gebhart/patrepeval huggingface dataset:
Computational Study of the Human Dystrophin Repeats: Interaction Properties and Molecular Dynamics (2011)

Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD). It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.
On the Origin of Pulse Shaping Control of Molecular Dynamics (2001)

Pulsed laser control of photodissociation in the strong and the weak coupling regimes is analyzed. Simple pulse shaping conditions are derived and are given explicitly in the weak coupling regime. Implicit equations in the strong coupling regime are also derived. Short, shaped pulses, yielding optimal control, are shown to work due to quantum interference among routes to the same final energy. This is contrary to the prevailing view that the role of a short pulse is to be fast enough so as to “beat the process of intramolecular vibrational redistribution (IVR)”.
NK CELL RECOGNITION (2004)

The integrated processing of signals transduced by activating and inhibitory cell surface receptors regulates NK cell effector functions. Here, I review the structure, function, and ligand specificity of the receptors responsible for NK cell recognition.
Vascular endothelial growth factor as a marker of tumor endothelium. (1998)

Vascular endothelial growth factor (VEGF) is an angiogenic growth factor that is a primary stimulant of the vascularization of solid tumors. VEGF production is induced by oncogenic gene mutations in the tumor cells and by hypoxic conditions inside the tumor mass. Hypoxia and the locally increased concentration of VEGF lead to an up-regulation of VEGF receptor expression on tumor endothelial cells. Therefore, in the tumor microenvironment, there is an up-regulation of both VEGF and its receptor, leading to a high concentration of occupied receptor on tumor vascular endothelium. The VEGF:receptor complex presents an attractive target for the specific delivery of drugs or other effectors to tumor endothelium. In the present study, several hybridomas that secrete monoclonal antibodies against the VEGF:receptor (Flk-1) complex or against VEGF itself have been raised. Three of the antibodies (3E7, GV39M, and 11B5) bind with high affinity to the VEGF:Flk-1 complex in ELISA and to tumor endothelium in frozen sections of human tumors, rodent tumors, and human tumor xenografts. 3E7 and GV39M localize selectively to tumor endothelium after i.v. injection into mice bearing human tumor xenografts. Additionally, one antibody (2C3) was raised that blocks the interaction between VEGF and KDR/Flk-1. 2C3 inhibits VEGF-mediated growth of endothelial cells in vitro and localizes strongly to connective tissue in tumors after injection into mice bearing human tumor xenografts. These findings suggest that 3E7, GV39M, and 2C3 are candidates for targeting and imaging the vasculature or connective tissue of tumors.
“Raisin Bun”-Type Composite Spheres of Silica and Semiconductor Nanocrystals (2000)

CdTe nanocrystals capped with 1-mercapto-2,3-propandiol, CdSe nanocrystals capped with sodium citrate, and core−shell CdSe/CdS nanocrystals capped with sodium citrate were synthesized in aqueous solutions, and their surface was modified by 3-mercaptopropyltrimethoxysilane (MPS) in water−ethanol mixtures. By addition of sodium silicate, “raisin bun”-type composite particles were formed, with either CdTe, CdSe, or CdSe/CdS nanocrystals being homogeneously incorporated as multiple cores into silica spheres of 40−80 nm size, accompanied by some alteration of optical properties of the nanoparticles and, in particular, the reduction of the luminescence quantum yield. Further, growth of larger silica spheres (100−700 nm) can be performed by the Stöber technique using either MPS-modified semiconductor nanocrystals or “raisin bun”-type composite particles as seeds, which gives semiconductor-doped silica globules of desirable sizes in the submicrometer range. The composite spheres can be used as building blocks for 3D colloidal crystals, prepared in this study for CdS/CdSe-doped 250 nm silica colloid. The shift of the photonic band gap to the red was observed in photonic crystals made of nanoparticles-doped silica due to the high refractive index of the semiconductors.
Iterative Oxazole Assembly via α‐Chloroglycinates: Total Synthesis of (−)‐Muscoride A (2003)

