gebhart/patrepeval huggingface dataset:
Time-lapse analysis and microgenomics profile the endogenous angiogenic phenotype in aggressive melanoma subpopulations (2008)

291 Beyond the elemental role of blood vessels in tumor growth, fluid conducting networks lacking endothelium were identified previously in metastatic melanoma and other cancer types (termed vasculogenic mimicry). The etiology remains unclear, though it appears to involve dysregulation of the tumor-specific phenotype and transdifferentiation. Instigating the molecular deciphering of this phenomenon, we established a novel technique for time-lapse imaging and topographical documentation of the spontaneously emerging vascular-like networks and randomly oriented cells (nests) followed by laser capture microdissection in living 3D cultures. The evolution of the vasculogenic mimicry phenotype was quantified in long-term cultures by 3 time-dependent variables: the distribution of network lengths, widths, and area coverage. Based on these morphological descriptors the networks were locally classified over time in “early” and “mature” stages. Microgenomics analysis of the network structures revealed for the first time that despite the shared genotype, transcription was differentially regulated among the phenotypically distinct melanoma structures in vasculogenic mimicry. Moreover the level of differential gene expression in network versus nest cells was shown to increase with the degree of network “maturity”. Several angiogenesis-specific genes were differentially expressed in higher levels in “mature” network cells of both uveal and cutaneous melanoma with intriguing representation of the ephrin family of angiogenesis factors. Moreover, the adjacent nest cells over-expressed ECM-related genes. Expression of angiogenesis-specific genes in melanoma resembled that of normal microvascular cells and was enhanced for melanoma disseminating hematogenously. The findings suggest that melanoma plasticity could enable autopoiesis of vascular-mimicking elements within the tumor infrastructure with significant clinical implications, such as response to anti-angiogenic treatments. Identifying factors regulating tumor plasticity and heterogeneity at the molecular level is essential in designing effective anti-cancer therapies.
Design Methods for 3D Membrane Projection Lithography Metasurface Unit Cells (2020)

Three dimensional metasurface structures hold the potential for better performing devices and interesting new properties. However, at optical frequencies it is very difficult to fabricate truly three dimensional designs. One of the most promising techniques is Membrane Projection Lithography (MPL), which can allow for dielectric and metallic inclusions to be deposited on the side wall of a cavity. However, the design process is difficult due to the large search space afforded by these 3D structures and the many coupling environments that arise between neighboring unit cells. Fortunately, advanced optimization techniques have been developed that allow for the space to be fully explored in an efficient manner for optimal designs.
Proteomics application exercise of the Swiss Proteomics Society: Report of the SPS'02 session (2003)

After the success of the mass spectrometry (MS) round table that was held at the first Swiss Proteomics Society congress (SPS'01) in Geneva, the SPS has organized a proteomics application exercise and allocated a full session at the SPS'02 congress. The main objective was to encourage the exchange of expertise in protein identification, with a focus on the use of mass spectrometry, and to create a bridge between the users' questions and the instrument providers' solutions. Two samples were sent to fifteen interested labs, including academic groups and MS hardware providers. Participants were asked to identify and partially characterize the samples. They consisted of a complex mixture of peptide/proteins (sample A) and an almost pure recombinant peptide carrying post-translational modifications (sample B). Sample A was an extract of snake venom from the species Bothrops jararaca. Sample B was a recombinant and modified peptide derived from the shrimp Penaeus vannamei penaeidin 3a. The eight labs that returned results reported the use of a wide range of MS instrumentation and techniques. They mentioned a variety of time and manpower allocations. The origin of sample A was generally identified together with a number of database protein entries. The difficulty of the sample identification lay in the incomplete knowledge of the Bothrops species genome sequence and is discussed. Sample B was generally and correctly identified as penaeidin. However, only one group reported the full primary structure. Interestingly, the approaches were again varied and are discussed in the text.
Length-based attacks in polycyclic groups (2014)

Abstract The Anshel–Anshel–Goldfeld (AAG) key-exchange protocol was implemented and studied with the braid groups as its underlying platform. The length-based attack, introduced by Hughes and Tannenbaum, has been used to cryptanalyze the AAG protocol in this setting. Eick and Kahrobaei suggest to use the polycyclic groups as a possible platform for the AAG protocol. In this paper, we apply several known variants of the length-based attack against the AAG protocol with the polycyclic group as the underlying platform. The experimental results show that, in these groups, the implemented variants of the length-based attack are unsuccessful in the case of polycyclic groups having high Hirsch length. This suggests that the length-based attack is insufficient to cryptanalyze the AAG protocol when implemented over this type of polycyclic groups. This implies that polycyclic groups could be a potential platform for some cryptosystems based on conjugacy search problem, such as non-commutative Diffie–Hellman, El Gamal and Cramer–Shoup key-exchange protocols. Moreover, we compare for the first time the success rates of the different variants of the length-based attack. These experiments show that, in these groups, the memory length-based attack introduced by Garber, Kaplan, Teicher, Tsaban and Vishne does better than the other variants proposed thus far in this context.
BoostMotion: Boosting a Discriminative Similarity Function for Motion Estimation (2006)

