gebhart/patrepeval huggingface dataset:
Elastographic Imaging of Thermal Lesions in Liver In-Vivo Using Diaphragmatic Stimuli (2004)

Radiofrequency or microwave ablations are interstitial focal ablative therapies that can be used in a percutaneous fashion for treating tumors in the liver, kidney, and prostate. These modalities provide in situ destruction of tumors. We present a method for in-vivo elastographic visualization of the ablated regions in the liver during and after thermal therapy. In-vivo elastographic imaging uses compressions of the liver due to movement of the diaphragm during the respiratory cycle. Elastography of the liver and other abdominal organs has not been attempted previously due to the difficulty in providing controlled compressions. Gating of the data acquisition to the respiratory waveform would provide access to data where the compression increments are similar in both magnitude and direction, thereby enabling reproducible imaging of the thermal lesion or tumor. Comparison of elastograms with gross-pathology of ablated tissue illustrates the correspondence between elastographic image features and pathology. Ultrasound is routinely used to guide the rf ablation procedure, so the same imaging system could be used for elastographic imaging. Since the technique utilizes physiological motion of the diaphragm due to respiration, it may also be employed in the visualization of cancerous tumors in the liver.
Reversible Photoswitching of Ferromagnetic FePt Nanoparticles at Room Temperature (2007)

There has been a great interest in developing photoswitchable magnetic materials because of their possible applications for future high-density information storage media. In fact, however, the examples reported so far did not show ferromagnetic behavior at room temperature. From the viewpoint of their practical application to magnetic recording systems, the ability to fix their magnetic moments such that they still exhibit room-temperature ferromagnetism is an absolute requirement. Here, we have designed reversible photoswitchable ferromagnetic FePt nanoparticles whose surfaces were coated with azobenzene-derivatized ligands. On the surfaces of core particles, reversible photoisomerization of azobenzene in the solid state was realized by using spacer ligands that provide sufficient free volume. These photoisomerizations brought about changes in the electrostatic field around the core-FePt nanoparticles. As a result, we have succeeded in controlling the magnetic properties of these ferromagnetic composite nanoparticles by alternating the photoillumination in the solid state at room temperature.
Spatial and movement-based heuristics for encoding pattern information through touch. (1985)

Seven experiments investigated the heuristics people use to encode spatial pattern information through touch. Observers traced a tangible pathway with one hand and then answered questions about either the euclidean line between the pathway endpoints or the pathway itself. Parameters of the euclidean line were held constant, while characteristics of the felt pathway were manipulated. Experiments 1-4 showed that blindfolded sighted and blind observers increasingly overestimated the length of the euclidean line as the length of the explored pathway increased. This indicates a movement-based heuristic for encoding distance. Experiments 5-7 indicated that judgments of the position of the euclidean line did not vary with the position of the felt pathway or the extent to which it deviated from that line. Instead, the results indicated that observers relied on implicit spatial axes, which are movement independent, to judge position. These and other results have implications for theories of haptic encoding of spatial pattern and for the construction of tangible graphics displays.
Expression and Secretion of a Cellulomonas fimi Exoglucanase in Saccharomyces cerevisiae (1988)

We used the yeast MEL1 gene for secreted alpha-galactosidase to construct cartridges for the regulated expression of foreign proteins from Saccharomyces cerevisiae. The gene for a Cellulomonas fimi beta-1,4-exoglucanase was inserted into one cartridge to create a fusion of the alpha-galactosidase signal peptide to the exoglucanase. Yeast transformed with plasmids containing this construction produced active extracellular exoglucanase when grown under conditions appropriate to MEL1 promoter function. The cells also produced active intracellular enzyme. The secreted exoglucanase was N-glycosylated and was produced continuously during culture growth. It hydrolyzed xylan, carboxymethyl cellulose, 4-methylumbelliferyl-beta-d-cellobiose, and p-nitrophenyl-beta-d-cellobiose. A comparison of the recombinant S. cerevisiae enzyme with the native C. fimi enzyme showed the yeast version to have an identical K(m) and pH optimum but to be more thermostable.
Single-Wall Carbon Nanotube Films (2002)

