gebhart/patrepeval huggingface dataset:
Second line therapy for advanced pancreatic adenocarcinoma: where are we and where are we going? Highlights from the "2010 ASCO Annual Meeting". Chicago, IL, USA. June 4-8, 2010. (2010)

Most patients with adenocarcinoma of the pancreas present with locally advanced or metastatic disease. Although single agent gemcitabine is widely accepted as first-line therapy, there is no current standard of care for gemcitabine-refractory patients. Common second-line chemotherapy regimens included oxaliplatin and 5-FU/leucovorin (OFF), gemcitabine and oxaliplatin (GEMOX), oxaliplatin and capecitabine (XELOX), and irinotecan-oxaliplatin. At the 2010 American Society of Clinical Oncology (ASCO) Annual Meeting, several new second-line chemotherapy regimens were presented, including gemcitabine and oxaliplatin with imatinib, single agent nab-paclitaxel, and the combination of high-dose capecitabine with oxaliplatin and sorafenib. These abstracts provide exciting new directions for the treatment of gemcitabine-refractory advanced pancreatic cancer.
Stable binding of recA protein to duplex DNA. Unraveling a paradox. (1987)

recA protein binding to duplex DNA is a complicated, multistep process. The final product of this process is a stably bound complex of recA protein and extensively unwound double-stranded DNA. recA monomers within the complex hydrolyze ATP with an apparent kcat of approximately 19-22 min-1. Once the final binding state is achieved, binding and ATP hydrolysis by this complex becomes pH independent. The weak binding of recA protein to duplex DNA reported in previous studies does not, therefore, reflect an intrinsically unfavorable binding equilibrium. Instead, this apparent weak binding reflects a slow step in the association pathway. The rate-limiting step in this process involves the initiation rather than the propagation of DNA binding and unwinding. This step exhibits no dependence on recA protein concentration at pH 7.5. Extension or propagation of the recA filament is fast relative to the overall process. Initiation of binding is pH dependent and represents a prominent kinetic barrier at pH 7.5. ATP hydrolysis occurs only after the duplex DNA is unwound. The binding density of recA protein on double-stranded DNA is approximately one monomer/4 base pairs. A model for this process is presented. These results provide an explanation for several paradoxical observations about recA protein-promoted DNA strand exchange. In particular, they demonstrate that there is no thermodynamic requirement for dissociation of recA protein from the heteroduplex DNA product of strand exchange.
Enzymatic activation of a doxorubicin-peptide prodrug by prostate-specific antigen. (1998)

New approaches to target cytotoxic therapy specifically to metastatic prostate cancer sites are urgently needed. As such an approach, an inactive prodrug was synthesized by coupling the primary amine of doxorubicin to the COOH-terminal carboxyl of a seven-amino acid peptide carrier (i.e., Mu-His-Ser-Ser-Lys-Leu-Gln-Leu). The seven-amino acid peptide was documented to be hydrolyzable specifically by the serine protease prostate-specific antigen (PSA) to liberate the active cytotoxin L-leucyl-doxorubicin. Primary cultures of PC-82 human prostate cancer cells secreted high levels of enzymatically active PSA (i.e., 70 +/- 5 ng of enzymatically active PSA/10(6) cells/24 h), whereas LNCaP human prostate cancer cells produced lower levels of enzymatically active PSA (i.e., 2.3 +/- 1 ng/10(6) cells/24 h). LNCaP cells, however, secreted sufficient amounts of enzymatically active PSA to activate the doxorubicin prodrug to a cytotoxic form in vitro. The specificity of the cytotoxic response to the prodrug was demonstrated by the fact that 70 nM of the prodrug killed 50% of the PSA-producing LNCaP cells, whereas doses as high as 1 microM had no cytotoxic effect on PSA-nonproducing TSU human prostate cancer cells in vitro.
The expression of TNF alpha by human muscle. Relationship to insulin resistance. (1996)

