gebhart/patrepeval huggingface dataset:
RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour (2000)

We have probed the effects of altering buffer conditions on the behaviour of two aptamer RNAs for the bacterio-phage MS2 coat protein using site-specific substitution of 2'-deoxy-2-aminopurine nucleotides at key adenosine positions. These have been compared to the wild-type operator stem-loop oligonucleotide, which is the natural target for the coat protein. The fluorescence emission spectra show a position and oligonucleotide sequence dependence which appears to reflect local conformational changes. These are largely similar between the differing oligonucleotides and deviations can be explained by the individual features of each sequence. Recognition by coat protein is enhanced, unaffected or decreased depending on the site of substitution, consistent with the known protein-RNA contacts seen in crystal structures of the complexes. These data suggest that the detailed conformational dynamics of aptamers and wild-type RNA ligands for the same protein target are remarkably similar.
Expression of p-STAT3 in human gastric carcinoma: significant correlation in tumour invasion and prognosis. (2007)

Signal transducers and activators of transcription (STATs) belong to a family of transcription factors activated in response to cytokines and growth factors. Constitutive activation of STAT3 has been observed in a growing number of tumour-derived cell lines, as well as in tumor specimens from human cancers. Our aim was to determine the relationship between the expression of phosphorylated STAT3 (p-STAT3) and clinicopathological factors in human gastric adenocarcinoma. One-hundred and eleven cases of surgically resected human gastric adenocarcinoma were studied by immunohistochemistry. Fifty-five (49.5%) cases showed positive staining for the p-STAT3 proteins. The expression of p-STAT3 was significantly correlated with several clinicopathological factors. Moreover, expression of p-STAT3 was detected by Western blot analysis in 2 different kinds of cultured human gastric carcinoma cell lines and 4 cases of gastric carcinoma tissue obtained at surgery. Western blot analysis confirmed the presence of p-STAT3 in these specimens. In univariate survival analysis, p-STAT3 expression was associated with inferior survival (p<0.05). Constitutive activation of STAT3 may play an important role in the tumorigenesis of gastric adenocarcinoma, and the detailed mechanism of STAT3 signaling pathway in gastric adenocarcinoma deserves further investigation.
Formation of ROS and RNS in Water Electro-Sprayed through Transient Spark Discharge in Air and their Bactericidal Effects (2013)

Chemical and bactericidal effects induced by plasma in water upon electro-spraying through DC-driven positive transient spark discharge in air were investigated. Inactivation of E. coli was determined in dependence on pH (controlled by buffers) and correlated with chemical changes induced in water. Productions of hydrogen peroxide, nitrites, nitrates, peroxynitrites, and pH changes were determined, and the extent of oxidative stress induced in bacteria was evaluated. The degree of inactivation and oxidative damage of bacteria increased with the increasing acidity of the solution. Acidified nitrites interacting with hydrogen peroxide were determined as the most important bactericidal ROS/RNS agents in plasma-treated water. A possible role of peroxynitrites, ozone, and metal nanoparticles is discussed.
RECEPTORS FOR EPIDERMAL GROWTH FACTOR AND OTHER POLYPEPTIDE MITOGENS (1987)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Microstructure and Mechanical Behavior of Porous Ti–6Al–4V Processed by Spherical Powder Sintering (2013)

Reducing the stiffness of titanium is an important issue to improve the behavior of this material when working together with bone, which can be achieved by generating a porous structure. The aim of this research was to analyze the porosity and mechanical behavior of Ti-6Al-4V porous samples developed by spherical powder sintering. Four different microsphere sizes were sintered at temperatures ranging from 1300 to 1400 °C for 2, 4 and 8 h. An open, interconnected porosity was obtained, with mean pore sizes ranging from 54.6 to 140 µm. The stiffness of the samples diminished by as much as 40% when compared to that of solid material and the mechanical properties were affected mainly by powder particles size. Bending strengths ranging from 48 to 320 MPa and compressive strengths from 51 to 255 MPa were obtained.
Portals and mirrors (1995)