An optically homogeneous solution/dispersion of single-wall carbon nanotubes (SWNTs) in oleum has been used to form isotropic films exhibiting fibrillar morphology. Tensile modulus, strength, and strain to failure of the film are 8 GPa, 30 MPa, and 0.5%, respectively. The electrical conductivity in the plane of the film is 1 × 105 S/m.
Connexin mimetic peptides: specific inhibitors of gap-junctional intercellular communication (2001)

Intercellular co-operation is a fundamental and widespread feature in tissues and organs. An important mechanism ensuring multicellular homoeostasis involves signalling between cells via gap junctions that directly connect the cytosolic contents of adjacent cells. Cell proliferation and intercellular communication across gap junctions are closely linked, and a number of pathologies in which communication is disrupted are known where connexins, the gap-junctional proteins, are modified. The proteins of gap junctions thus emerge as therapeutic targets inviting the development and exploitation of chemical tools and drugs that specifically influence intercellular communication. Connexin mimetic peptides that correspond to short specific sequences in the two extracellular loops of connexins are a class of benign, specific and reversible inhibitors of gap-junctional communication that have been studied recently in a broad range of cells, tissues and organs. This review summarizes the properties and uses of these short synthetic peptides, and compares their probable mechanism of action with those of a wide range of other less specific traditional gap-junction inhibitors.
Highly Luminescent Tetradentate Bis-Cyclometalated Platinum Complexes: Design, Synthesis, Structure, Photophysics, and Electroluminescence Application (2010)

N,N-Di(6-phenylpyridin-2-yl)aniline (L1), N,N-di(6-(2,4-difluorophenyl)pyridin-2-yl)aniline (L2), N,N-di(3-(pyridin-2-yl)phenyl)aniline (L3), N,N-di(3-(1H-pyrazol-1-yl)phenyl)aniline (L4), N,N-di(3-(3-methyl-1H-pyrazol-1-yl)phenyl)aniline (L5), and N,N-di(3-(4-methyl-1H-pyrazol-1-yl)phenyl)aniline (L6) undergo cyclometalation to produce two types of tetradentate bis-cyclometalated platinum(II) complexes: C--N*N(wedge)C platinum complexes 1 and 2 and N--C*C--N platinum complexes 3-6, respectively, where an "X--Y" (X, Y = C or N) denotes a bidentate coordination to the platinum to form a five-membered metallacycle and "X*Y" denotes a coordination to form a six-membered metallacycle. The crystal structures of 1, 3, and 5 were determined by the single-crystal X-ray diffraction analysis, showing distorted square-planar geometry, that is, two C--N coordination moieties are twisted. Complex 5 showed much greater distortion with largest deviation of 0.193 A from the mean NCCNPt coordination plane, which is attributed to the steric interaction between the two 3-methyl groups on the pyrazolyl rings. Density functional theory (DFT) calculations were carried out on the ground states of 1 and 3-6. The optimized geometries are consistent with the crystal structures. The highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs) of the molecules displayed a localized characteristic with the contribution (18-45%) of the platinum metal to the HOMOs. All complexes are emissive at ambient temperature in fluid with quantum yields of 0.14 to 0.76 in 2-methyltetrahydrofuran. The emission of the complexes covers from blue to red region with lambda(max) ranging from 474 to 613 nm. Excimer emission was observed for 1 and 2 at high concentration of the complexes. The emission lifetime at infinite dilution for 1 and 2 was determined to be 7.8 and 11.4 micros, respectively. Concentration quenching was observed for 3 and 4, but the excimer emission was not observed. The life times for 3-6 were determined to be in the range of micro seconds, but those of 4-6 (3.4-5.7 micros) were somewhat shorter than that of 3 (7.6 micros). The highly structured emission spectra, long life times, and DFT calculations suggested that the emissive state is primarily a (3)LC state with metal-to-ligand charge-transfer (MLCT) admixture. The ZFS of 23 cm(-1) for the emissive triplet state was observed directly by high resolution spectroscopy for 1 in a Shpol'skii matrix, which also suggested an emission from a triplet ligand centered ((3)LC) state with admixture of MLCT character. Complex 1 was incorporated into an organic light-emitting diode (OLED) device as an emitter at 4 wt % in the mixed host of 4,4',4''-tris(N-carbazolyl)triphenylamine (TCTA) and 2,2',2''-(1,3,5-benzenetriyl)tris(1-phenyl-1-H-benzimidazole) (TPBI) and demonstrated excellent performance with maximum external quantum efficiency of 14.7% at the current density of 0.01 mA/cm(-1).
A noncommutative algorithm for multiplying 3×3 matrices using 23 multiplications (1976)

