoplasmic locations for GEL and GIIB. The latter findings suggest that mRNAs may follow different geographic pathways as they progress from premessage to transcriptionally active message.
Matrix Components and Scaffolds for Sustained Islet Function (2011)

The clinical treatment of diabetes by islet transplantation is limited by low islet survival rates. A fundamental reason for this inefficiency is likely due to the removal of islets from their native environment. The isolation process not only disrupts interactions between blood vessels and endocrine cells, but also dramatically changes islet cell interaction with the extracellular matrix (ECM). Biomolecular cues from the ECM are important for islet survival, proliferation, and function; however, very little is known about the composition of islet ECM and the role each component plays. Without a thorough understanding of islet ECM, current endeavors to prolong islet survival via scaffold engineering lack a systematic basis. The following article reviews current knowledge of islet ECM and attempts to explain the roles they play in islet function. In addition, the effects of in vitro simulations of the native islet scaffold will be evaluated. Greater understanding in these areas will provide a preliminary platform from which a sustainable bioartificial pancreas may be developed.
Loss tangent and complex modulus estimated by acoustic radiation force creep and shear wave dispersion (2012)

Elasticity imaging methods have been used to study tissue mechanical properties and have demonstrated that tissue elasticity changes with disease state. In current shear wave elasticity imaging methods typically only shear wave speed is measured and rheological models, e.g. Kelvin-Voigt, Maxwell and Standard Linear Solid, are used to solve for tissue mechanical properties such as the shear viscoelastic complex modulus. This paper presents a method to quantify viscoelastic material properties in a model-independent way by estimating the complex shear elastic modulus over a wide frequency range using time-dependent creep response induced by acoustic radiation force. This radiation force induced creep method uses a conversion formula that is the analytic solution of a constitutive equation. The proposed method in combination with shearwave dispersion ultrasound vibrometry is used to measure the complex modulus so that knowledge of the applied radiation force magnitude is not necessary. The conversion formula is shown to be sensitive to sampling frequency and the first reliable measure in time according to numerical simulations using the Kelvin-Voigt model creep strain and compliance. Representative model-free shear complex moduli from homogeneous tissue mimicking phantoms and one excised swine kidney were obtained. This work proposes a novel model-free ultrasound-based elasticity method that does not require a rheological model with associated fitting requirements.
Adapted nonlinear multiresolution decomposition with applications in progressive lossless image coding (2002)

We present an adapted nonlinear multiresolution decomposition (with some derivatives) of still images that permits perfect reconstruction. A hierarchical pyramidal decomposition with maximal decimation is used. For one level of decomposition, the input image I is partitioned into two subimages I/sub 1/ and I/sub 2/ obtained by downsampling. The subimage I/sub 1/ is unchanged. The subimage I/sub 2/ is replaced by the rounded output I/sub h/ of a 2D FIR filter whose coefficients have first been adapted to I and which has the entries I/sub 1/ and I/sub 2/. A similar processing is then applied one time to each of the subimages I/sub 1/ and I/sub 2/. The nonlinearity introduced by the rounding permits us to perfectly inverse the process, even when inverse filters (which are all ARMA) are not BIBO stable. Applications are given in lossless image coding, with possibility of embedded zerotree coding.