Motion estimation for applications where appearance undergoes complex changes is challenging due to lack of an appropriate similarity function. In this paper, we propose to learn a discriminative similarity function based on an annotated database that exemplifies the appearance variations. We invoke the LogitBoost algorithm to selectively combine weak learners into one strong similarity function. The weak learners based on local rectangle features are constructed as nonparametric 2D piecewise constant functions, using the feature responses from both images, to strengthen the modeling power and accommodate fast evaluation. Because the negatives possess a location parameter measuring their closeness to the positives, we present a locationsensitive cascade training procedure, which bootstraps negatives for later stages of the cascade from the regions closer to the positives. This allows viewing a large number of negatives and steering the training process to yield lower training and test errors. In experiments of estimating the motion for the endocardial wall of the left ventricle in echocardiography, we compare the learned similarity function with conventional ones and obtain improved performances. We also contrast the proposed method with a learning-based detection algorithm to demonstrate the importance of temporal information in motion estimation. Finally, we insert the learned similarity function into a simple contour tracking algorithm and find that it reduces drifting.
Synthesis of Dimethyl 2‐Phenylcyclopropane‐1,1‐Dicarboxylate Using an Iodonium Ylide Derived from Dimethyl Malonate (2010)

Abstract Potassium hydroxide Dimethyl malonate Iodosobenzene diacetate Bis[rhodium(a,a,a′a′‐tetramethyl‐1,3‐benznedipropionic acid)] Styrene Thiourea
T-Cell and B-Cell Responses to Viral Antigens at the Clonal Level (1983)

Etude de la reconnaissance des determinants viraux en particulier quand ils sont exprimes sur les cellules injectees par les systemes a la fois des cellules B et T
High level bacterial expression of uteroglobin, a dimeric eukaryotic protein with two interchain disulfide bridges, in its natural quaternary structure. (1990)

Bacterial expression of eukaryotic proteins is a tool of ever-increasing importance in biochemistry and molecular biology. However, the majority of the recombinant eukaryotic proteins that have been expressed in bacteria are produced as fusion proteins and not in their native conformation. In particular, correct formation of quaternary structures by recombinant proteins in bacterial hosts has been reported very rarely. To our knowledge, correct intracellular formation of multimeric structures containing more than one interchain disulfide bridge has not been reported so far. We have constructed three plasmids which are able to direct expression of recombinant rabbit uteroglobin, a homodimeric protein with two interchain disulfide bridges, in Escherichia coli. Among these, the plasmid pLE103-1, in which the expression of recombinant uteroglobin is controlled by a bacteriophage T7 late promoter, is by far the most efficient. With pLE103-1, recombinant uteroglobin production reached about 10% of total bacterial soluble proteins. This protein accumulated in bacterial cells in dimeric form, as it is naturally found in the rabbit uterus. Recombinant uteroglobin was purified to near-homogeneity and its NH2-terminal amino acid sequence was confirmed to be identical to that of its natural counterpart, except for 2 Ala residues the codons for which were added during the plasmid construction. This protein was found to be as active a phospholipase A2 inhibitor as natural uteroglobin on a molar basis. To our knowledge, this is the first report of high level bacterial expression of a full length eukaryotic homodimeric protein with two interchain disulfide bridges in its natural, biologically active form. The plasmid pLE103-1 may be useful to explore structure-function relationships of rabbit uteroglobin. In addition, this plasmid may be useful in obtaining high level bacterial expression of other eukaryotic proteins with quaternary structure, as well as for other general applications requiring efficient bacterial expression of cDNAs.
A synapomorphic disulfide bond is critical for the conformational stability and cytotoxicity of an amphibian ribonuclease (2000)

Onconase((R)) (ONC) is a homolog of ribonuclease A (RNase A) that has unusually high conformational stability and is toxic to human cancer cells in vitro and in vivo. ONC and its amphibian homologs have a C-terminal disulfide bond, which is absent in RNase A. Replacing this cystine with a pair of alanine residues greatly decreases the conformational stability of ONC. In addition, the C87A/C104A variant is 10-fold less toxic to human leukemia cells. These data indicate that the synapomorphic disulfide bond of ONC is an important determinant of its cytotoxicity.
The Prediction of Thermal Performance for Outdoor Swimming Pools (2021)