TNFalpha is orverexpressed in the adipose tissue of obese rodents and humans, and is associated with insulin resistance. To more closely link TNF expression with whole body insulin action, we examined the expression of TNF by muscle, which is responsible for the majority of glucose uptake in vivo. Using RT-PCR, TNF was detected in human heart, in skeletal muscle from humans and rats, and in cultured human myocytes. Using competitive RT-PCR, TNF was quantitated in the muscle biopsy specimens from 15 subjects whose insulin sensitivity had been characterized using the glucose clamp. technique. TNF expression in the insulin resistant subjects and the diabetic patients was fourfold higher than in the insulin sensitive subjects, and there was a significant inverse linear relationship between maximal glucose disposal rate and muscle TNF (r = -0.60, P < 0.02). In nine subjects, muscle cells from vastus lateralis muscle biopsies were placed into tissue culture for 4 wk, and induced to differentiate into myotubes. TNF was secreted into the medium from these cells, and cells from diabetic patients expressed threefold more TNF than cells from nondiabetic subjects. Thus, TNF is expressed in human muscle, and is expressed at a higher level in the muscle tissue and in the cultured muscle cells from insulin resistant and diabetic subjects. These data suggest another mechanism by which TNF may play an important role in human insulin resistance.
MBE growth of cubic GaN on GaAs substrates (1996)

Abstract We review our recent results on plasma‐assisted molecular beam epitaxy of cubic GaN films on GaAs(001). The crucial role of the nucleation stage for obtaining epitaxial growth is highlighted by reflection high‐energy electron diffraction and transmission electron microscopy. For the subsequent growth, it is found that the surface stoichiometry determines the phase composition of the epilayers as determined by X‐ray reciprocal space mapping, Raman and cathodoluminescence spectroscopy. For an in situ control of the surface stoichiometry, we develop a method based on the transitions of the surface reconstructions of cubic (001)GaN. Films grown under conditions optimized by this method are single‐phase cubic and exhibit intense excitonic luminescence up to room temperature.
Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities (2008)

High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic), BRCA1 loss (epigenetic), and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways.
Pulse Laser Sulfur-Hyperdoping of Germanium and High Quantum Efficiency Photodiodes (2016)

Germanium was successfully hyperdoped with sulfur by means of nanosecond pulse laser and SF6 gas. A photodiode was fabricated based on sulfur-hyperdoped germanium. Rectifying current-voltage characteristics were observed for the device. The sulfur-hyperdoped germanium photodiode showed an internal quantum efficiency close to 150% from visible to near infrared and increased to 275% for the ultraviolet region. The -3 dB bandwidth was measured to be 20 MHz. Sulfur was demonstrated to be an effective deep level dopant for realizing high-performance germanium photodiodes.
Multi-modality tissue-mimicking phantom for thermal therapy (2004)

A tissue-mimicking phantom material has been developed for use with thermal therapy devices and techniques. This material has magnetic resonance properties (primarily T2) which change drastically upon thermal coagulation, enabling its use for device characterization and treatment verification using simple T2-weighted imaging techniques. The coagulation temperature of the phantom can be changed from 50-60 degrees C by adjusting the pH from 4.3 to 4.7. The energy absorption properties can be adjusted to match the acoustical and optical properties of tissues. T2 relaxation measurements are provided as a function of temperature, along with T2-weighted MR images to illustrate the visualization of heating patterns. A complete recipe for fabricating phantoms is provided.
Black Flower Coloration in Wild Lisianthius nigrescens: Its Chemistry and Ecological Consequences (2004)

The major pigments responsible for the flower color within the black flowered Gentianaceae, Lisianthius nigrescens, were characterized by HPLC and chemical analyses HPLC analysis showed one major and one minor anthocyanin and 3 major and 3 minor flavone glycosides. The anthocyanins [delphinidin-3-O-rhamnol(1-6)galactoside and its 5-O-glucoside] comprised an extraordinary 24% of the dry weight of wild collected L. nigrescens corallas, and were accompanied in a 1:1 ratio by a range of apigenin and luteolin 8-C-glucosides and their 7-O-methyl ethers. The high levels of anthocyanins and flavones (and their co-pigmentation) is thought to account for the almost complete absorption of both UV and visible wavebands observed by reflectance photography.
Nanobelts, Nanowires, and Nanodiskettes of Semiconducting Oxides—From Materials to Nanodevices (2003)

Abstract Novel nanostructures of semiconducting oxides are reviewed here. It is shown that nanobelts, nanowires, and nanodiskettes of materials such as zinc oxide, gallium oxide, silica, and tin oxide can be fabricated using a vapor‐phase evaporation method. Two applications of these materials—in field effect transistors and as gas sensors—are highlighted.
A Sensitive and Quantitative Assay for Measuring Cleavage of Presenilin Substrates (2002)