An efficient iterative synthesis of oxazoles involves the cyclization of 2-alkynyl glycinates (see scheme) formed from the reaction of 1-alkynyl aluminum reagents with α-chloroglycinates. This approach was used in the total synthesis of the bisoxazole natural product, (−)-muscoride A.
Heterogeneity of apolipoprotein B: isolation of a new species from human chylomicrons. (1980)

Low density lipoproteins and the triglyceride-rich lipoproteins of human serum each contain proteins of high molecular weight termed apolipoprotein B, which have previously been thought to be identical. We have isolated four species of apolipoprotein B with unique molecular weights and amino acid compositions. We have assigned numerical designations to these species in a centile system based upon their relative apparent Mr in NaDodSO4. One which we term B-100, with an apparent Mr of 549,000 +/- 7650 (SD) determined by NaDodSO4 gel electrophoresis, predominates in low density and very low density lipoproteins and is also present in chylomicrons from thoracic duct lymph or from plasma. Substantial amounts of two large proteins designated B-74 (apparent Mr 407,000 +/- 5790) and B-26 (apparent Mr 144,500 +/- 8970), which appear to be complementary fragments or constituents of the B-100 protein, are found in the low density lipoproteins of many individuals. A distinct protein, B-48, with an apparent Mr of 264,000 +/- 8150 is a major and constant constituent of chylomicrons from thoracic duct lymph or from plasma.
Multispectral texture characterization: application to computer aided diagnosis on prostatic tissue images (2012)

Abstract Various approaches have been proposed in the literature for texture characterization of images. Some of them are based on statistical properties, others on fractal measures and some more on multi-resolution analysis. Basically, these approaches have been applied on mono-band images. However, most of them have been extended by including the additional information between spectral bands to deal with multi-band texture images. In this article, we investigate the problem of texture characterization for multi-band images. Therefore, we aim to add spectral information to classical texture analysis methods that only treat gray-level spatial variations. To achieve this goal, we propose a spatial and spectral gray level dependence method (SSGLDM) in order to extend the concept of gray level co-occurrence matrix (GLCM) by assuming the presence of texture joint information between spectral bands. Thus, we propose new multi-dimensional functions for estimating the second-order joint conditional probability density of spectral vectors. Theses functions can be represented in structure form which can help us to compute the occurrences while keeping the corresponding components of spectral vectors. In addition, new texture features measurements related to (SSGLDM) which define the multi-spectral image properties are proposed. Extensive experiments have been carried out on 624 textured multi-spectral images for use in prostate cancer diagnosis and quantitative results showed the efficiency of this method compared to the GLCM. The results indicate a significant improvement in terms of global accuracy rate. Thus, the proposed approach can provide clinically useful information for discriminating pathological tissue from healthy tissue.
Surgery with molecular fluorescence imaging using activatable cell-penetrating peptides decreases residual cancer and improves survival (2010)

The completeness of tumor removal during surgery is dependent on the surgeon’s ability to differentiate tumor from normal tissue using subjective criteria that are not easily quantifiable. A way to objectively assess tumor margins during surgery in patients would be of great value. We have developed a method to visualize tumors during surgery using activatable cell-penetrating peptides (ACPPs), in which the fluorescently labeled, polycationic cell-penetrating peptide (CPP) is coupled via a cleavable linker to a neutralizing peptide. Upon exposure to proteases characteristic of tumor tissue, the linker is cleaved, dissociating the inhibitory peptide and allowing the CPP to bind to and enter tumor cells. In mice, xenografts stably transfected with green fluorescent protein show colocalization with the Cy5-labeled ACPPs. In the same mouse models, Cy5-labeled free ACPPs and ACPPs conjugated to dendrimers (ACPPDs) delineate the margin between tumor and adjacent tissue, resulting in improved precision of tumor resection. Surgery guided by ACPPD resulted in fewer residual cancer cells left in the animal after surgery as measured by Alu PCR. A single injection of ACPPD dually labeled with Cy5 and gadolinium chelates enabled preoperative whole-body tumor detection by MRI, intraoperative guidance by real-time fluorescence, intraoperative histological analysis of margin status by fluorescence, and postoperative MRI tumor quantification. Animals whose tumors were resected with ACPPD guidance had better long-term tumor-free survival and overall survival than animals whose tumors were resected with traditional bright-field illumination only.
Rapid production of ultralong amorphous ceramic nanofibers by laser spinning (2007)

