gebhart/patrepeval huggingface dataset:
Enhanced cartilage tissue engineering by sequential exposure of chondrocytes to FGF‐2 during 2D expansion and BMP‐2 during 3D cultivation (2001)

Bovine calf articular chondrocytes, either primary or expanded in monolayers (2D) with or without 5 ng/ml fibroblast growth factor-2 (FGF-2), were cultured on three-dimensional (3D) biodegradable polyglycolic acid (PGA) scaffolds with or without 10 ng/ml bone morphogenetic protein-2 (BMP-2). Chondrocytes expanded without FGF-2 exhibited high intensity immunostaining for smooth muscle alpha-actin (SMA) and collagen type I and induced shrinkage of the PGA scaffold, thus resembling contractile fibroblasts. Chondrocytes expanded in the presence of FGF-2 and cultured 6 weeks on PGA scaffolds yielded engineered cartilage with 3.7-fold higher cell number, 4.2-fold higher wet weight, and 2.8-fold higher wet weight glycosaminoglycan (GAG) fraction than chondrocytes expanded without FGF-2. Chondrocytes expanded with FGF-2 and cultured on PGA scaffolds in the presence of BMP-2 for 6 weeks yielded engineered cartilage with similar cellularity and size, 1.5-fold higher wet weight GAG fraction, and more homogenous GAG distribution than the corresponding engineered cartilage cultured without BMP-2. The presence of BMP-2 during 3D culture had no apparent effect on primary chondrocytes or those expanded without FGF-2. In summary, the presence of FGF-2 during 2D expansion reduced chondrocyte expression of fibroblastic molecules and induced responsiveness to BMP-2 during 3D cultivation on PGA scaffolds.
Controlling Charge States of Large Ions (1999)

The charge state of ions produced in electrospray ionization (ESI) was reduced in a controlled manner to yield predominantly singly charged species by exposure of the aerosol to a bipolar ionizing gas. Analysis of the resulting ions on an orthogonal time-of-flight mass spectrometer yielded mass spectra greatly simplified compared with conventional ESI spectra. The decreased spectral complexity afforded by the charge reduction facilitates the analysis of mixtures by ESI mass spectrometry.
Blood: Principles and Practice of Hematology (1995)

<i>Blood: Principles and Practice of Hematology</i>is the third major hematology text to appear in 1995 and raises such interesting questions as, How does one review a text of more than 11½ lb and 2300 pages? Is the world ready for another hematology text? And, what is the role of a textbook in the age of CD-ROM and computer-based literature searches? I answered the first question by deciding that the book was an immovable item and concentrated on 21 selected chapters (about one third) of particular interest to an intellectually curious practicing hematologist. Thus, chapter 2 on laboratory methods used in analyzing blood is very complete, and I know where to find answers to questions about automated blood cell counters or FACS (fluorescence-activated cell sorter) analysis. Similarly, section 4 on molecular genetics minimizes jargon and provides helpful diagrams to explain (to me) complicated concepts. Chapter 10 on acquired aplastic anemia
Mutations in the NS1 Protein of Swine Influenza Virus Impair Anti-Interferon Activity and Confer Attenuation in Pigs (2005)

It has been shown previously that the nonstructural protein NS1 of influenza virus is an alpha/beta interferon (IFN-alpha/beta) antagonist, both in vitro and in experimental animal model systems. However, evidence of this function in a natural host has not yet been obtained. Here we investigated the role of the NS1 protein in the virulence of a swine influenza virus (SIV) isolate in pigs by using reverse genetics. The virulent wild-type A/Swine/Texas/4199-2/98 (TX/98) virus and various mutants encoding carboxy-truncated NS1 proteins were rescued. Growth properties of TX/98 viruses with mutated NS1, induction of IFN in tissue culture, and virulence-attenuation in pigs were analyzed and compared to those of the recombinant wild-type TX/98 virus. Our results indicate that deletions in the NS1 protein decrease the ability of the TX/98 virus to prevent IFN-alpha/beta synthesis in pig cells. Moreover, all NS1 mutant viruses were attenuated in pigs, and this correlated with the amount of IFN-alpha/beta induced in vitro. These data suggest that the NS1 protein of SIV is a virulence factor. Due to their attenuation, NS1-mutated swine influenza viruses might have a great potential as live attenuated vaccine candidates against SIV infections of pigs.
The Rise of Bots (2017)

This work documents the recent rise in popularity of messaging bots: chatterbot-like agents with simple, textual interfaces that allow users to access information, make use of services, or provide entertainment through online messaging platforms. Conversational interfaces have been often studied in their many facets, including natural language processing, artificial intelligence, human-computer interaction, and usability. In this work we analyze the recent trends in chatterbots and provide a survey of major messaging platforms, reviewing their support for bots and their distinguishing features. We then argue for what we call "Botplication", a bot interface paradigm that makes use of context, history, and structured conversation elements for input and output in order to provide a conversational user experience while overcoming the limitations of text-only interfaces.
Formalisation de la création de services dans le réseau intelligent (1997)

