gebhart/patrepeval huggingface dataset:
GenBank (1998)

The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send their sequence data. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez , which integrates data from the major DNA and protein sequence databases along with taxonomy, genome and protein structure information. MEDLINE(R) abstracts from published articles describing the sequences are also included as an additional source of biological annotation. Sequence similarity searching is offered through the BLAST series of database search programs. In addition to FTP, e-mail and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services of interest to biologists.
Repair of the Tibiofibular Syndesmosis with a Flexible Implant (1991)

Fractures of the adult ankle with disruption of the tibiofibular syndesmosis require adequate stabilization of the ankle mortise to ensure satisfactory healing of the syndesmotic ligaments. Numerous internal fixation techniques for stabilization of the syndesmosis have been used. However, most techniques require partial device removal before weight bearing can be initiated. The "flexible syndesmosis repair" uses simple, inexpensive, readily available synthetic materials to restore distal tibiofibular stability. Once early fracture healing has been obtained, weight bearing is begun (average 6 weeks). Biomechanical testing on paired cadaver ankles demonstrated a suture tensile strength of 60 lbs and consistent suture-button strength of 49 lbs, whereas tricortical screw fixation was found to have a higher 82 lbs average pull-out strength, but demonstrated a wide variability depending on bone quality. Twelve patients have been managed with flexible syndesmosis repair and followed for 2-4 years. All fractures have healed without deformity and there are no cases of mortise instability. Subsequent analysis of devices removed 8-12 months following implantation has shown that all have remained intact without failure. The flexible syndesmosis repair is a reliable, stable way to restore syndesmosis integrity, allowing early weight bearing without need for interim surgery.
Antineoplastic agents 429. Syntheses of the combretastatin A-1 and combretastatin B-1 prodrugs. (2000)

The original synthesis of combretastatin A-1 (1) was modified to allow an efficient scale-up procedure for obtaining this anti-neoplastic stilbene. Subsequent conversion to a useful prodrug was accomplished by diphosphorylation (to 10), with in situ formation of dibenzylchlorophosphite, followed by cleavage of the benzyl ester protecting groups with trimethyliodosilane. The phosphoric acid intermediate was treated with sodium methoxide to complete a practical route to the sodium phosphate prodrug (4). Selective hydrogenation of phosphate 10 and treatment of the product with sodium methoxide led to combretastatin B-1 prodrug (5). The phosphoric acid precursor of prodrug 4 was employed in a parallel series of reactions to produce a selection of metal and ammonium cation prodrug candidates. Each of the phosphate salts was evaluated from the perspective of relative solubility behavior and cancer cell growth inhibition. The sodium phosphate prodrug of combretastatin A-1 (4) was selected for detailed antineoplastic studies.
SPECIAL APPLICATION OF CAST-IN-PLACE WALLS FOR TUNNELS IN SOFT CLAY IN OSLO (1972)

