gebhart/patrepeval huggingface dataset:
Transcript identification by analysis of short sequence tags--influence of tag length, restriction site and transcript database (2003)

There exist a number of gene expression profiling techniques that utilize restriction enzymes for generation of short expressed sequence tags. We have studied how the choice of restriction enzyme influences various characteristics of tags generated in an experiment. We have also investigated various aspects of in silico transcript identification that these profiling methods rely on. First, analysis of 14 248 mRNA sequences derived from the RefSeq transcript database showed that 1-30% of the sequences lack a given restriction enzyme recognition site. Moreover, 1-5% of the transcripts have recognition sites located less than 10 bases from the poly(A) tail. The uniqueness of 10 bp tags lies in the range 90-95%, which increases only slightly with longer tags, due to the existence of closely related transcripts. Furthermore, 3-30% of upstream 10 bp tags are identical to 3' tags, introducing a risk of misclassification if upstream tags are present in a sample. Second, we found that a sequence length of 16-17 bp, including the recognition site, is sufficient for unique transcript identification by BLAST based sequence alignment to the UniGene Human non-redundant database. Third, we constructed a tag-to-gene mapping for UniGene and compared it to an existing mapping database. The mappings agreed to 79-83%, where the selection of representative sequences in the UniGene clusters is the main cause of the disagreement. The results of this study may serve to improve the interpretation of sequence-based expression studies and the design of hybridization arrays, by identifying short tags that have a high reliability and separating them from tags that carry an inherent ambiguity in their capacity to discriminate between genes. To this end, supplementary information in the form of a web companion to this paper is located at http:// biobase.biotech.kth.se/tagseq.
The prospect of laser fusion in the 21st century (2002)

Inertial confinement fusion (ICF) has developed remarkably in the last 30 years. In the 21st century, we can expect fusion energy for civilian use. After the cold war era, the value of ICF has shifted from defense demands to peaceful applications. The megajoule laser systems are under construction expecting the development of spark ignition. However there are many problems to solve in science and technology. One alternative way is to use a petawatt short-pulse laser aiming for fast ignition. On the way to the final goal, we would like to contribute for various applications of high power lasers such as laboratory astrophysics, X-ray lasers, laser-induced lightning as well as laser processing.
Novel Family of Single-Stage Three-Level AC Choppers (2010)

The capacitor-clamped base cell is presented. Based on the base cell, a novel family of single-stage three-level (TL) ac choppers is proposed. The converters can directly transfer unsteady high ac voltage with distortion into regulated sinusoidal voltage with low THD. The circuit configuration is constituted of a TL converter, and input and output filters. The topological family includes buck, boost, buck-boost, Cuk, Sepic, and Zeta modes. In order to achieve a reliable TL ac-ac conversion, a double transient voltage feedback control strategy of output voltage and the voltage across the clamp capacitor is introduced in this paper. A prototype of a 500 VA 220 V ± 10% 50 Hz ac/180-240 V 50 Hz ac converter is presented with the experimental results to prove that the converters have four improved advantages simultaneously, including the lower voltage stress of power switches, the bidirectional power flow, the low total harmonic distortion of output voltage, and the higher input power factor.
Development of a Force and Torque Hybrid Display "GyroCubeStick" (2005)

Multimodal interfaces with the five senses attract a great deal of attention as for the next generation multimedia interface. Especially, the interfaces with additional tactile sensation and force feedback enable us to perform pointing and manipulation operations and navigation operations easily rather than the conventional interfaces without them. The display device using pin array and manipulation arms is the most popular to display tactile sensation and force feedback. The arms and wires restrict user's movement and reachable area around the device base connected to the arms. These devices are relative larger and are not convenient for mobile uses. Therefore, in this paper, a torque and force feedback device of non-grounding and no reaction base on the human body has been developed, which displays the torque of virtual objects and normal and tangential force on the surfaces as the resistance force and tactile sensation.
A statistical sampling algorithm for RNA secondary structure prediction (2003)

