gebhart/patrepeval huggingface dataset:
Osteoclasts express high levels of p60<sup>c‐<i>src</i></sup>, preferentially on ruffled border membranes (1992)

Expression of p60c-src, the normal cellular counterpart of the transforming protein of Rous sarcoma virus (RSV), p60v-src, was examined in mouse and rat authentic osteoclasts and mouse osteoclast-like multinucleated cells (MNCs) formed in vitro. In co-cultures of mouse osteoblastic cells and spleen cells, the expression of p60c-src strikingly increased on day 5 in parallel with the appearance of MNCs in the presence of 1 alpha,25-dihydroxyvitamin D3 (1 alpha,25(OH)2D3). Immunohistochemical examination confirmed the high level expression of p60c-src in both mouse authentic osteoclasts and MNCs. Electron microscopic examination revealed that p60c-src was primarily localized on ruffled border membranes and vacuoles, but not on the clear zone in rat authentic osteoclasts. These results suggest that p60c-src is important in osteoclastic bone resorption.
Image spaces and video trajectories: using Isomap to explore video sequences (2003)

Dimensionality reduction techniques seek to represent a set of images as a set of points in a low dimensional space. Here we explore a video representation that considers a video as two parts - a space of possible images and a trajectory through that space. The non-linear dimensionality reduction technique of Isomap, gives, for many interesting scenes, a very low dimensional representation of the space of possible images. Analysis of the shape of the video trajectory through these image spaces gives new tools for video analysis. Experiments with natural video sequences illustrate methods for the very different tasks of classifying video clips and temporal super-resolution.
Relation between Aneurysm Volume, Packing, and Compaction in 145 Cerebral Aneurysms Treated with Coils (2004)

The common practice of inserting as many coils as possible in cerebral aneurysms is sensible in trying to avoid compaction. In aneurysms with packing of 24% or more, no compaction occurred at 6-month angiographic follow-up. In aneurysms with a volume of more than 600 mm(3), high packing could not be achieved, which resulted in compaction in the majority of aneurysms.
A Novel Coordination Polymer as Positive Electrode Material for Lithium Ion Battery (2007)

A new coordination polymer based on an aromatic carbonyl ligand is prepared and investigated as a positive active material for lithium ion batteries, namely, [Li2(C6H2O4)] (1). It is synthesized by the dehydration of [Li2(C6H2O4)·2H2O] (2). These compounds are characterized by Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), elemental analysis (EA), single crystal X-ray diffraction methods and powder X-ray diffraction (XRD). As positive material, compound 1 has an initial discharge capacity of 176 mAh·g−1 and a columbic efficiency of 93.18% in the first cycle. It might provide a new method for finding new positive-electrode materials in lithium ion batteries.
Multiple alignment using hidden Markov models. (1995)

A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the performance of other HMM training methods and the ClustalW program. Simulated annealing is better able to find near-global optima in the multiple alignment probability landscape than the other tested HMM training methods. Neither ClustalW nor simulated annealing produce consistently better alignments compared to each other. Examination of the specific cases in which ClustalW outperforms simulated annealing, and vice versa, provides insight into the strengths and weaknesses of current hidden Markov model approaches.
Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data (2011)

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.
New Polymers for Special Applications (2012)

This book comprises the contributions of several authors in the area of polymer physics by application of conducting polymers; hydrogel films on optical fiber core; thin film polymers; PDLC films application; photopolymers for holographic media; microwave absorption and EMI shielding behavior of nanocomposites based on intrinsically conducting polymers and graphene and carbon nanotubes; in the area of polymer synthesis of conducting polymers; oxidative polymerization of aniline; electro reductive polymerization; polysilanes with ordered sequences; radiation cross-linking poly(urethane-imide) and nitrogen-rich polymers as candidates for energetic applications; development of ruthenium complexes to novel functional nanocomposites. We hope that this book will help inspire readers to pursue study and research in this field.
Novel method for genomic analysis of<i>PKD1</i>and<i>PKD2</i>mutations in autosomal dominant polycystic kidney disease (2008)