WESTERN SUBURBAN LINES AND ONE FOR THE RAILWAY LINK FROM EAST TO WEST THROUGH THE CENTER OF OSLO ARE TO BE CONSTRUCTED TOGETHER OVER A LENGTH OF APPROXIMATELY 250 METERS THROUGH A DEEP CLAY FILLED CANYON. THE CLAY IS SOFT TO MEDIUM IN STIFFNESS AND THE MAXIMUM DEPTH TO THE BEDROCK IS APPROXIMATELY 40 METERS. THE RAILWAY TUNNEL WILL BE THE DEEPER OF THE TWO, WITH AN EXCAVATED DEPTH OF APPROXIMATELY 16 METERS. THIS IS TWICE AS DEEP AS IT IS POSSIBLE TO CARRY OUT AN OPEN STRUTTED EXCAVATION, WITH RESPECT TO THE DANGER OF BOTTOM HEAVE FAILURE AT THIS SITE. IN ADDITION, THE CONSTRUCTION WILL PASS WITHIN A FEW METERS OF THE NATIONAL THEATER BUILDING. THIS OLD HISTORIC BUILDING IS FOUNDED ON FLOATING PILES AND HAS SUCH SERIOUS SETTLEMENT DAMAGE THAT IT WILL NOT WITHSTAND ANY FURTHER UNEVEN SETTLEMENTS. THIS ARTICLE DESCRIBES THE SITE CONDITIONS AND DISCUSSES THE ALTERNATIVE SOLUTIONS WHICH HAVE BEEN CONSIDERED. THE CHOSEN METHOD IS BASED ON THE USE OF CAST-IN-PLACE WALLS WHICH ARE EXTENDED WELL BELOW THE EXCAVATION LEVEL, BUT WHICH DO NOT EXTEND TO ROCK AT THE DEEPEST SECTION. A SPECIAL FACTOR IN THIS PROJECT IS THAT THE LONGITUDINAL WALLS ARE STRUTTED BY DIGGING TRANSVERSE TRENCHES AND CASTING CROSS WALLS BENEATH THE EXCAVATION LEVEL. THE LONGITUDINAL AND TRANSVERSE WALLS THEN FORM A STIFF SYSTEM OF RIBS BELOW THE LEVEL OF THE EXCAVATION SO THAT THE SHEAR STRENGTH BETWEEN THE CLAY AND THE CONCRETE WALLS PREVENT BOTTOM HEAVE. LATERAL MOVEMENTS OF THE WALLS AND SETTLEMENTS WILL BE SMALL DUE TO THE STRUTS, AS TRANSVERSE WALLS ARE PLACED BEFORE THE MAIN EXCAVATION IS STARTED. CASINGS WILL BE PLACED IN THE LONGITUDINAL WALLS FOR THE RAMMING OF STEEL PILES TO ROCK, AND THE PILING WILL BE DONE BEFORE THE MAIN EXCAVATOR COMMENCES. A TRIAL EXCAVATION TO A DEPTH OF 28 METERS WAS UNDERTAKEN IN 1970. TO DETERMINE THE SHEARING STRENGTH BETWEEN CLAY AND CAST-IN-PLACE CONCRETE, PULLING OUT TESTS ON PILES WERE CARRIED OUT. PILES CAST IN WATER, CLAY, OR MIKROSIL SLURRY GAVE RESULTS SIMILAR TO THOSE OBTAINED FROM VANE BORINGS; FOR CONCRETE CAST IN BENTONITE SLURRY, HOWEVER, THE SHEAR STRENGTH WAS 25% LOWER. /TRRL/
The role of conditioning and verbal expectancy in the placebo response (1990)

Both conditioning and expectancy models have been offered in recent years as explanations for the placebo response. Following our earlier work on conditioning placebo responses in human subjects the current study examined the relative contribution made by conditioning and verbal expectancy. Group 1 received a Combined Expectancy and Conditioning Manipulation; group 2 received Expectancy Alone; group 3, Conditioning Alone; and group 4 was the control group. Subjects' responses were compared with and without a placebo cream, using iontophoretic pain stimulation. The results suggest that conditioning was more powerful than verbal expectancy in creating a placebo response.
Genome alignment with graph data structures: a comparison (2014)

We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools.
Recombinant plasminogen activator inhibitor type 1 (1994)

Plasminogen activator inhibitor type 1 (PAI-1), a member of the serpin family of serine protease inhibitors, inhibits both tissue-type plasminogen activator (t-PA) and urokinase type plasminogen activator (u-PA). High PAI-1 levels are associated with an increased risk of thromboembolic disease while PAI-1 deficiency may represent an inherited autosomal recessive bleeding disorder. This review describes the biochemistry of PAI-1 including its purification, conversion between active and latent forms, and interaction with its target serine proteases and its protein cofactor, vitronectin. In addition, an overview of animal studies with PAI-1 is presented to examine its role in regulating fibrinolysis in vivo. For this review, particular emphasis is placed on studies with a recombinant form of bacterially expressed PAI-1 (rPAI-1), which shares many features in common with the active form of native PAI-1.
A role for TREM2 ligands in the phagocytosis of apoptotic neuronal cells by microglia (2009)