We describe an approach for determining potentially visible sets in dynamic architectural models. Our scheme divides the models into cells and portals, computing a conservative estimate of which cells are visible at render time. The technique is simple to implement and can be easily integrated into existing systems, providing increased interactive performance on large architectural models.
Temperature-Induced Protein Release from Water-in-Oil-in-Water Double Emulsions (2008)

A model water-in-oil-in-water (W1/O/W2) double emulsion was prepared by a two-step emulsification procedure and subsequently subjected to temperature changes that caused the oil phase to freeze and thaw while the two aqueous phases remained liquid. Our previous work on individual double-emulsion globules1 demonstrated that crystallizing the oil phase (O) preserves stability, while subsequent thawing triggers coalescence of the droplets of the internal aqueous phase (W1) with the external aqueous phase (W2), termed external coalescence. Activation of this instability mechanism led to instant release of fluorescently tagged bovine serum albumin (fluorescein isothiocyanate (FITC)-BSA) from the W 1 droplets and into W2. These results motivated us to apply the proposed temperature-induced globule-breakage mechanism to bulk double emulsions. As expected, no phase separation of the emulsion occurred if stored at temperatures below 18 degrees C (freezing point of the model oil n-hexadecane), whereas oil thawing readily caused instability. Crucial variables were identified during experimentation, and found to greatly influence the behavior of bulk double emulsions following freeze-thaw cycling. Adjustment of these variables accounted for a more efficient release of the encapsulated protein.
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding (2009)

We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding approximately 18x haploid coverage of aligned sequence and close to 300x clone coverage. Over 98% of the reference genome is covered with at least one uniquely placed read, and 99.65% is spanned by at least one uniquely placed mate-paired clone. We identify over 3.8 million SNPs, 19% of which are novel. Mate-paired data are used to physically resolve haplotype phases of nearly two-thirds of the genotypes obtained and produce phased segments of up to 215 kb. We detect 226,529 intra-read indels, 5590 indels between mate-paired reads, 91 inversions, and four gene fusions. We use a novel approach for detecting indels between mate-paired reads that are smaller than the standard deviation of the insert size of the library and discover deletions in common with those detected with our intra-read approach. Dozens of mutations previously described in OMIM and hundreds of nonsynonymous single-nucleotide and structural variants in genes previously implicated in disease are identified in this individual. There is more genetic variation in the human genome still to be uncovered, and we provide guidance for future surveys in populations and cancer biopsies.
miRNA-embedded shRNAs for Lineage-specific BCL11A Knockdown and Hemoglobin F Induction (2015)

RNA interference (RNAi) technology using short hairpin RNAs (shRNAs) expressed via RNA polymerase (pol) III promoters has been widely exploited to modulate gene expression in a variety of mammalian cell types. For certain applications, such as lineage-specific knockdown, embedding targeting sequences into pol II-driven microRNA (miRNA) architecture is required. Here, using the potential therapeutic target BCL11A, we demonstrate that pol III-driven shRNAs lead to significantly increased knockdown but also increased cytotoxcity in comparison to pol II-driven miRNA adapted shRNAs (shRNA(miR)) in multiple hematopoietic cell lines. We show that the two expression systems yield mature guide strand sequences that differ by a 4 bp shift. This results in alternate seed sequences and consequently influences the efficacy of target gene knockdown. Incorporating a corresponding 4 bp shift into the guide strand of shRNA(miR)s resulted in improved knockdown efficiency of BCL11A. This was associated with a significant de-repression of the hemoglobin target of BCL11A, human γ-globin or the murine homolog Hbb-y. Our results suggest the requirement for optimization of shRNA sequences upon incorporation into a miRNA backbone. These findings have important implications in future design of shRNA(miR)s for RNAi-based therapy in hemoglobinopathies and other diseases requiring lineage-specific expression of gene silencing sequences.
Fiber grating sensors (1997)

We review the recent developments in the area of optical fiber grating sensors, including quasi-distributed strain sensing using Bragg gratings, systems based on chirped gratings, intragrating sensing concepts, long period-based grating sensors, fiber grating laser-based systems, and interferometric sensor systems based on grating reflectors.
Tc-99m Sestamibi Uptake in Metastatic Prostate Carcinoma (2000)