A noncommutative algorithm, as opposed to a commutative algorithm, performs matrix multiplication without requiring the matrix elements to be commutative under the operation of multiplication. Such an algorithm is most desirable since it can be employed to multiply two matrices whose elements are themselves matrices.
Real-Time Nucleic Acid Sequence-Based Amplification Is More Convenient than Real-Time PCR for Quantification of Plasmodium falciparum (2005)

Determination of the number of malaria parasites by routine or even expert microscopy is not always sufficiently sensitive for detailed quantitative studies on the population dynamics of Plasmodium falciparum, such as intervention or vaccine trials. To circumvent this problem, two more sensitive assays, real-time quantitative nucleic acid sequence-based amplification (QT-NASBA) and real-time quantitative PCR (QT-PCR) were compared for quantification of P. falciparum parasites. QT-NASBA was adapted to molecular beacon real-time detection technology, which enables a reduction of the time of analysis and of contamination risk while retaining the specificity and sensitivity of the original assay. Both QT-NASBA and QT-PCR have a sensitivity of 20 parasites/ml of blood, but QT-PCR requires a complicated DNA extraction procedure and the use of 500 microl of venous blood to achieve this sensitivity, compared to 50 microl of finger prick blood for real-time QT-NASBA. Both techniques show a significant correlation to microscopic parasite counts, and the quantification results of the two real-time assays are significantly correlated for in vitro as well as in vivo samples. However, in comparison to real-time QT-PCR, the results of real-time QT-NASBA can be obtained 12 h earlier, with relatively easy RNA extraction and use of finger prick blood samples. The prospective development of multiplex QT-NASBA for detection of various P. falciparum developmental stages increases the value of QT-NASBA for malaria studies. Therefore, for studies requiring sensitive and accurate detection of P. falciparum parasites in large numbers of samples, the use of real-time QT-NASBA is preferred over that of real-time QT-PCR.
Protection Provided by a Herpes Simplex Virus 2 (HSV-2) Glycoprotein C and D Subunit Antigen Vaccine against Genital HSV-2 Infection in HSV-1-Seropositive Guinea Pigs (2013)

A prophylactic vaccine for genital herpes disease remains an elusive goal. We report the results of two studies performed collaboratively in different laboratories that assessed immunogenicity and vaccine efficacy in herpes simplex virus 1 (HSV-1)-seropositive guinea pigs immunized and subsequently challenged intravaginally with HSV-2. In study 1, HSV-2 glycoproteins C (gC2) and D (gD2) were produced in baculovirus and administered intramuscularly as monovalent or bivalent vaccines with CpG and alum. In study 2, gD2 was produced in CHO cells and given intramuscularly with monophosphoryl lipid A (MPL) and alum, or gC2 and gD2 were produced in glycoengineered Pichia pastoris and administered intramuscularly as a bivalent vaccine with Iscomatrix and alum to HSV-1-naive or -seropositive guinea pigs. In both studies, immunization boosted neutralizing antibody responses to HSV-1 and HSV-2. In study 1, immunization with gC2, gD2, or both immunogens significantly reduced the frequency of genital lesions, with the bivalent vaccine showing the greatest protection. In study 2, both vaccines were highly protective against genital disease in naive and HSV-1-seropositive animals. Comparisons between gD2 and gC2/gD2 in study 2 must be interpreted cautiously, because different adjuvants, gD2 doses, and antigen production methods were used; however, significant differences invariably favored the bivalent vaccine. Immunization of naive animals with gC2/gD2 significantly reduced the number of days of vaginal shedding of HSV-2 DNA compared with that for mock-immunized animals. Surprisingly, in both studies, immunization of HSV-1-seropositive animals had little effect on recurrent vaginal shedding of HSV-2 DNA, despite significantly reducing genital disease.
High-throughput RNAi Screening Identifies a Role for TNK1 in Growth and Survival of Pancreatic Cancer Cells (2011)