Amorphous nanofibers of several centimeters in length can be grown in microseconds during laser cutting of ceramics if a supersonic gas jet is used to clear the cut edge. Such rapid growth is not achievable with vapor phase or solution based methods. Instead, the growth mechanism involves elongation of very small volumes of molten ceramic by frictional drag action of the gas jet. Analysis of the elongation process shows that rapid elongation and cooling are essential to prevent surface tension causing spheroid formation. Using a modified geometry, the process can be adapted to produce near-continuous nanofibers with tailored compositions.
Sepsis in an aging population* (2005)

Division of Pulmonary and, Critical Care Medicine, Department of Medicine, UMDNJ-Robert Wood, Johnson Medical School, New Brunswick, NJ Dr. Paz received advisory board and consultancy fees from Johnson and Johnson from 2002 to 2004. Dr. Martin has no financial interests to disclose.
Mutual relationships between soils and biological carrier systems (2005)

Improved viability and antagonistic activity of biocontrol agents during soil inoculation is of crucial importance to their effective application. The chitinolytic bacterium Serratia marcescens was used as a model organism to study the efficacy of freeze-dried alginate beads (in comparison to their non-dried counterparts) as possible carriers for immobilized biocontrol agents. The release of bacteria and chitinolytic enzyme from alginate beads, before and during their application in soil, was examined, and the beads' physical properties characterized. Dispersal of the alginate bead-entrapped S. marcescens in the soil resulted in high soil cell densities throughout the 35 days of the experiment. Chitin inclusion in the beads resulted in significantly higher chitinolytic activity of S. marcescens, increased dry-bead porosity and decreased stiffness. Rehydration of the dried beads (after immersion in soil) resulted in a sixfold increase in weight due to water absorption. No significant differences were found in bacterial count inside the non-dried (gel) versus dried beads. However, higher cell densities and chitinase activity were detected in soil containing dried beads with chitin than in that containing their non-dried counterparts. The biological performance of S. marcescens was examined in the greenhouse: a free cell suspension reduced bean (Phaseolus vulgaris L.) disease by 10%, while immobilized bacteria found in the dried, chitin-containing beads reduced disease by 60%.
Infrared imaging with a wavefront-coded singlet lens (2009)

We describe the use of wavefront coding for the mitigation of optical aberrations in a thermal imaging system. Diffraction-limited imaging is demonstrated with a simple singlet which enables an approximate halving in length and mass of the optical system compared to an equivalent two-element lens.
Electronic linearization of piezoelectric actuators and noise budget in scanning probe microscopy (2006)

The maximum resolution achievable with a scanning probe microscope is limited by the probe size, by the mechanism of interaction with the sample, as is widely known, and by the electronic noise in the instrument. The evaluation of this noise for the three motion axes of a linearized high resolution scanning electrochemical microscope has been carried through and the intrinsic maximum resolution is discussed.
An Efficient Probabilistic Context-Free Parsing Algorithm that Computes Prefix Probabilities (1994)

We describe an extension of Earley's parser for stochastic context-free grammars that computes the following quantities given a stochastic context-free grammar and an input string: a) probabilities of successive prefixes being generated by the grammar; b) probabilities of substrings being generated by the nonterminals, including the entire string being generated by the grammar; c) most likely (Viterbi) parse of the string; d) posterior expected number of applications of each grammar production, as required for reestimating rule probabilities. (a) and (b) are computed incrementally in a single left-to-right pass over the input. Our algorithm compares favorably to standard bottom-up parsing methods for SCFGs in that it works efficiently on sparse grammars by making use of Earley's top-down control structure. It can process any context-free rule format without conversion to some normal form, and combines computations for (a) through (d) in a single algorithm. Finally, the algorithm has simple extensions for processing partially bracketed inputs, and for finding partial parses and their likelihoods on ungrammatical inputs.
The stimulation of pp60v-src kinase activity by vanadate in intact cells accompanies a new phosphorylation state of the enzyme. (1984)