Chest pain developed in a 67-year-old man with a history of prostate carcinoma and he was referred for a myocardial perfusion scan. A Tc-99m sestamibi–dipyridamole study showed impaired coronary artery flow reserve to the interventricular septum and a fixed perfusion defect in the inferior wall of the left ventricle, consistent with previous myocardial infarction. Increased sestamibi uptake in an irregular pattern in multiple ribs was noted incidentally. The serum prostate-specific antigen concentration was markedly elevated at 84.3 μg/l (normal, <4.0 μg/l). A whole-body bone scan showed corresponding multiple foci of increased tracer accumulation in the ribs and elsewhere in the axial and appendicular skeleton, consistent with widespread prostatic carcinoma metastases in bone. Tc-99m sestamibi uptake has been reported in a wide range of benign and malignant tumors, but accumulation in prostate carcinoma has not been previously described. FIGURE 1Fig. 1: Anterior and left anterior oblique views of the left thorax after intravenous injection of Tc-99m sestamibi at rest (left and right images) and left anterior oblique view after sestamibi injection during exercise (center image) show irregular uptake of tracer in multiple ribs.FIGURE 2Fig. 2: A Tc-99m MDP whole-body bone scan shows multiple foci of increased tracer accumulation throughout the axial and appendicular skeleton consistent with widely disseminated prostate carcinoma metastases in the bone.
Intranasal Immunization of Mice with a Mixture of the Pneumococcal Proteins PsaA and PspA Is Highly Protective against Nasopharyngeal Carriage ofStreptococcus pneumoniae (2000)

Acquisition of pneumococci is generally from carriers rather than from infected individuals. Therefore, to induce herd immunity against Streptococcus pneumoniae it will be necessary to elicit protection against carriage. Capsular polysaccharide-protein conjugates, PspA, and PsaA are known to elicit some protection against nasopharyngeal carriage of pneumococci but do not always completely eliminate carriage. In this study, we observed that PsaA elicited better protection than did PspA against carriage. Pneumolysin elicited no protection against carriage. Immunization with a mixture of PsaA and PspA elicited the best protection against carriage. These results indicate that PspA and PsaA may be useful for the elicitation of herd immunity in humans. As PspA and pneumolysin are known to elicit immunity to bacteremia and pneumonia, their inclusion in a mucosal vaccine may enable such a vaccine to prevent invasive disease as well as carriage.
Activity of rapamycin (AY-22,989) against transplanted tumors. (1984)

Rapamycin exhibits activity against several ascites and solid transplantable tumors; it is slightly active to inactive against leukemias. On a weight basis, rapamycin was less active than 5-fluorouracil, cyclophosphamide and adriamycin, but rapamycin's maximal activity against Colon 38 tumor was similar to that of 5-fluorouracil and cyclophosphamide. Its activity was such that it significantly inhibited tumor growth at any stage of development. In the active dose range, rapamycin appeared less toxic than the other drugs. In the Colon 38 tumor model, rapamycin at a given dose exhibited the same activity when administered ip, iv, im and sc; upon oral administration, its activity was reduced but not abolished. Rapamycin was compatible with 5-fluorouracil and cyclophosphamide. The sequential treatment 5-fluorouracil-rapamycin-cyclophosphamide was superior to the sequence 5-fluorouracil-adriamycin-cyclophosphamide in protecting Colon 38 tumor-bearing mice. 29-Demethoxyrapamycin exerted only marginal activity against P388 lymphocytic leukemia; it was inactive against B16 melanocarcinoma and Colon 38 solid tumor.
A conjoint pattern recognition approach to nonintrusive load monitoring (1993)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1993.
Real-time 3D particle manipulation visualized using volume holographic gratings (2014)

Holographic optical tweezers (HOTs) extend optical trapping into three dimensions. Volume imaging then becomes a concern as trapped objects are easily moved out of focus of the imaging objective lens. Here we demonstrate a three-dimensional real-time interactive optical trapping, manipulating, and imaging system based on HOTs incorporated with volume holographic microscope. Intensity information about the trapped objects at multiple depths can be captured in a single measurement. This method is compatible with most imaging modes such as bright-field and fluorescence.
Perry's chemical engineers' handbook (2008)