To identify novel targets in pancreatic cancer cells, we used high-throughput RNAi (HT-RNAi) to select genes that, when silenced, would decrease viability of pancreatic cancer cells. The HT-RNAi screen involved reverse transfecting the pancreatic cancer cell line BxPC3 with a siRNA library targeting 572 kinases. From replicate screens, approximately 32 kinases were designated as hits, of which 22 kinase targets were selected for confirmation and validation. One kinase identified as a hit from this screen was tyrosine kinase nonreceptor 1 (TNK1), a kinase previously identified as having tumor suppressor-like properties in embryonic stem cells. Silencing of TNK1 with siRNA showed reduced proliferation in a panel of pancreatic cancer cell lines. Furthermore, we showed that silencing of TNK1 led to increased apoptosis through a caspase-dependent pathway and that targeting TNK1 with siRNA can synergize with gemcitabine treatment. Despite previous reports that TNK1 affects Ras and NF-κB signaling, we did not find similar correlations with these pathways in pancreatic cancer cells. Our results suggest that TNK1 in pancreatic cancer cells does not possess the same tumor suppressor properties seen in embryonic cells but seems to be involved in growth and survival. The application of functional genomics by using HT-RNAi screens has allowed us to identify TNK1 as a growth-associated kinase in pancreatic cancer cells.
Restoration of Viral Immunity in Immunodeficient Humans by the Adoptive Transfer of T Cell Clones (1992)

The adoptive transfer of antigen-specific T cells to establish immunity is an effective therapy for viral infections and tumors in animal models. The application of this approach to human disease would require the isolation and in vitro expansion of human antigen-specific T cells and evidence that such T cells persist and function in vivo after transfer. Cytomegalovirus-specific CD8+ cytotoxic T cell (CTL) clones could be isolated from bone marrow donors, propagated in vitro, and adoptively transferred to immunodeficient bone marrow transplant recipients. No toxicity developed and the clones provided persistent reconstitution of CD8+ cytomegalovirus-specific CTL responses.
Contacts between the lac repressor and the thymines in the lac operator. (1977)

We have identified important points of contact between the lac repressor and the lac operator by crosslinking the repressor to bromouracil-substituted operator. We substituted bromouracils for thymines in a 55-base-long restriction fragment containing the lac operator and labeled one or the other 5' end with 32P. Ultraviolet irradiation of this fragment produced single-strand breakds at the bromouracils. We examined breakage at each bromouracil in the sequence by denaturing the DNA and displaying the UV-generated fragments on a polyacrylamide gel. In the presence of lac repressor, UV radiation failed to break at specific sites. We attribute this to a competing reaction in which the DNA crosslinks to the repressor rather than breaking. These crosslinkable sites thus define positions at which the lac repressor protein lies close to the methyl group of a thymine in the major groove of DNA.
Biochemical characterization and mechanism of action of a thermostable β-glucosidase purified from Thermoascus aurantiacus (2000)

An extracellular beta-glucosidase from Thermoascus aurantiacus was purified to homogeneity by DEAE-Sepharose, Ultrogel AcA 44 and Mono-P column chromatography. The enzyme was a homotrimer, with a monomer molecular mass of 120 kDa; only the trimer was optimally active at 80 degrees C and at pH 4.5. At 90 degrees C, the enzyme showed 70% of its optimal activity. It was stable at pH 5.2 and at temperatures up to 70 degrees C for 48 h, but stability decreased above 70 degrees C and at pH values above and below 5.0. The enzyme hydrolysed aryl and alkyl beta-d-glucosides and cello-oligosaccharides, and was specific for substrates with a beta-glycosidic linkage. The hydroxy groups at positions 2, 4 and 6 of a glucose residue at the non-reducing end of a disaccharide appeared to be essential for catalysis. The enzyme had the lowest K(m) towards p-nitrophenyl beta-d-glucoside (0.1137 mM) and the highest k(cat) towards cellobiose and beta,beta-trehalose (17052 min(-1)). It released one glucose unit at a time from the non-reducing end of cello-oligosaccharides, and the rate of hydrolysis decreased with an increase in chain length. Glucose and d-delta-gluconolactone inhibited the beta-glucosidase competitively, with K(i) values of 0.29 mM and 8.3 nM respectively, while methanol, ethanol and propan-2-ol activated the enzyme. The enzyme catalysed the synthesis of methyl, ethyl and propyl beta-d-glucosides in the presence of methanol, ethanol and propan-2-ol respectively with either glucose or cellobiose, although cellobiose was preferred. An acidic pH favoured hydrolysis and transglycosylation, but high concentrations of alcohols favoured the latter reaction. The stereochemistry of cellobiose hydrolysis revealed that beta-glucosidase from T. aurantiacus is a retaining glycosidase, while N-terminal amino acid sequence alignment indicated that it is a member of glycoside hydrolase family 3.
ATM-ATR–dependent up-regulation of DNAM-1 and NKG2D ligands on multiple myeloma cells by therapeutic agents results in enhanced NK-cell susceptibility and is associated with a senescent phenotype (2008)