We have observed that intact wild type Rous sarcoma virus-transformed chicken embryo fibroblasts (CEF), when incubated with micromolar sodium orthovanadate for as little as 4 h, results in a 2-3-fold increase in pp60v-src kinase activity as judged by the IgG kinase assay. The addition of sodium vanadate or vanadyl sulfate to transformed cell lysates or the immunoprecipitate assay was without effect on the activity of isolated pp60v-src kinase activity. The increased kinase activity is reflected intracellularly by an increased phosphotyrosine content of a known substrate of pp60v-src, a 36-kDa phosphoprotein, without a change in total phosphate incorporation into cellular proteins. Pulse and pulse-chase experiments with [35S]methionine indicated that there was no change in the net or rate of biosynthesis of pp60v-src which might have accounted for the elevated kinase activity. Along with this stimulation of pp60v-src kinase activity, we found a parallel increase in the phosphate content of the enzyme and the appearance of an electrophoretic variant after vanadate treatment. The increased phosphorylation of the kinase is accounted for by an increase in phosphotyrosine content without a change in phosphoserine content. The increased phosphotyrosine content is shown to be resident in the carboxyl-terminal fragment and, unexpectedly, in the amino-terminal fragment of the kinase. The phosphotyrosine present in the amino-terminal portion may be a de novo phosphorylation, but could also represent a tyrosine site(s) not easily detected under unstimulated conditions in the absence of vanadate.
Beneficial Effects of Vitamin E Treatment in Acute Myocardial Infarction (2000)

These results indicate that Vit E may exert beneficial effects on the heart by reducing oxidative stress in acute myocardial infarction.
Chemical synthesis and sequence studies of deoxyribooligonucleotides which constitute the duplex sequence of the lactose operator of Escherichia coli. (1975)

We have synthesized the deoxyribooligonucleotide fragments, constituting the sequence of the lac operator of Escherichia coli. Two of these fragments, d(pApApTpTpGpTpTpApT) (nonamer) and d(pApApTpTpGpTpGpApG) (nonamer), corresponding to the 5' termini of lac operator have been synthesized by the phosphodiester method. The remaining four fragments, d(ApCpApApTpT) (hexamer), d(ApTpApApCpApApTpT) (nonamer), d(ApApTpTpGpTpGpApGpCpGpG) (dodecamer), and d(ApApTpTpGpTpTpApTpCpCpGpCpTpC) (pentadecamer), have been synthesized by an improved phosphotriester method. All of the compounds were first characterized by venom and spleen phosphodiesterase digestion to obtain their base composition. The sequence of these oligonucleotides was fully confirmed by the characteristic mobility shifts of their partial venom phosphodiesterase digestion products on two-dimensional homochromatography. A comparative study of the two methods for the synthesis of oligonucleotides has revealed that the phosphotriester method is more convenient than the phosphodiester method because of higher yields and ease of handling large scale preparations.
Improved tumor targeting of anti–epidermal growth factor receptor Nanobodies through albumin binding: taking advantage of modular Nanobody technology (2008)