The definitive reference for more than half a century,—updated for the first time in more than a decade. Since 1934, Perry9s Chemical Engineer9s Handbook has delivered unrivaled, state-of-the-art coverage of all aspects of chemical engineering—from the fundamentals to details on computer applications and control. Featuring 2,700 pages and 1900 illustrations, the eighth edition is a comprehensive source for the newest developments, advances, achievements, and methods in the field.
Molecular Cloning and Expression of Major Structural Protein VP1 of the Human Polyomavirus JC Virus: Formation of Virus-Like Particles Useful for Immunological and Therapeutic Studies (1999)

The major structural viral protein, VP1, of the human polyomavirus JC virus (JCV), the causative agent of progressive multifocal leukoencephalopathy (PML), was expressed by using recombinant baculoviruses. Recombinant VP1 formed virus-like particles (VLP) with the typical morphology of empty JCV capsids. Purified VP1 VLP bind to SVG, B, and T cells, as well as to monkey kidney cells. After binding, VP1 VLP were also internalized with high efficiency and transported to the nucleus. Immunization studies revealed these particles as highly immunogenic when administered with adjuvant, while immunization without adjuvant induced no immune response. VP1 VLP hyperimmune serum inhibits binding to SVG cells and neutralizes natural JCV. Furthermore, the potential of VP1 VLP as an efficient transporter system for gene therapy was demonstrated. Exogenous DNA could be efficiently packaged into VP1 VLP, and the packaged DNA was transferred into COS-7 cells as shown by the expression of a marker gene. Thus, VP1 VLP are useful for PML vaccine development and represent a potential new transporter system for human gene therapy.
The isolation and attenuation of a virus causing rhinotracheitis in turkeys in South Africa. (1989)

In March 1978, a number of turkeys with severe respiratory symptoms affecting over 80% of the flock were investigated for a possible causative agent. With the standard techniques used for the isolation of bacteriae, mycoplasmae and viruses, only Mycoplasma gallisepticum, Mycoplasma meleagridis and Newcastle disease virus were isolated. Tracheal organ cultures were subsequently prepared from 27-day-old turkey embryos and inoculated with sinus exudate from affected turkeys. After an incubation period of 4 days a virus was isolated with which the typical symptoms, as observed in the field, could be reproduced in susceptible turkeys after 3-5 days. Following primary isolation in tracheal organ cultures, the virus grew readily in embryonated eggs and Vero cells. With the electron microscope, virus-like particles, varying in size from 40 nm-500 nm, were observed, having a pleomorphic shape and studded with fine surface projections. The virus seems to fall into the family Paramyxoviridae. A vaccine produced from attenuated virus in embryonated eggs afforded good protection against mortalities due to airsacculitis that normally follows on to turkey rhinotracheitis infection. The serological and clinical effects of the virus on chickens are also reported on.
Near field detector for integrated surface plasmon resonance biosensor applications (2009)

Integrated surface plasmon resonance biosensors promise to enable compact and portable biosensing at high sensitivities. To replace the far field detector traditionally used to detect surface plasmons we integrate a near field detector below a functionalized gold film. The evanescent field of a surface plasmon at the aqueous-gold interface is converted into photocurrent by a thin film organic heterojunction diode. We demonstrate that use of the near field detector is equivalent to the traditional far field measurement of reflectivity. The sensor is stable and reversible in an aqueous environment for periods of 6 hrs. For specific binding of neutravidin, the detection limit is 4 microg/cm(2). The sensitivity can be improved by reducing surface roughness of the gold layers and optimization of the device design. From simulations, we predict a maximum sensitivity that is two times lower than a comparable conventional SPR biosensor.
Efficacy of the Dynamic Interspinous Assisted Motion system in clinical treatment of degenerative lumbar disease. (2010)