Empirical methods and industrial guidelines are conventionally used for arriving at heating needs of outdoor community swimming pools which seldom account for local climatic conditions. This paper presents a comprehensive model to estimate the water temperature of an outdoor swimming pool and then to estimate heating-plant size. The important feature of the present model is that all comprehensible modes of heat and mass transfer and topographic conditions are incorporated. The notables are the heat and mass transfer to/from swimming pools through free and forced convection, radiative cooling to the sky, and climatic changes such as cloud cover and rainfall. The ambient weather conditions and solar contributions are also found to be significant contributors. The consequent predictions of pool-water temperature are evaluated vis-à-vis measurements from an Olympic size open air swimming pool in Perth, Australia. Based on a comparison among some models in the literature, it is found that the present model is able to replicate the measured data to within ±0.5°C for nearly 68% of the results over a three year time frame. The subsequent heating-capacity calculations are found to be satisfied in 82% of the measured values to within ±25 kW.
Millimeter-wave imaging of composite materials (1993)

This work addresses the application and evaluates the potential of mm-wave imaging in the W-band (75-110 GHz) using samples of low-loss dielectric and composite materials with artificial defects. The initial focus is on the measurement of amplitude changes in the back scattered and forward-scattered fields. The c-scan system employs a focused beam antenna to provide spatial resolution of about one wavelength. A plane-wave model is used to calculate the effective reflection (or transmission) coefficient of multilayer test sample geometry. Theoretical analysis is used to optimize the measurement frequency for higher image contrast and to interpret the experimental results. Both reflection and transmission images, based on back scattered and forward-scattered powers, were made with Plexiglas and Kevlar/epoxy samples containing artificially introduced defects such as subsurface voids and disbonds. The results clearly indicate that mm-wave imaging has high potential for non-contact interrogation of low-loss materials.
Data from Antibody Targeting GRP78 Enhances the Efficacy of Radiation Therapy in Human Glioblastoma and Non–Small Cell Lung Cancer Cell Lines and Tumor Models (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Non–small cell lung cancer (NSCLC) and glioblastoma multiforme (GBM) have poor median survival. NSCLC and GBM overexpress glucose regulated protein 78 (GRP78), which has a role in radioresistance and recurrence. In this study, we determined the effect of anti-GRP78 antibody and the combined effect of the anti-GRP78 antibody with ionizing radiation (XRT) on NSCLC and GBM cell lines both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; NSCLC and GBM cancer cell lines were treated with anti-GRP78 antibodies and evaluated for proliferation, colony formation, cell death, and PI3K/Akt/mTOR signaling. The efficacy of anti-GRP78 antibodies on tumor growth in combination with XRT was determined &lt;i&gt;in vivo&lt;/i&gt; in mouse xenograft models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; GBM and NSCLC cells treated with anti-GRP78 antibodies showed attenuated cell proliferation, colony formation, and enhanced apoptosis. GBM and NSCLC cells treated with anti-GRP78 antibodies also showed global suppression of PI3K/Akt/mTOR signaling. Combining antibody with XRT resulted in significant tumor growth delay in both NSCLC and GBM heterotopic tumor models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Antibodies targeting GRP78 exhibited antitumor activity and enhanced the efficacy of radiation in NSCLC and GBM both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. GRP78 is a promising novel target, and anti-GRP78 antibodies could be used as an effective cancer therapy alone or in combination with XRT. &lt;i&gt;Clin Cancer Res; 23(10); 2556–64. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Physiologic and Metabolic Factors in the Pathogenesis of Neonatal Enteric Infections in Calves (1972)

SUMMARY Some of the physiologic and metabolic disturbances that occur in neonatal calves with acute enteric infections were investigated. All calves were remarkably dehydrated and in most cases there was evidence of hemoconcentration. Significant metabolic acidosis in such calves was believed to be the result of primary intestinal bicarbonate ion loss, increased organic acid production, and decreased hydrogen ion excretion by the kidneys. Plasma sodium values were normal or moderately reduced in most cases; hypertonic dehydration was observed infrequently. Plasma potassium values were characteristically increased; increased blood urea nitrogen and serum inorganic phosphorous content indicated significant renal insufficiency. The importance of fluid and electrolyte replacement in neonatal diarrheal disease is emphasized.
Channel Estimation in Millimeter Wave Systems with Inter Cell Interference (2019)