The service creation in Intelligent Network is a software quality problem that encompasses several activities, namely specification, design, implementation, deployment and maintenance. In order to ensure the software quality, validation and formal verification are required. Validation of a service consists of verifying the global coherence of its specification and design, while verification consists of formal proof of structural and behavioral expected properties.We propose in this paper a multi-formalism approach, coupling the use of Object-Oriented (OO) and Petri Nets (PN) paradigms, which enables a designer to validate and to verify a service specification. We provide him a proving toolset in order to achieve these activities. This paper describes this proving toolset and its experience on an exemple.
Prostate specific antigen (PSA) in breast and ovarian cancer. (1998)

Prostatic specific antigen (PSA) is commonly used for the diagnosis and monitoring of prostatic adenocarcinoma, and has recently been detected in breast cancer and it is also thought to be produced by ovarian cancer. To examine the prognostic value of PSA tumor expression, we investigated the tumor cytosols of 26 patients with breast cancer and of 16 women with ovarian cancer. We used a chemiluminescence immunoassay for the quantitative determination of PSA (detection limit 0.003 ng/ml). The median PSA level in breast cancer patients was 0.31 ng/mg (minimum 0.003, maximum 4.4). PSA expression was significantly lower in poorly differentiated breast cancers compared to moderately and highly differentiated tumors. Advanced lymph node metastases were also correlated with lower PSA expression. We found no correlation with relapse free or overall survival. Median PSA level in our ovarian cancer patient collective was 0.014 ng/mg (minimum 0.003, maximum 0.046). We found a significant correlation between PSA expression and the estrogen receptor content of the tumor. PSA expression showed no correlation with histological grading, tumor size or other tumor characteristics in ovarian cancer. There was no correlation with relapse free or overall survival in ovarian cancer patients. Our study demonstrates that PSA is expressed in ovarian malignancies but at a lower level compared to breast cancer tissue. PSA was not able to identify a subset of patients with good prognosis in breast and in ovarian cancer patients.
Twenty Years of Embryonic Stem Cell Research in Farm Animals (2012)

Notable distinctions between an embryonic stem cell (ESC) and somatic cell are that an ESC can maintain an undifferentiated state indefinitely, self-renew, and is pluripotent, meaning that the ESC can potentially generate cells representing all the three primordial germ layers and contribute to the terminally differentiated cells of a conceptus. These attributes make the ESC an ideal source for genome editing for both agricultural and biomedical applications. Although, ESC lines have been successfully established from rodents and primates, authentic ungulate stem cell lines on the contrary are still not available. Outstanding issues including but not limited to differences in pluripotency characteristics among the existing ESC lines, pre-implantation embryo development, pluripotency pathways, and culture conditions plague our efforts to establish authentic ESC lines from farm animals. In this review, we highlight some of these issues and discuss how the recent derivation of induced pluripotent stem cells (iPSCs) might augur the establishment of robust authentic ESC lines from farm animals.
Water, 3. Treatment by Ion Exchange Processes (2016)

The article contains sections titled: 1. Fundamentals 1.1. Characterization of the Chemical State of Water 1.2. Representation of the Chemical State of Water 1.3. Ion Exchangers 2. Cation-Exchange Processes 2.1. Strongly Acidic Resins in the Na+ Form 2.2. Strongly Acidic Resins in the H+ Form 2.3. Weakly Acidic Resins in the Hydrogen Form 3. Anion-Exchange Processes 3.1. Strongly Basic Resins in the Cl− Form 3.2. Strongly Basic Resins in the OH− Form 3.3. Strongly Basic Resins in the HCO 3 − Form 3.4. Weakly Basic Resins 4. Combined Processes 4.1. Demineralization 4.2. Partial Demineralization
Increasing Chemotherapy in Small-Cell Lung Cancer: From Dose Intensity and Density to Megadoses (2007)

The hypothesis that increasing cytotoxic dose intensity will improve cancer cure rates is compelling. Although supporting evidence for this hypothesis has accrued for several tumor types, including lymphomas, breast cancer, and testicular cancers, it remains unproven. Small-cell lung cancer is extremely chemo- and radiosensitive, with a response rate of 80% achieved routinely, but few patients are cured by chemoradiotherapy. In this setting, increased cytotoxic dose intensity might improve cure rates. The finding that response rates in small-cell lung cancer correlate with received cytotoxic dose intensity merely confirms that "less is worse" and "more is better." Within conventional ranges, dose intensity can be increased with the support of hematopoietic growth factors and/or by shortening treatments intervals; however, dose intensity could be increased by only 20%-30%, and a survival advantage has not been clearly demonstrated. Given its high chemosensitivity, small-cell lung cancer was one of the first malignancies deemed suitable for increasing dose intensity and even for the use of a megadose with the support of autologous bone marrow transplantation. Some interest is emerging again due to improvements in supportive care, such as the availability of hematopoietic growth factors and peripheral blood progenitor cells.
Nanosized Emulsions Stabilized by Semisolid Polymer Interphase (2010)