The DIAM system appears to be a useful and effective treatment in the surgical management of degenerative lumbar disease in certain patients. However, long-term follow-up is needed to evaluate the clinical outcomes of the device.
Correction: Comparative Reliability Studies and Analysis of Au, Pd-Coated Cu and Pd-Doped Cu Wire in Microelectronics Packaging (2014)

This paper compares and discusses the wearout reliability and analysis of Gold (Au), Palladium (Pd) coated Cu and Pd-doped Cu wires used in fineline Ball Grid Array (BGA) package. Intermetallic compound (IMC) thickness measurement has been carried out to estimate the coefficient of diffusion (D o ) under various aging conditions of different bonding wires. Wire pull and ball bond shear strengths have been analyzed and we found smaller variation in Pd-doped Cu wire compared to Au and Pd-doped Cu wire. Au bonds were identified to have faster IMC formation, compared to slower IMC growth of Cu. The obtained weibull slope, b of three bonding wires are greater than 1.0 and belong to wearout reliability data point. Pd-doped Cu wire exhibits larger time-to-failure and cycles-to-failure in both wearout reliability tests in Highly Accelerated Temperature and Humidity (HAST) and Temperature Cycling (TC) tests. This proves Pd-doped Cu wire has a greater potential and higher reliability margin compared to Au and Pd-coated Cu wires.
Virilization of Young Children After Topical Androgen Use by Their Parents (2004)

Children were virilized by contact with adults using cutaneous steroid preparations. Parents were unaware of the dangers of passive transfer. Laboratory data were consistent with exogenous androgen exposure. Each child had opportunity for passive exposure, and discontinuation of contact resulted in a decrease of androgen levels or regression of symptoms.
Object-related-navigation for mobile robots (2012)

Motivated by cognitive considerations about human knowledge representation we introduce a new approach for robot motion planning and control. Instead of reasoning about positions in a global cartesian coordinate frame we utilize relative orientation and distance information between the robot and perceived objects in the environment. A representation built upon these considerations enables on the one hand a tight coupling between perception, planning, and robot control, while on the other hand a means for precise robot control is established. With our approach we try to encourage for a new view in robotic planning problems by illustrating how it allows for plan generation and execution in a human comprehensible fashion by incorporating plans like: ”Overtake vehicle X on the right side, then follow lane Y”.
On the Theory of Infinitely Repeated Games with Discounting (1988)

Presentation d'un cadre systematique pour etudier des jeux repetes indefiniment avec actualisation, en s'attachant plus particulierement aux equilibres parfaits de strategie pure
Sequence comparison of open reading frames 2 to 5 of low and high virulence United States isolates of porcine reproductive and respiratory syndrome virus (1995)

The sequences of ORFs 2 to 5 of five United States (US) porcine reproductive and respiratory syndrome virus (PRRSV) isolates with differing virulence were determined. The nucleotide and deduced amino acid sequences of these isolates were compared with those of other known PRRSV isolates. The amino acid sequence identity between seven US PRRSV isolates was 91-99% in ORF 2, 86-98% in ORF 3, 92-99% in ORF 4 and 88-97% in ORF 5. The low virulence US isolate had highest sequence variation in ORFs 2 to 4 compared to the other US isolates. A hypervariable region with antigenic potential was identified within the major envelope glycoprotein. Phylogenetic analysis of ORFs 2 to 7 indicated the existence of at least three minor genotypes within the major US genotype. The low virulence US isolate formed a branch distinct from the other US isolates. The results of this study have implications for both the taxonomy of PRRSV and vaccine development.
Palladium‐katalysierte Kreuzkupplungen zwischen sp‐ und sp2‐hybridisierten Kohlenstoffatomen (2003)

Palladium-katalysierte Bindungsbildungen zwischen Alkinen und Arylhalogeniden oder -triflaten sind heute so faszinierend wie vor nahezu 30 Jahren, als sie von Sonogashira eingeführt wurden (siehe Schema). Einfachere Verfahren, neuartige Acetylid-Kupplungspartner sowie effizientere Katalysatoren und Ligandensysteme tragen zu ihren vielseitigeren Verwendungsmöglichkeiten bei.