There is much evidence to support a role for natural killer (NK) cells in controlling the progression of multiple myeloma (MM), a malignancy characterized by an abnormal plasma cell proliferation in the bone marrow (BM). Induction of DNA damage response has been recently shown capable of enhancing NKG2D ligand (NKG2DL) expression, but nothing is known about DNAM-1 ligand (DNAM-1L) regulation. In this study, we show that myeloma cells treated with low doses of therapeutic agents commonly used in the management of patients with MM, such as doxorubicin, melphalan, and bortezomib, up-regulate DNAM-1 and NKG2D ligands. Accordingly, therapeutic drug treatment of MM cells increases NK-cell degranulation, the NKG2D and DNAM-1 receptors being the major triggering molecules. Similar data were also obtained using ex vivo primary plasma cells derived from MM patients. Drug-induced DNAM-1 and NKG2D ligand expression was abolished after treatment with the ATM (ataxia telangiectasia mutated) and ATR (ATM- and RAD3-related) pharmacologic inhibitors caffeine and KU-55933, and was preferentially associated with senescent cells arrested in the G2 phase of the cell cycle. Altogether, our findings have identified a common pathway that can trigger the up-regulation of different NK cell-activating ligands and suggest that NK cells represent an immunosurveillance mechanism toward cells undergoing stress-induced senescent programs.
Effects of noise, image resolution, and ROI definition on the accuracy of standard uptake values: a simulation study. (2004)

The poor accuracy of the SUV under various conditions may hamper its use for diagnosis, especially in multicenter trials. SUV ratios used to measure response to treatment, however, are less dependent on noise, image resolution, and ROI definition. Therefore, the SUV might be more suitable for response-monitoring purposes.
A critical review of the role of Fc gamma receptor polymorphisms in the response to monoclonal antibodies in cancer (2013)

Antibody-dependent cellular cytotoxicity (ADCC) is a major mechanism of action of therapeutic monoclonal antibodies (mAbs) such as cetuximab, rituximab and trastuzumab. Fc gamma receptors (FcgR) on human white blood cells are an integral part of the ADCC pathway. Differential response to therapeutic mAbs has been reported to correlate with specific polymorphisms in two of these genes: FCGR2A (H131R) and FCGR3A (V158F). These polymorphisms are associated with differential affinity of the receptors for mAbs. This review critically examines the current evidence for genotyping the corresponding single nucleotide polymorphisms (SNPs) to predict response to mAbs in patients with cancer.
Adult mesenchymal stem cells and cell-based tissue engineering. (2003)

The identification of multipotential mesenchymal stem cells (MSCs) derived from adult human tissues, including bone marrow stroma and a number of connective tissues, has provided exciting prospects for cell-based tissue engineering and regeneration. This review focuses on the biology of MSCs, including their differentiation potentials in vitro and in vivo, and the application of MSCs in tissue engineering. Our current understanding of MSCs lags behind that of other stem cell types, such as hematopoietic stem cells. Future research should aim to define the cellular and molecular fingerprints of MSCs and elucidate their endogenous role(s) in normal and abnormal tissue functions.
A Role for Immune Complexes in Enhanced Respiratory Syncytial Virus Disease (2002)

Respiratory syncytial virus (RSV) is the leading cause of bronchiolitis and viral pneumonia in infants and young children. Administration of a formalin inactivated vaccine against RSV to children in the 1960s resulted in increased morbidity and mortality in vaccine recipients who subsequently contracted RSV. This incident precluded development of subunit RSV vaccines for infants for over 30 years, because the mechanism of illness was never clarified. An RSV vaccine for infants is still not available. Here, we demonstrate that enhanced RSV disease is mediated by immune complexes and abrogated in complement component C3 and B cell-deficient mice but not in controls. Further, we show correlation with the enhanced disease observed in children by providing evidence of complement activation in postmortem lung sections from children with enhanced RSV disease.