We introduce a new approach for stabilizing oil-in-water nanoemulsions using a semisolid interphase formed by the phase separation of amphiphilic block copolymers from the organic phase. This system is illustrated using an amphiphilic diblock copolymer, poly(ethylene oxide)-block-poly(epsilon-caprolactone) (PEO-b-PCL), with commonly used oils. PEO-b-PCL can be miscible with oil at elevated temperatures (70-80 degrees C); however, polymer/oil demixing occurs as the temperature drops below the melting temperature of PEO-b-PCL (approximately 55 degrees C). A homogeneous polymer/oil mixture was dispersed in water at 80 degrees C to generate embryonic emulsions, and then the emulsion size was reduced to a nanometer range through microfluidic homogenization. The structure of the generated nanoemulsions is irreversibly frozen as they are cooled down to ambient temperature. The nanoemulsions stabilized by PEO-b-PCL show the excellent colloidal stability against thermal and chemical stresses, exhibiting no significant changes in the size distribution during incubation for 4 months at ambient temperature or 10 days at 60 degrees C. This study demonstrates that PEO-b-PCL is an attractive emulsifying material for practical nanoemulsion formulations requiring structural stability under a broad range of conditions.
Genome complexity reduction for SNP genotyping analysis (2002)

Efficient single nucleotide polymorphism (SNP) genotyping methods are necessary to accomplish many current gene discovery goals. A crucial element in large-scale SNP genotyping is the number of individual biochemical reactions that must be performed. An efficient method that can be used to simultaneously amplify a set of genetic loci across a genome with high reliability can provide a valuable tool for large-scale SNP genotyping studies. In this paper we describe and characterize a method that addresses this goal. We have developed a strategy for reducing genome complexity by using degenerate oligonucleotide primer (DOP)-PCR and applied this strategy to SNP genotyping in three complex eukaryotic genomes; human, mouse, and Arabidopsis thaliana. Using a single DOP-PCR primer, SNP loci spread throughout a genome can be amplified and accurately genotyped directly from a DOP-PCR product mixture. DOP-PCRs are extremely reproducible. The DOP-PCR method is transferable to many species of interest. Finally, we describe an in silico approach that can effectively predict the SNP loci amplified in a given DOP-PCR, permitting the design of an efficient set of reactions for large-scale, genome-wide SNP studies.
Antisense Oligonucleotides, A Novel Developing Targeting Therapy (2019)

Antisense oligonucleotides (ASOs) have been validated as therapeutic agents and an important tool in molecular biology. Indeed, ASOs are used either in vitro or in vivo to generate mRNA selective knockouts. They can be used for human therapy since ASOs can inhibit specifically target genes especially whose are difficult to target with small molecules inhibitors or neutralizing antibodies. However, despite their specificity and broadness of use, some practical obstacles remain unsolved in antisense pharmacology, such as insufficient stability due to nucleases degradation activity, and poor cellular delivery as a result of low cellular uptake difficult biological membrane crossing. Moreover, in many cases, potential off-target effects and immunostimulation are also part of the problems derived from their use. In this review, we will discuss ASOs, their chemistry, limitation of use, some solutions to increase stability, and finally some of their therapeutical application.
The Lac Operon: A Short History of a Genetic Paradigm (1996)

A description of the history and present knowledge of a paradigmatic system, the lac operon of Escherichia coli. A unique combination of personal anecdotes and present-day science makes this book appealing to students, postdocs, active and retired researchers alike.
DNA Codes for Nanoscience (2004)

The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.
Alternative Monomers Based on Lignocellulose and Their Use for Polymer Production (2015)

Polymeric materials play a key role in modern industry. Owing to outstanding and very versatile properties of polymers, they have rather quickly occupied the great niche of commodities. World plastic production is continuously growing from 1.7 Mton/year in 1950 to 288 Mton/year in 2012. Fossil sources are still required for production of the major part of polymers, as only 5% of chemicals are currently produced from renewable feedstocks. Nevertheless, the application of natural chemicals as feedstocks for the manufacture of polymers is steadily increasing. Different motivations induce such a high interest toward new biobased materials. First of all, the global depletion of petroleum resources and their uneven spread over the world stimulate the rational use of biomass as a renewable and ubiquitous resource. Additionally, overwhelming of dumps with nondegradable plastics causes serious ecological problems, stimulating the developments toward new biodegradable materials. Here we have to point at the distinction between the terms “biobased” and “biodegradable”. Biobased products are manufactured from renewable sources, but several examples of biobased and nonbiodegradable products, e.g., biopolyethylene, biopolyamide 11, exist. It should be noted that each new material has to be tested for biodegradability before it can be claimed to be so. For example, linear polymers produced from itaconic acid are biodegradable, but cross-linking of the polymer chains slows down the biodegradation
Tycoon: A Distributed Market-based Resource Allocation System (2004)