An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a representation of the ensemble of probable structures is of interest. We present a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures. The forward step of the algorithm computes the equilibrium partition functions of RNA secondary structures with recent thermodynamic parameters. Using conditional probabilities computed with the partition functions in a recursive sampling process, the backward step of the algorithm quickly generates a statistically representative sample of structures. With cubic run time for the forward step, quadratic run time in the worst case for the sampling step, and quadratic storage, the algorithm is efficient for broad applicability. We demonstrate that, by classifying sampled structures, the algorithm enables a statistical delineation and representation of the Boltzmann ensemble. Applications of the algorithm show that alternative biological structures are revealed through sampling. Statistical sampling provides a means to estimate the probability of any structural motif, with or without constraints. For example, the algorithm enables probability profiling of single-stranded regions in RNA secondary structure. Probability profiling for specific loop types is also illustrated. By overlaying probability profiles, a mutual accessibility plot can be displayed for predicting RNA:RNA interactions. Boltzmann probability-weighted density of states and free energy distributions of sampled structures can be readily computed. We show that a sample of moderate size from the ensemble of an enormous number of possible structures is sufficient to guarantee statistical reproducibility in the estimates of typical sampling statistics. Our applications suggest that the sampling algorithm may be well suited to prediction of mRNA structure and target accessibility. The algorithm is applicable to the rational design of small interfering RNAs (siRNAs), antisense oligonucleotides, and trans-cleaving ribozymes in gene knock-down studies.
Principles and Practice of Biological Mass Spectrometry (2000)

Introduction to Mass Spectrometry. Ionization Methods. Mass Analysis and Ion Detection. Tandem Mass Spectrometry. Molecular Mass Measurement. Quantitative Analysis. Coupling of Separation Techniques with Mass Spectrometry. Structural Analysis of Proteins. Structural Characterization of Peptides. Analysis of Glycoproteins and Oligosaccharides. Folding-Unfolding and Higher-order Structures of Proteins. Investigation of Noncovalent Interactions. Structure Determination of Lipids and Glycolipids. Screening Combinatorial Libraries. Characterization of Oligonucleotides. Applications to Real-World Problems. Index.
T3 monoclonal antibody activation of nonspecific cytolysis: a mechanism of CTL inhibition. (1985)

The T3 antigen is expressed on all cytotoxic T lymphocytes (CTL). Monoclonal antibodies (MAb) to the T3 antigen previously have been shown to inhibit CTL-mediated killing of cells expressing the relevant target antigens. The mechanism of T3 MAb inhibition, however, remains undefined. In this report, we describe a novel effect of the T3 MAb: the stimulation of allospecific CTL clones to kill target cells that do not express the relevant HLA antigens. The stimulation of nonspecific killing was seen only with MAb to the T3 antigen; MAb to other function-associated antigens (e.g., LFA-1, LFA-2, LFA-3, T4, T8, HLA-A,B,C, and DR) had no effect. T3 MAb stimulated nonspecific killing by CTL clones expressing both the T4+ and T8+ phenotype and by CTL clones specific for both class I and class II HLA alloantigens. Target cell susceptibility to T3 MAb stimulated killing was variable. CTL clones lysed some target cell lines very efficiently (e.g., K562, Daudi, and M124.1) but lysed other cell lines much less efficiently (e.g., 23.1, Mann, and L cells). In CTL-mediated cytotoxicity assays with target cells expressing the relevant HLA antigens, T3 MAb demonstrated the expected inhibition of cytolysis. Thus, the ability of T3 MAb to stimulate and inhibit CTL-mediated cytolysis suggests that both effects may be the result of a common mechanism of activation.
Quantifying the development of the peripheral naive CD4+ T-cell pool in humans (2009)