Following neuronal injury, microglia initiate repair by phagocytosing dead neurons without eliciting inflammation. Prior evidence indicates triggering receptor expressed by myeloid cells-2 (TREM2) promotes phagocytosis and retards inflammation. However, evidence that microglia and neurons directly interact through TREM2 to orchestrate microglial function is lacking. We here demonstrate that TREM2 interacts with endogenous ligands on neurons. Staining with TREM2-Fc identified TREM2 ligands (TREM2-L) on Neuro2A cells and on cultured cortical and dopamine neurons. Apoptosis greatly increased the expression of TREM2-L. Furthermore, apoptotic neurons stimulated TREM2 signaling, and an anti-TREM2 mAb blocked stimulation. To examine the interaction between TREM2 and TREM2-L in phagocytosis, we studied BV2 microglial cells and their engulfment of apoptotic Neuro2A. One of our anti-TREM2 mAb, but not others, reduced engulfment, suggesting the presence of a functional site on TREM2 interacting with neurons. Further, Chinese hamster ovary cells transfected with TREM2 conferred phagocytic activity of neuronal cells demonstrating that TREM2 is both required and sufficient for competent uptake of apoptotic neuronal cells. Finally, while TREM2-L are expressed on neurons, TREM2 is not; in the brain, it is found on microglia. TREM2 and TREM2-L form a receptor-ligand pair connecting microglia with apoptotic neurons, directing removal of damaged cells to allow repair.
Anthrax (2001)

Bacillus anthracis was shown to be the etiological agent of anthrax by R. Koch and L. Pasteur at the end of the nineteenth century. The concepts on which medical microbiology are based arose from their work on this bacterium. The link between plasmids and major virulence factors of B. anthracis was not discovered until the 1980s. The three toxin components are organized in two A-B type toxins, and the bacilli are covered by an antiphagocytic polyglutamic capsule. Structure-function analysis of the toxins indicated that the common B-domain binds to a ubiquitous cell receptor and forms a heptamer after proteolytic activation. One enzyme moiety is an adenylate cyclase and the other is a Zn(2+) metalloprotease, which is able to cleave MAPKKs. The capsule covers an S-layer sequentially composed of two distinct proteins. Knowledge of the toxins facilitates the design of safer veterinary vaccines. Spore-structure analysis could contribute to the improvement of human nonliving vaccines. The phylogeny of B. anthracis within the Bacillus cereus group is also reviewed.
Nanoporous Biodegradable Elastomers (2008)

A nanoporous biodegradable elastomer based on citric acid is described. Nanopores are used to control the mechanical and degradation properties of the elastomer. Furthermore, macromolecular drugs can be entrapped under mild conditions via pore collapse, which also delays the release of the drug. The nanoporous elastomer is biocompatible and a promising platform technology for engineering soft tissues. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Transcription of the Escherichia coli fumarate reductase genes (frdABCD) and their coordinate regulation by oxygen, nitrate, and fumarate (1985)

The fumarate reductase enzyme complex allows Escherichia coli to grow anaerobically with fumarate as a terminal electron acceptor for oxidative phosphorylation when the preferred compounds oxygen and nitrate are not available. We used the pKO promoter test vectors to identify a single promoter for the frdABCD genes which encode fumarate reductase. Expression of galactokinase from the frd promoter-galK operon fusion plasmid was repressed by oxygen and by nitrate and was induced by fumarate, indicating that frd gene expression is regulated at the transcriptional level by these terminal electron acceptors. S1 nuclease analysis, using a single-stranded DNA probe from the frd promoter region and mRNA isolated from a fumarate reductase-induced culture, revealed that the frd mRNA transcript initiates with an adenine residue 93 bases prior to the start of frdA translation. No promoters internal to the frd genes were revealed with the plasmid promoter screening system. S1 nuclease analysis revealed that the frd mRNA terminates in a uridine-rich region centered at 46 bases after the last codon of frdD. A stem and loop structure previously described as the growth rate-dependent attenuator for the linked ampC gene precedes the frd mRNA terminus. This result confirms the proposal that the stem and loop structure serves the dual role of a frd terminator anaerobically and an ampC attenuator aerobically. The four frd genes encoding the subunits of the fumarate reductase complex thus comprise an operon which is regulated at the transcriptional level in response to the cellular availability of the alternate electron acceptors oxygen, nitrate, and fumarate.
Video object annotation, navigation, and composition (2008)