P2P clusters like the Grid and PlanetLab enable in principle the same statistical multiplexing efficiency gains for computing as the Internet provides for networking. The key unsolved problem is resource allocation. Existing solutions are not economically efficient and require high latency to acquire resources. We designed and implemented Tycoon, a market based distributed resource allocation system based on an Auction Share scheduling algorithm. Preliminary results show that Tycoon achieves low latency and high fairness while providing incentives for truth-telling on the part of strategic users.
Purification and Preliminary Sequencing of Tc45, an Immunodominant Trypanosoma cruzi Antigen: Absence of Homology with Cruzipain, Cruzain, and a 46-Kilodalton Protein (1995)

In spite of being separated by more than 20 million years of evolution, the murine and human immune systems share extensive similarities. Thus, experimental results obtained with the murine model may have predictive value for human Chagas' disease. Challenge of the H-2 congenic mouse stains A.SW (H-2s) and A.CA (H-2f) with Trypanosoma cruzi yields different results. The A.CA animals die approximately 12 days postinfection, while A.SW mice survive indefinitely. A 45-kD protein (Tc45), an antigen differentially recognized by the A.SW strain, is present in cultured epimastigotes and blood trypomastigotes. We describe here its purification from epimastigotes. The presence of Tc45 was monitored and a single band was detected. Since the molecular weights of Tc45, cruzipain, cruzain, and a 46-kD parasite polypeptide are similar, it was important to determine if these molecules are related. A complete lack of homology was observed when the sequence of cruzain, cruzipain, and the 46-kD polypeptide were compared with the preliminary sequence of Tc45.
Isolation of a gene encoding a human reduced folate carrier (RFC1) and analysis of its expression in transport-deficient, methotrexate-resistant human breast cancer cells. (1995)

Our laboratory has previously reported the isolation of a murine cDNA which restores reduced folate carrier (RFC) activity and methotrexate (MTX) sensitivity to a MTX-resistant, transport-deficient human breast cancer cell line (MTXR ZR-75-1) (K. H. Dixon et al., J. Biol. Chem., 269: 17-20, 1994). Using this murine cDNA as a probe, we have isolated two homologous overlapping partial cDNAs from a human testis cDNA library. In addition, using human cDNA as a probe, we have isolated a 20-kb human genomic fragment which contains RFC coding regions. Analysis of the nucleotide sequence of these clones revealed that the human RFC gene, RFC1, is approximately 65% homologous to the murine and hamster genes. Using a human genomic P1 plasmid clone containing RFC1, we mapped the location of RFC1 by fluorescence in situ hybridization to the end of the long arm of chromosome 21 (21q22.2-q22.3). Fluorescence in situ hybridization analysis also showed that two copies of RFC1 were present in MTXR ZR-75-1 cells, and showed no evidence of rearrangement of this gene. Northern blot analysis of MTXR ZR-75-1 cells demonstrated a marked decrease in the level of the 3-kb RFC1 transcript relative to the parental cell line, and Western blot analysis using a polyclonal antibody raised against a peptide generated from the RFC1 sequence showed decreased expression of an approximately M(r) 56,000 protein in MTXR ZR-75-1 cells. Finally, MTXR ZR-75-1 cells transfected with an RFC1 gene showed increased MTX uptake, which was more sensitive to competition by folinic acid than by folic acid. Therefore, decreased RFC1 expression appears to be the molecular mechanism of decreased MTX uptake in this MTX-resistant cell line.
Total reflection of light from a corrugated surface of a dielectric waveguide (1985)

It is shown that reflection of a plane monochromatic wave by the surface of a corrugated waveguide structure may excite a guided mode in one of the diffraction orders and thus alter greatly the reflection and transmission coefficients of the incident wave until total reflection or total transmission are achieved.
HTSeq – A Python framework to work with high-throughput sequencing data (2014)

ABSTRACT Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard work flows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data such as genomic coordinates, sequences, sequencing reads, alignments, gene model information, variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability: HTSeq is released as open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index https://pypi.python.org/pypi/HTSeq . Contact: sanders@fs.tum.de
HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data (2015)

HLA-VBSeq is an efficient and accurate HLA typing method using high-throughput sequencing data without the need of primer design for HLA loci. Moreover, it does not assume any prior knowledge about HLA allele frequencies, and hence HLA-VBSeq is broadly applicable to human samples obtained from a genetically diverse population.