What are the rules that govern a naive T cell's prospects for survival or division after export from the thymus into the periphery? To help address these questions, we combine data from existing studies with robust mathematical models to estimate the absolute contributions of thymopoiesis, peripheral division, and loss or differentiation to the human naive CD4+ T-cell pool between the ages of 0 and 20 years. Despite their decline in frequency in the blood, total body numbers of naive CD4+ T cells increase throughout childhood and early adulthood. Our analysis shows that postthymic proliferation contributes more than double the number of cells entering the pool each day from the thymus. This ratio is preserved with age; as the thymus involutes, the average time between naive T-cell divisions in the periphery lengthens. We also show that the expected residence time of naive T cells increases with time. The naive CD4+ T-cell population thus becomes progressively less dynamic with age. Together with other studies, our results suggest a complex picture of naive T-cell homeostasis in which population size, time since export from the thymus, or time since the last division can influence a cell's prospects for survival or further divisions.
Crystal growth and the steady-state grain size during high-energy ball-milling (2001)

The change in crystal size during high-energy ball-milling of hematite and zinc sulphide powders with initial average crystal size of 8 nm and 4 nm, respectively, has been investigated by X-ray powder diffraction and transmission electron microscopy.It is found that the crystal size increases with ball-milling time.This result shows that the steady-state grain size in ball-milling experiments of bigger particles can be explained by an equilibrium between fracturing and crystal growth.The kinetics of crystal growth during ball-milling of nanoparticles is discussed with reference to a simple empirical model.
Document Structure Integrity: A Robust Basis for Cross-site Scripting Defense. (2009)

Cross-site scripting (or XSS) has been the most dominant class of web vulnerabilities in 2007. The main underlying reason for XSS vulnerabilities is that web markup and client-side languages do not provide principled mechanisms to ensure secure, ground-up isolation of user-generated data in web application code. In this paper, we develop a new approach that combines randomization of web application code and runtime tracking of untrusted data both on the server and the browser to combat XSS attacks. Our technique ensures a fundamental integrity property that prevents untrusted data from altering the structure of trusted code throughout the execution lifetime of the web application. We call this property document structure integrity (or DSI). Similar to prepared statements in SQL, DSI enforcement ensures automatic syntactic isolation of inline usergenerated data at the parser-level. This forms the basis for confinement of untrusted data in the web browser based on a server-specified policy. We propose a client-server architecture that enforces document structure integrity in a way that can be implemented in current browsers with a minimal impact to compatibility and that requires minimal effort from the web developer. We implemented a proof-of-concept and demonstrated that such DSI enforcement with a simple default policy is sufficient to defeat over 98 % of the 5,328 real-world reflected XSS vulnerabilities documented in 2007, with very low performance overhead both on the client and server. 1
Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA. (1982)

An E. coli mutant that lacks tRNA-guanine transglycosylase was isolated by random screening from a collection of Escherichia coli mutants obtained with N-methyl-N'-nitro-N-nitrosoguanidine. The defective gene, named tgt, was mapped at about 9 min on the E. coli chromosome, and the gene order was shown to be phoB-tgt-tsx. tgt was transferred to an E. coli strain with a defined genetic background by P1 transduction to investigate its function. The mutant thus obtained lacked queuosine (2-amino-5-[3S, 4R, 5S)-4,5-dihydroxycyclopent-1-en-3-ylaminomethyl]-7-(beta-D-ribofuranosyl)-pyrro lo-[2,3-D]-pyrimidin-4-one) in tRNA, indicating that the enzyme is actually involved in the biosynthesis of queuosine in tRNA. No clear biological defect was observed in the mutant, and, in fact, it grew slightly faster than the control isogenic strain. tRNATyr lacking queuosine, isolated from the mutant, showed no significant biological difference from normal queuosine-containing tRNA in amino acid acceptor activity or amino acid transfer in a cell-free protein synthesizing system directed by synthetic polynucleotide. The only phenotypic change observed in the mutant thus far is marked reduction of viability when the cells are kept under unsuitable conditions for growth, suggesting that the presence of queuosine in tRNA is important to E. coli for survival in the natural environment.
The cancer-immunity cycle as rational design for synthetic cancer drugs: Novel DC vaccines and CAR T-cells (2017)