Genetic testing of PKD1 and PKD2 is useful for diagnosis and prognosis of autosomal dominant polycystic kidney disease (ADPKD), particularly in asymptomatic individuals or those without a family history. PKD1 testing is complicated by the large transcript size, complexity of the gene region, and the extent of gene variations. A molecular assay was developed using Transgenomic's SURVEYOR Nuclease and WAVE Nucleic Acid High Sensitivity Fragment Analysis System to screen for PKD1 and PKD2 variants, followed by sequencing of variant gene segments, thereby reducing the sequencing reactions by 80%. This method was compared to complete DNA sequencing performed by a reference laboratory for 25 ADPKD patients from 22 families. The pathogenic potential of gene variations of unknown significance was examined by evolutionary comparison, effects of amino acid substitutions on protein structure, and effects of splice-site alterations. A total of 90 variations were identified, including all 82 reported by the reference laboratory (100% sensitivity). A total of 76 variations (84.4%) were in PKD1 and 14 (15.6%) in PKD2. Definite pathogenic mutations (seven nonsense, four truncation, and three splicing defects) were detected in 64% (14/22) of families. The remaining 76 variants included 26 missense, 33 silent, and 17 intronic changes. Two heterozygous nonsense mutations were incorrectly determined by the reference laboratory as homozygous. "Probably pathogenic" mutations were identified in an additional five families (overall detection rate 86%). In conclusion, the SURVEYOR nuclease method was comparable to direct sequencing for detecting ADPKD mutations, achieving high sensitivity with lower cost, providing an important tool for genetic analysis of complex genes.
Photothermal Heating of Plasmonic Nanoantennas: Influence on Trapped Particle Dynamics and Colloid Distribution (2018)

Plasmonic antennas are well-known and extremely powerful platforms for optical spectroscopy, sensing, and manipulation of molecules and nanoparticles. However, resistive antenna losses, resulting in highly localized photothermal heat generation, may significantly compromise their applicability. Here we investigate how the interplay between plasmon-enhanced optical and thermal forces affects the dynamics of nanocolloids diffusing in close proximity to gold bowtie nanoantennas. The study is based on an anti-Stokes thermometry technique that can measure the internal antenna temperature with an accuracy of ∼5 K over an extended temperature range. We argue that Kapitza resistances have a significant impact on the local thermal landscape, causing an interface temperature discontinuity of up to ∼20% of the total photothermal temperature increase of the antenna studied. We then use the bowties as plasmonic optical tweezers and quantify how the antenna temperature influences the motion and distribution of nearby fluorescent colloids. We find that colloidal particle motion within the plasmonic trap is primarily dictated by a competition between enhanced optical forces and enhanced heating, resulting in a surprising insensitivity to the specific resonance properties of the antenna. Furthermore, we find that thermophoretic forces inhibit diffusion of particles toward the antenna and drive the formation of a thermal depletion shell that extends several microns. The study highlights the importance of thermal management at the nanoscale and points to both neglected problems and new opportunities associated with plasmonic photothermal effects in the context of nanoscale manipulation and analysis.
Preparing Libraries in Saccharomyces cerevisiae (2003)

High recombination frequency and ease of manipulation made the budding yeast, Saccharomyces cerevisiae, the model eukaryotic organism for studies on homologous recombination (1,2). Mutagenesis of intrinsic genes (3) and the construction of vectors (4) are applications of in vivo recombination in molecular biology. Next to Escherichia coli, S. cerevisiae is the most commonly used host organism in directed evolution (5–9). Its well developed recombination apparatus facilitates mutant library construction. Ligation of mutant genes into expression vectors is in many cases a tedious and non-robust step that needs fine tuning for new plasmid-gene combinations. Yeast gap repair can substitute for ligation to give more reliable high transformation frequency and shortening the protocol for library expression. In gap repair, the mutant gene inserts are cotransformed with open plasmid that contains sequences homologous to the ends of the inserts on both ends. Homologous recombination combines these to form complete plasmids.
Antihistamine use and breast cancer risk (2003)

Antihistamines are structurally similar to DPPE, a tamoxifen derivative known to promote tumor growth, and to antidepressants. Animal experiments have linked certain antihistamines and antidepressants with enhanced tumor growth in mice. The few epidemiologic studies examining antihistamine use have not indicated an increased risk. In light of suggestive animal data, structural similarities between antihistamines and DPPE, the widespread use of antihistamines, and the lack of epidemiologic investigation into their use and breast cancer risk, it is important to examine this issue. Female cases aged 25-74 years, diagnosed 1996 to 1998, were identified through the Ontario Cancer Registry. Controls were a random, age-matched sample of women. Cases (n=3,133) and controls (n=3,062) completed a mailed questionnaire that included questions about antihistamines used regularly (undefined), type and duration. Age-adjusted odds ratio (OR) estimates and 95% confidence intervals (CIs) were obtained using logistic regression. Antihistamine users were at no increased risk for breast cancer (OR=0.93, 95% CI: 0.81, 1.06), and no trend in risk was observed for age starting or duration of use. Antihistamine users were at no increased risk. No confounding or effect modification was identified in multivariate modeling. Our findings do not support the hypothesis that women who use antihistamines are at a greater breast cancer risk than those who do not.
Mediator join indices (2002)