The approximately 15-kDa variable domains of camelid heavy-chain-only antibodies (called Nanobodies) can easily be formatted as multivalent or multispecific single-chain proteins. Because of fast excretion, however, they are less suitable for therapy of cancer. In this study, we aimed for improved tumor targeting of a bivalent anti-epidermal growth factor receptor (EGFR) Nanobody (alphaEGFR-alphaEGFR) by fusion to a Nanobody unit binding to albumin (alphaAlb). Biodistributions of alphaEGFR-alphaEGFR, alphaEGFR-alphaEGFR-alphaAlb ( approximately 50 kDa), alphaTNF-alphaTNF-alphaAlb (control, binding tumor necrosis factor-alpha), and the approximately 150-kDa anti-EGFR antibody cetuximab were compared in A431 xenograft-bearing mice. The proteins were radiolabeled with (177)Lu to facilitate quantification. Tumor uptake of (177)Lu-alphaEGFR-alphaEGFR decreased from 5.0 +/- 1.4 to 1.1 +/- 0.1 %ID/g between 6 and 72 h after injection. Due to its rapid blood clearance, tumor-to-blood ratios >80 were obtained within 6 h after injection. Blood clearance became dramatically slower and tumor uptake became significantly higher by introduction of alphaAlb. Blood levels of alphaEGFR-alphaEGFR-alphaAlb were 21.2 +/- 2.5, 11.9 +/- 0.6, and 4.0 +/- 1.4 and tumor levels were 19.4 +/- 5.5, 35.2 +/- 7.5, and 28.0 +/- 6.8 %ID/g at 6, 24, and 72 h after injection, respectively. Tumor uptake was at least as high as for cetuximab (15.5 +/- 3.9, 27.1 +/- 7.9, and 25.6 +/- 6.1 %ID/g) and significantly higher than for alphaTNF-alphaTNF-alphaAlb. alphaEGFR-alphaEGFR-alphaAlb showed faster and deeper tumor penetration than cetuximab. These data show that simple fusion of alphaEGFR and alphaAlb building blocks results in a bifunctional Nanobody format, which seems more favorable for therapy as far as pharmacokinetics and tumor deposition are concerned.
Soft-materials elastic and shear moduli measurement using piezoelectric cantilevers (2005)

We have developed a soft-material elastic modulus and shear modulus sensor using piezoelectric cantilevers. A piezoelectric cantilever is consisted of a highly piezoelectric layer, e.g., lead–zirconate–titanate bonded to a nonpiezoelectric layer, e.g., stainless steel. Applying an electric field in the thickness direction causes a piezoelectric cantilever to bend, generating an axial displacement or force. When a piezoelectric cantilever is in contact with an object, this electric field-generated axial displacement is reduced due to the resistance by the object. With a proper design of the piezoelectric cantilever’s geometry, its axial displacements with and without contacting the object could be accurately measured. From these measurements the elastic modulus of the object can be deduced. In this study, we tailored the piezoelectric cantilevers for measuring the elastic and shear moduli of tissue-like soft materials with forces in the submilli Newton to milliNewton range. Elastic moduli and shear moduli of soft materials were measured using piezoelectric cantilevers with a straight tip and an L-shaped tip, respectively. Using gelatin and commercial rubber material as model soft tissues, we showed that a piezoelectric cantilever 1.5–2cm long could measure the elastic modulus and the shear modulus of a small soft material sample (1–3mm wide) in the small strain range (&amp;lt;1%). For samples 5mm high, the resultant compressive (shear) strains were less than 0.5% (1%). The measurements were validated by (1) comparing the measured Young’s modulus of the commercial rubber sample with its known value and (2) by measuring both the Young’s modulus and shear modulus on the samples and confirming the thus deduced Poisson’s ratios with the separately measured Poisson’s ratios.
The detection of Salmonella in skimmed milk powder enrichments using conventional methods and immunomagnetic separation (1995)

Skimmed milk powders were spiked with one of three Salmonella serovars and incubated in buffered peptone water for 24 h. No false-negative results were obtained by immunomagnetic separation (IMS), compared to seven for selenite cysteine, one for Müller-Kauffmann tetrathionate and two for Rappaport-Vassiliadis enrichment broths. Salmonella virchow was detected and enumerated during the pre-enrichment incubation by IMS and indirect conductance techniques. The Salm. virchow cell number did not increase after 12 h incubation and remained at 3 x 10(6) cfu ml-1. IMS was able to capture Salm. virchow cells at cell numbers ca 50 ml-1 in the presence of a 1000 greater number of non-salmonella cells.