Cell therapy is an advanced form of cancer immunotherapy that has had remarkable clinical progress in the past decade in the search for cure of cancer. Most success has been achieved for chimeric antigen receptor (CAR) T-cells where CAR T-cells targeting CD19 show very high complete response rates for patients with refractory acute B-cell acute lymphoblastic leukemia (ALL) and are close to approval for this indication. CD19 CAR T-cells are also effective against B-cell chronic lymphoblastic leukemia (CLL) and B-cell lymphomas. Although encouraging, CAR T-cells have not yet proven clinically effective for solid tumors. This is mainly due to the lack of specific and homogenously expressed targets to direct the T-cells against and a hostile immunosuppressive tumor microenvironment in solid tumors. Cancer vaccines based on dendritic cells (DC) are also making progress although clinical efficacy is still lacking. The likelihood of success is however increasing now when individual tumors can be sequences and patient-specific neoepitopes identified. Neoepitopes and/or neoantigens can then be included in patient-based DC vaccines. This review discusses recent advancements of DC vaccines and CAR T-cells with emphasis on the cancer-immunity cycle, and current efforts to design novel cell therapies.
Armchair graphene nanoribbons: Electronic structure and electric-field modulation (2008)

We report electronic structure and electric-field modulation calculations in the width direction for armchair graphene nanoribbons (acGNRs) using a semiempirical extended H\"uckel theory. Important band-structure parameters are computed, e.g., effectives masses, velocities, and band gaps. For the three types of acGNRs, the ${p}_{z}$ orbital tight-binding parameters are extracted if feasible. Furthermore, the effect of electric field in the width direction on acGNRs dispersion is explored. It is shown that for the two types of semiconducting acGNRs, an external electric field can reduce the band gap to a few meV with different quantitative behaviors.
Steroid-hormone receptors in breast cancer (1984)

An obvious problem for the surgeon or oncologist treating breast cancer has been to identify the patients likely to respond to endocrine manipulation. Until recently, clinical factors such as previous response to hormone therapy, disease-free interval, age and menopausal status, and location of the dominant metastatic lesion were the principal criteria for selecting therapeutic regimens for these women. Recently, the measurement of steroid hormone receptors has become an important laboratory test. Progress during the last decade has shown that: the most reliable methods of determining estrogen receptors (ER) and progestin receptors (PR) are multipoint titration analysis using dextran-coated charcoal, and sucrose density gradient centrifugation; 55% to 65% of primary breast tumors contain more than 10 femtomole/mg cytosol protein of ER; 45% to 55% of metastatic breast tumors contain more than 10 fmol/mg cytosol protein of ER; ER are present more often in tumors of postmenopausal women compared with those of premenopausal women; benign breast lesions such as fibrocystic disease and fibroadenomas usually contain less than 10 fmol/mg cytosol protein of ER; 90% of male breast carcinomas contain ER; approximately 55% of women with breast tumors containing ER respond objectively to endocrine therapy, either additive or ablative; less than 3% of women with breast tumors lacking ER respond objectively to hormone therapy. In addition, it has been suggested that the absence of ER in a breast tumor correlates well with an increased response to cytotoxic chemotherapy; 45% to 60% of primary or metastatic breast tumors contain PR. Also, the presence of both ER and PR in a breast tumor indicates a 75% to 80% likelihood that the patient will respond to endocrine manipulation, either additive or ablative; it has been suggested that the presence of the 8 Svedberg form of ER in a breast tumor (as detected by sucrose gradient centrifugation) improves the accuracy of selecting the patient likely to respond to endocrine therapy; and there appears to be a relationship between the quantity of ER in a breast tumor and a patient's response to endocrine therapy. The incidence of response to hormone therapy increases with increasing ER levels.
Interactions Between Cultured Neurons and Carbon Nanotubes: A Nanoneuroscience Vignette (2009)