A mediator join index (MJI) is proposed to speed up N-way inter-database joins by reducing the amount of data transfer during evaluation. A family of algorithms, the query scrubbing algorithms (QSA), are developed to maintain MJI and to evaluate queries using MJI. QSA algorithms use query scrubbing to cope with update and query anomalies related to materialized views in the mediator context. Compared with existing algorithms, QSA algorithms incur less overhead in handling the anomalies and makes MJI a promising technique for efficient mediator query processing.
Dynamics of biofilm processes (1979)

Biofilms can develop on almost any surface exposed to an aqueous environment. The biofilm systems that result can be used beneficially, as exemplified by fixed-film wastewater treatment processes (for example, trickling filters and rotating biological contactors). In addition, biofilms play a major positive role in stream purification processes. However, biofilms can be quite troublesome in certain engineering systems. In water distribution systems and heat transfer equipment, for example, biofilms can cause substantial energy losses resulting from increased fluid frictional resistance and increased heat transfer resistance. The significance of biofilm development on various processes is summarized.
Binding and Invasion of Liver Cells by Plasmodium falciparum Sporozoites (2002)

Plasmodium sporozoites display circumsporozoite (CS) protein on their surface, which is involved in the attachment of sporozoites to liver cells. CS protein is a member of the thrombospondin type I repeat (TSR) domain family and possess a single copy of TSR domain toward its carboxyl terminus. We show by a direct measurement the correlation between the binding activity of various segments of the CS protein and their ability to inhibit the invasion of liver cells by the sporozoites. We made eight truncated versions of Plasmodium falciparum CS protein to elucidate the role of various regions in the binding and invasion process. Deletion of the TSR domain actually enhanced binding activity by 2-3-fold without the loss of receptor specificity, indicating that TSR may not be the only domain in defining the specificity of binding. These same deletions blocked invasion of live sporozoites more efficiently than proteins that include the TSR domain. Deletion of as little as six amino acids from amino terminus of the protein, however, renders it incapable of binding to liver cells and as an inhibitor of sporozoite invasion. Hence, the binding of CS protein to liver cells and its ability to inhibit the invasion process are affected in a parallel manner, both positively and negatively, by sequence changes in the encoded CS gene. This indicates that both assays are measuring interrelated phenomenon and points to the essential involvement for the amino-terminal portion of the CS protein in these processes.
Complications induced by decompressive craniectomies after traumatic brain injury. (2003)

To reduce the incidence of iatrogenic side effects, surgical craniectomy should be performed according to the strict indication and standard and any abuse should be avoided.
The influences of O<sub>3</sub>reaction on physico‐chemical characteristics of activated carbon for benzene adsorption (1995)

Volatile organic compounds (VOCs) emitted from industrial manufacturing processes are commonly controlled by combustion and condensation methods: however, the most promising method is through adsorption by activated carbon. Ozone is used to oxidize activated carbon thus increasing the specific surface area, pore volume, and functional groups. As the results indicate, the specific surface area of activated carbon was increased from 783 m2/g to 851 m2/g. Pore size distribution analysis found the specific surface area on the activated carbon increases mainly at micropores. Oxygen functional group increases from 196 ueq/g to 240 ueq/g after ozone treatment. The adsorption capacity of benzene on activated carbon (AC) and on oxidized activated carbon (AO3) at various temperatures was decreased from 268 mg/g (10°C) to 179 mg/g(120°C) at AC and from 262 mg/g to 158 mg/g, at the same respective temperatures, for AO3. The results show that reaction temperature has a greater effect on AO3 than on AC. According to factor analysis and correspondence analysis, we found physical characteristics (BET surface area and micropore area) on the AC could consider as the major factor affecting the adsorption rate.
Stimulated Emission and Absorption near Resonance for Driven Systems (1972)

The rate of absorption of energy from a weak signal field by an atom driven by a strong pump field is evaluated. The pump field and the signal field are assumed to induce transitions between the same pair of states, and their frequencies are both assumed to lie near the atomic resonance frequency for the transition in question. We find that the signal-field absorption line-shape function takes on negative values, representing stimulated emission rather than absorption, even though population inversion does not occur. This amplification of the signal field, which is most pronounced at high pump intensities, is shown to occur primarily at the expense of the pump field, which suffers an increased rate of attenuation. The results are discussed in the context of a theorem which expresses the absorption line-shape function for general atomic systems in terms of a suitable atomic correlation function.
Porphyrin Monolayer-Modified Gold Clusters as Photoactive Materials (2001)