Millimeter wave (mmWave) systems rely on accurate channel state information (CSI) for the design of the precoding and combining matrices. Acquiring accurate CSI, however, is challenging due to the large number of antennas, the low signal-to-noise (SNR) ratio before beamforming, and possible interference from neighboring base stations (BSs). Prior work on channel estimation focused on the first two challenges and did not address inter- cell interference. Interference from neighboring BSs deteriorates the already low SNR and introduces errors in the channel estimate. This leads to additional interference in the system. This paper studies the effects of inter- cell interference on compressed sensing (CS) mmWave channel estimation techniques. A CS measurement matrix design is then proposed to jointly estimate the mmWave channel and null interference from neighboring BSs. Simulation results show that channel estimate errors strongly depend on the interference power and the number of interfering BSs. Moreover, in the presence of interference, the proposed techniques are shown to achieve channel estimates comparable to interference-free systems.
T‐cell trafficking in the central nervous system (2012)

To perform their distinct effector functions, pathogen-specific T cells have to migrate to target tissue where they recognize antigens and produce cytokines that elicit appropriate types of protective responses. Similarly, migration of pathogenic self-reactive T cells to target organs is an essential step required for tissue-specific autoimmunity. In this article, we review data from our laboratory as well as other laboratories that have established that effector function and migratory capacity are coordinately regulated in different T-cell subsets. We then describe how pathogenic T cells can enter into intact or inflamed central nervous system (CNS) to cause experimental autoimmune encephalomyelitis or multiple sclerosis. In particular, we elaborate on the role of CCR6/CCL20 axis in migration through the choroid plexus and the involvement of this pathway in immune surveillance of and autoimmunity in the CNS.
Determination of partial molar volumes from free energy perturbation theory (2015)

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.
The ATP‐driven primary Na+ pump in subcellular vesicles of Vibrio alginolyticus (1988)

Subcellular vesicles of Vibrio alginolyticus hydrolyze ATP and accumulate Na+ in an ATP-dependent fashion. The Na+ uptake is (i) strongly stimulated by delta psi-discharging agents, i.e., the protonophorous uncoupler CCCP or valinomycin + K+ and (ii) arrested by DCCD at a concentration strongly inhibiting ATP hydrolysis. Lower concentrations of DCCD stimulate the Na+ accumulation supported by ATP hydrolysis as well as by NADH oxidation. It is concluded that there is an electrogenic DCCD-sensitive Na+-ATPase in the cytoplasmic membrane of V. alginolyticus.
CONSTANT PRESSURE MD SIMULATION METHOD (2004)

Abstract By introducing an anisotropic factor in the cell dynamics of constant pressure molecular dynamics simulations, we dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under hydrostatic pressure. The method is especially effective for anisotropic liquids, such as smectic liquid crystals and membranes, however it can also be used for crystals and isotropic liquid as well. Crystal-smectic-nematicisotropic phase transitions in systems of soft spherocylinders are observed. Keywords: crystal-smectic phase transitionmolecular dynamics simulationsmectic-nematic phase transition
Assembly and Organization Processes in DNA-Directed Colloidal Crystallization* (2020)

We present an analysis of the key steps involved in the DNA-directed assembly of nanoparticles into crystallites and polycrystalline aggregates. Additionally, the rate of crystal growth as a function of increased DNA linker length, solution temperature, and self-complementary versus non-self-complementary DNA linker strands (1- versus 2-component systems) has been studied. The data show that the crystals grow via a 3-step process: an initial “random binding’’ phase resulting in disordered DNA-AuNP aggregates,940followed by localized reorganization and subsequent growth of crystalline domain size, where the resulting crystals are well-ordered at all subsequent stages of growth.
Clinical Development of Gamitrinib, a Novel Mitochondrial-Targeted Small Molecule Hsp90 Inhibitor (2014)

Abstract : The past funding cycle of the above-referenced award has supported important advances in each of the milestones and specific tasks set forth in the original SOW. Work carried out during the last budget period focused on three experimental directions towards the accomplishments of the original specific aims. First, considerable progress has been made in the full preclinical characterization of Gamitrinib in anticipation of IND filing and human testing. Specifically, ADME (adsorption, distribution, metabolism and excretion)studies and a complete plasma distribution and pharmacokinetics profile of Gamitrinib in rats have been obtained. Second, we expanded the safety characterization of Gamitrinib in vitro and in vivo, and completed a non-GLP, 7 day repeated-dose study of Gamitrinib intravenous administration to Sprague-Dawley rats and Beagle dogs. These studies demonstrated encouraging drug-like properties and a favorable safety profile for Gamitrinib in vivo, with no systemic or organ toxicity in two animal species. Third, molecular studies have been carried out to further the characterization of Gamitrinib mechanism of action, antitumor efficacy in combination regimens, and the underlying role of its target, namely mitochondrial protein folding quality control in tumor progression. Supported by the present award and published in the premiere, peer-reviewed literature (JCI, PLOS Biol and Cancer Cell), these studies further validated the role of mitochondrial Hsp90sas important therapeutic targets in cancer, and established Gamitrinib as a first-in-class, subcellularly-directed anticancer agent.