We explore the use of tracked 2D object motion to enable novel approaches to interacting with video. These include moving annotations, video navigation by direct manipulation of objects, and creating an image composite from multiple video frames. Features in the video are automatically tracked and grouped in an off-line preprocess that enables later interactive manipulation. Examples of annotations include speech and thought balloons, video graffiti, path arrows, video hyperlinks, and schematic storyboards. We also demonstrate a direct-manipulation interface for random frame access using spatial constraints, and a drag-and-drop interface for assembling still images from videos. Taken together, our tools can be employed in a variety of applications including film and video editing, visual tagging, and authoring rich media such as hyperlinked video.
Locating a nucleotide-binding site in the thymidine kinase of vaccinia virus and of herpes simplex virus by scoring triply aligned protein sequences. (1985)

Computer techniques were used to locate related segments of amino acid sequences in the thymidine kinases of vaccinia virus and of herpes simplex virus type 1 and in porcine adenylate kinase. As determined by a procedure that evaluates triply aligned sequences, the probability that the similarities among the segments described here arose by chance was no greater than 0.001. Because the sequence in porcine adenylate kinase is a nucleotide phosphate-binding site it is concluded that the segments in the vaccinia virus and herpes simplex virus thymidine kinases perform similar functions. The segments are residues 16-23 in porcine adenylate kinase, 11-19 in vaccinia virus thymidine kinase, and 56-64 in herpes simplex virus thymidine kinase.
Heparan Sulfate: A Complex Polymer Charged with Biological Activity (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Development of a laser photothermoacoustic frequency-swept system for subsurface imaging: Theory and experiment (2004)

In conventional biomedical photoacoustic imaging systems, a pulsed laser is used to generate time-of-flight acoustic information of the subsurface features. This paper reports the theoretical and experimental development of a new frequency-domain (FD) photo-thermo-acoustic (PTA) principle featuring frequency sweep (chirp) and heterodyne modulation and lock-in detection of a continuous-wave laser source at 1064 nm wavelength. PTA imaging is a promising new technique which is being developed to detect tumor masses in turbid biological tissue. Owing to the linear relationship between the depth of acoustic signal generation and the delay time of signal arrival to the transducer, information specific to a particular depth can be associated with a particular frequency in the chirp signal. Scanning laser modulation with a linear frequency sweep method preserves the depth-to-delay time linearity and recovers FD-PTA signals from a range of depths. Preliminary results performed on rubber samples and solid tissue phantoms indicate that the FD-PTA technique has the potential to be a reliable tool for biomedical depth-profilometric imaging.
Differences in neurogenic potential in floor plate cells along an anteroposterior location: midbrain dopaminergic neurons originate from mesencephalic floor plate cells (2007)

Directed differentiation and purification of mesencephalic dopaminergic (mesDA) neurons from stem cells are crucial issues for realizing safe and efficient cell transplantation therapies for Parkinson's disease. Although recent studies have identified the factors that regulate mesDA neuron development, the mechanisms underlying mesDA neuron specification are not fully understood. Recently, it has been suggested that mesencephalic floor plate (FP) cells acquire neural progenitor characteristics to generate mesDA neurons. Here, we directly examined this in a fate mapping experiment using fluorescence-activated cell sorting (FACS) with an FP cell-specific surface marker, and demonstrate that mesencephalic FP cells have neurogenic activity and generate mesDA neurons in vitro. By contrast, sorted caudal FP cells have no neurogenic potential, as previously thought. Analysis of dreher mutant mice carrying a mutation in the Lmx1a locus and transgenic mice ectopically expressing Otx2 in caudal FP cells demonstrated that Otx2 determines anterior identity that confers neurogenic activity to FP cells and specifies a mesDA fate, at least in part through the induction of Lmx1a. We further show that FACS can isolate mesDA progenitors, a suitable transplantation material, from embryonic stem cell-derived neural cells. Our data provide insights into the mechanisms of specification and generation of mesDA neurons, and illustrate a useful cell replacement approach for Parkinson's disease.
One-Step Rapid Reverse Transcription–PCR Assay for Detecting and Typing Dengue Viruses with GC Tail and Induced Fluorescence Resonance Energy Transfer Techniques for Melting Temperature and Color Multiplexing (2007)

A single-tube, 1-step reverse transcription-PCR assay based on T(m) and color multiplexing was developed for detecting and typing all 4 DV serotypes.
Submilliamp threshold vertical-cavity laser diodes (1990)