Porphyrin monolayer-modified gold clusters (three-dimensional system) have been prepared successfully. Their electrochemical and photophysical properties have been compared to those of the corresponding two-dimensional system of self-assembled monolayers (SAMs) of the porphyrin as well as the bis(porphyrin) disulfide reference in solutions. In particular, the time-resolved single-photon counting fluorescence studies have indicated that the undesirable quenching of the porphyrin excited singlet state via energy transfer to the gold surface of the three-dimensional system is much suppressed, as compared to the quenching of the porphyrin SAMs on the two-dimensional flat gold surface. Thus, the present systems have a variety of potential utility for development of the artificial photosynthetic materials, photocatalysts, and chemical and biochemical sensors using fluorescent chromophore-monolayer modified gold clusters.
ONE STEP FORWARD, TWO STEPS BACK? : THE DEBATE OVER RIGHT OF ESTABLISHMENT GOES ON - AND ON - BUT PROGRESS IS MEASURED IN INCHES (2003)

Right of establishment (RoE)is being pushed by advocates of more liberal European aviation markets so that outsider airlines could operate as locals if they follow local requirements. RoE however has several hurdles before it will sweep Europe. First, the European Court of Justice ruled that the European Commission does not have the authority to represent EU members in talks with the U.S. It also said that crucial elements of existing open skies agreements with U.S. violate EU law, crippling bilateralism. That was further exacerbated when a transport commissioner called on EU members to void their open skies agreements rather than wait for court challenges to complete. If RoE fails, other options exist. They include seventh freedom flights, which allow airlines designated by one country to fly between a second country and the U.S. as long as it didn't carry homeland traffic. But if those agreements disproportionately benefit alliance members, the court could void the agreements. Discussions and debates over how and if to open European markets will continue.
Molecular modes of action of cantharidin in tumor cells. (2004)

2020 Cantharidin (CAN), a compound derived from Lytta vesicatoria reveals profound cytotoxicity against tumor cells. We investigated molecular mechanisms that determine the cellular response to CAN. Alkaline and neutral comet assays showed that CAN induces DNA single and double-strand breaks that were repaired in a dose- and concentration-dependent manner. Cell lines harboring endogeneous wild-type (CHO-9), mutant (43-3B), or wild-type transfected ERCC1 (43-3B/ERCC1) were, however, similar sensitive to CAN indicating that the nucleotide excision repair pathway is not responsible for repair of CAN-induced DNA damage. CAN was less active in WTK1 lymphoblastoid cells with mutated p53 than in TK1 lymphoblastoid cells expressing wild-type p53. Multidrug-resistant MDR1-expressing CEM/ADR5000 cells did not exhibit cross-resistance to CAN as compared to drug-sensitive parental cells. The IC50 values for CAN did not correlate with the mRNA expression of the MDR1 gene in 60 cell lines of the National Cancer Institute (N.C.I.) indicating no role of the MDR-phenotype for CAN. Mining the microarray database of the NCI by standard and reverse COMPARE analyses provided 50 out of 9706 genes whose mRNA expression correlated with IC50 values for CAN in the NCI cell line panel. If the mRNA expression of the 50 genes was subjected to hierarchical cluster analysis, sensitivity or resistance of the 60 cell lines to CAN could be predicted. The present investigation represents a starting point to dissect the genes and molecular pathways involved in cellular response to CAN in greater detail.
Single Antenna Interference Cancellation for 8PSK Signals in EGPRS (2009)

In this paper, we explore a method for interference suppression in EGPRS (also commonly known as EDGE) systems, wherein 8PSK is used as the modulation for the desired signal and the interferer is modulated using GMSK. Previous methods for single antenna interference cancellation (SAIC) have concentrated on the case when both the desired and interfering signals are GMSK modulated, or have relied on highly complex methods such as joint demodulation. We derive a simple method that exploits the redundancy inherent in the interferer signal to suppress it. The interference suppression method causes a well- modeled nonlinear distortion to the 8PSK signal. This non-linear distortion is handled using a modified equalizer that deals with a time-varying input symbol constellation applied to a matrix channel. Simulation results using the method show great promise.
Reverse Engineering for Industrial-Plant CAD Models (2008)

Industrial-plant CAD models are commonly represented by triangular meshes, which do not preserve original information about implicit surfaces used during design. The reverse-engineering algorithms presented in this paper focus on reconstructing implicit information, recovering original data. We propose two different approaches, a numerical one and an original topological approach. We explore specificities found in CAD meshes to achieve high effectiveness, reconstructing 90% of information from massive models (with millions of triangles) after few minutes of processing.