Carbon nanotubes, owing to their electrical, chemical, mechanical, and thermal properties, are one of the most promising nanomaterials for the electronics, computer, and aerospace industries. More recently, these unique materials are finding their niche in neuroscience. Here, we discuss the use of carbon nanotubes as scaffolds for neuronal growth. The chemical properties of carbon nanotubes can be systematically varied by attaching different functional groups. Such functionalized carbon nanotubes can be used to control the outgrowth and branching pattern of neuronal processes. We also discuss electrical interactions between neurons and carbon nanotubes. The electrical properties of nanotubes can provide a mechanism to monitor or stimulate neurons through the scaffold itself. The ease of which carbon nanotubes can be patterned makes them attractive for studying the organization of neural networks and has the potential to develop new devices for neural prosthesis. We note that additional toxicity studies of carbon nanotubes are necessary so that exposure guidelines and safety regulations can be set.
Characterization and elimination of trench dislocations (2002)

Trench dislocations in a 0.25 μm BiCMOS SRAM technology were traced to defects arising during S/D processing. It is argued that these defects coalesce to form dislocations, typically near the trench edge, under the combined influence of mechanical stress and high temperature processing. Process variables impacting the generation of these dislocations, including layout geometry; trench depth, profile, and densification; the presence of a liner under the gate spacer nitride; and S/D implant condition and anneal are studied. Based on this analysis, a defect-free BiCMOS process is proposed. It is shown that although the incidence of trench dislocations could be decreased by reducing the overall stress in the flow, eliminating S/D implant defects is the key to completely removing the trench dislocations.
Atomic Layer Epitaxy of Copper: Growth and Selectivity in the Cu(II)‐2,2,6,6‐tetramethyl‐3,5‐heptanedionate/ Process (1998)

The deposition of copper by means of atomic layer epitaxy is reported. Using Cu(II)‐2,2,6,6‐tetramethyl‐3,5‐heptanedionate as the precursor, pure and specular copper films were deposited at deposition temperatures below 200°C. This is more than 150°C lower than in previous reports for the same precursor where chemical vapor deposition has been employed. The process was self‐limited in the temperature range 190 to 260°C. Area‐selective deposition was achieved on platinum seeded substrates vs. unseeded glass slides or oxidized metal surfaces in the temperature range 175 to 300°C. At higher temperatures, the selectivity was lost, and nucleation was independent of substrate material because of a thermal decomposition of the precursor.
A System for Automatic Notification and Severity Estimation of Automotive Accidents (2013)

New communication technologies integrated into modern vehicles offer an opportunity for better assistance to people injured in traffic accidents. Recent studies show how communication capabilities should be supported by artificial intelligence systems capable of automating many of the decisions to be taken by emergency services, thereby adapting the rescue resources to the severity of the accident and reducing assistance time. To improve the overall rescue process, a fast and accurate estimation of the severity of the accident represent a key point to help emergency services better estimate the required resources. This paper proposes a novel intelligent system which is able to automatically detect road accidents, notify them through vehicular networks, and estimate their severity based on the concept of data mining and knowledge inference. Our system considers the most relevant variables that can characterize the severity of the accidents (variables such as the vehicle speed, the type of vehicles involved, the impact speed, and the status of the airbag). Results show that a complete Knowledge Discovery in Databases (KDD) process, with an adequate selection of relevant features, allows generating estimation models that can predict the severity of new accidents. We develop a prototype of our system based on off-the-shelf devices and validate it at the Applus+ IDIADA Automotive Research Corporation facilities, showing that our system can notably reduce the time needed to alert and deploy emergency services after an accident takes place.