We report for the first time room-temperature, continuous-wave operation of individual vertical-cavity laser diodes with submilliampere threshold currents. A single quantum well active region emitting at 979 nm surrounded by GaAs/AlAs Bragg reflector mirrors was used. Threshold currents were as low as 0.7 mA. A record low linewidth-power product of 5 MHz mW and a linewidth as narrow as 85 MHz was measured. High yield and good uniformity were demonstrated.
Proviral Structure, Chromosomal Location, and Expression of HERV-K-T47D, a Novel Human Endogenous Retrovirus Derived from T47D Particles (1998)

We previously described that type B retrovirus-like particles released from the human mammary carcinoma cell line T47D are pseudotypes and package retroviral RNA of different origins (W. Seifarth, H. Skladny, F. Krieg-Schneider, A. Reichert, R. Hehlmann, and C. Leib-Mösch, J. Virol. 69:6408-6416, 1995). One preferentially packaged retroviral sequence, ERV-MLN, has now been used to isolate the corresponding full-length provirus from a human genomic library. The 9,315-bp proviral genome comprises a complete retroviral structure except for a 3' long terminal repeat (LTR) truncation. A lysine tRNA primer-binding site and phylogenetic analyses assign this human endogenous retroviral element, now called HERV-K-T47D, to the HML-4 subgroup of the HERV-K superfamily. The gag, prt, pol, and env genes exhibit 40 to 60% amino acid identity to HERV-K10. HERV-K-T47D is located on human chromosome 10, with five closely related elements on chromosomes 8, 9, 15, 16, and 19 and several hundred HERV-K-T47D-related solitary LTRs dispersed over the human genome. HERV-K-T47D-related sequences are detected in the genomes of higher primates and Old World monkeys but not in those of New World monkeys. High HERV-K-T47D transcription levels were observed in human placenta tissue, whereas transcription in T47D cells was strictly steroid dependent.
Photocured, Styrenated Gelatin-Based Microspheres for de Novo Adipogenesis through Corelease of Basic Fibroblast Growth Factor, Insulin, and Insulin-Like Growth Factor I (2004)

De novo adipose tissue formation appears to proceed via two different biological events: neovascularization and spontaneous accumulation of preadipocytes and subsequent differentiation to mature adipocytes. In this article, we perform accelerated de novo adipose tissue engineering using photocured, styrenated, gelatin-based microspheres (SGMs) with different drug release rates of immobilized angiogenic and adipogenic factors. The concept of this system is to induce neovascularization and migration of endogenous preadipocytes by the rapid delivery of the angiogenic factor basic fibroblast growth factor (bFGF), followed by the proliferation and differentiation of preadipocytes into adipocytes by the prolonged delivery of the adipogenic factors, insulin and insulin-like growth factor I (IGF-I). Bioactive substance-immobilized SGMs with different drug release rates were prepared with different gelatin concentrations. An in vitro study showed the prolonged release of an immobilized model protein and the dependence of drug release rate on gelatin concentration. After the subcutaneous injections of SGMs immobilized with these bioactive substances in different combinations, the formation of masses or clusters of adipocytes was observed in rats. Triglyceride content in the injection site for the group that received bFGF-, insulin-, and IGF-I-immobilized SGMs was significantly higher than that for the group that received insulin- and IGF-I-immobilized SGMs 4 weeks after the injection of microspheres. These results suggest that the system developed here is effective for the de novo formation of adipose tissue as it enables the induction of the two-step biological reaction by single injection.
Anionic synthesis of secondary amine functionalized polymers by reaction of polymeric organolithiums with N-benzylidenemethylamine (2002)

Functionalization of poly(styryl)lithium and poly(butadienyl)lithiums (PBDLi) with N-benzylidenemethylamine was investigated in hydrocarbon solvents at room temperature. The resulting secondary amine functionalized polymers were characterized by size exclusion chromatography, titration, 1H NMR, 13C NMR, and thin-layer chromatography. No dimeric side-products were observed by SEC. The secondary amine functionalized polystyrene was obtained in high yields (96%) in benzene solvent. The functionalization reactions of PBDLi in the absence or presence of 12 vol.-% triethylamine gave high yields (≥ 96%), whereas the same reaction in the presence of 12 vol.-% diethyl ether was less efficient (yield = 61%). The low functionalization yields in the presence of diethyl ether were attributed to the increased reactivity of PBDLi in the presence of diethyl ether, which promotes side reactions such as metalation between PBDLi and N-benzylidenemethylamine.