The presenilin (PS) proteins are components of the gamma-secretase activity, which is central in the pathogenesis of Alzheimer's disease. Here we present a novel cell-based reporter gene assay for the quantification of PS-controlled gamma-secretase cleavage of the Alzheimer amyloid precursor protein (APP). We show that this assay offers several advantages, including increased sensitivity and specificity, improved quantification of cleavage, and simultaneous detection of all gamma-secretase cleavages in APP. Furthermore, the APP assay can be used in parallel with a similar assay that records gamma-secretase cleavage of a Notch receptor. The use of these assays to analyze the effects of two known gamma-secretase inhibitors and postulated PS active site mutants on APP and Notch processing demonstrated that inhibitors and mutants that differently affect Notch and APP cleavage can be identified rapidly. The possibility in using these assays for high throughput screening of candidate gamma-secretase inhibitors for APP and Notch in parallel opens up new vistas to systematically search for novel inhibitors that selectively block APP cleavage while not affecting Notch signaling.
Discrimination Between Perfect and Mismatched Duplexes with Oligonucleotide Gel Microchips: Role of Thermodynamic and Kinetic Effects During Hybridization (2005)

The efficiency of discrimination between perfect and mismatched duplexes during hybridization on microchips depends on the concentrations of target DNA in solution and immobilized probes, buffer composition, and temperature of hybridization and is determined by both thermodynamic relationships and hybridization kinetics. In this work, optimal conditions of discrimination were studied using hybridization of fluorescently labeled target DNA with custom-made gel-based oligonucleotide microchips. The higher the concentration of immobilized probes and the higher the association constant, the higher the concentration of the formed duplexes and the stronger the corresponding fluorescence signal, but, simultaneously, the longer the time needed to reach equilibrium. Since mismatched duplexes hybridize faster than their perfect counterparts, perfect-to-mismatch signal ratio is lower in transient regime, and short hybridization times may hamper the detection of mutations. The saturation time can be shortened by decreasing the probe concentration or augmenting the gel porosity. This improves the detection of mutations in transient regime. It is shown that the decrease in the initial concentration of oligonucleotide probes by an order of magnitude causes only 1.5-2.5-fold decrease of fluorescence signals after hybridization of perfect duplexes for 3-12 h. At the same time, these conditions improve the discrimination between perfect and mismatched duplexes more than two-fold. A similar improvement may be obtained using an optimized dissociation procedure.
Nitric oxide production and inducible nitric oxide synthase expression in peritoneal macrophages of cirrhotic patients (1999)

The present study assessed whether peritoneal macrophages isolated from cirrhotic patients produce nitric oxide (NO) and express NO synthase type II (NOS II) mRNA and protein. Patients with cirrhosis and ascites without peritonitis or with unresolved or resolved spontaneous bacterial peritonitis (SBP) were studied. Following paracentesis, ascites NO(2)(-) + NO(3)(-) content (NOx) was measured. Peritoneal macrophages from ascites were seeded on well plates, and NO(2)(-) in the medium was determined. NOx was higher in patients with unresolved or resolved SBP than in cirrhotic patients without peritonitis. Macrophages of patients with SBP or resolved SBP produced NO(2)(-) after 30 hours in culture, but those obtained from patients without peritonitis did not. Reverse-transcription polymerase chain reaction (RT-PCR) and immunocytochemical analysis revealed the presence of a clear signal for NOS II mRNA and protein in macrophages of SBP patients, regardless of whether or not the infection subsided. Therefore, peritoneal macrophages isolated from cirrhotic patients with unresolved or resolved SBP produce NO and express the NOS II mRNA and protein, suggesting that NOS II may contribute to the control of SBP, or to its associated pathology, in human cirrhosis.
Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis (2014)

Eukaryotic 18S ribosomal RNA (rRNA) gene primers that feature a wide coverage are critical in detecting the composition of eukaryotic microscopic organisms in ecosystems. Here, we predicted 18S rRNA primers based on consecutive conserved sites and evaluated their coverage efficiency and scope of application to different eukaryotic groups. After evaluation, eight of them were considered as qualified 18S primers based on coverage rate. Next, we examined common conserved regions in prokaryotic 16S and eukaryotic 18S rRNA sequences to design 16S/18S universal primers. Three 16S/18S candidate primers, U515, U1390 and U1492, were then considered to be suitable for simultaneous amplification of the rRNA sequences in three domains. Eukaryotic 18S and prokaryotic 16S rRNA genes in a sponge were amplified simultaneously using universal primers U515 and U1390, and the subsequent sorting of pyrosequenced reads revealed some distinctive communities in different parts of the sample. The real difference in biodiversity between prokaryotic and eukaryotic symbionts could be discerned as the dissimilarity between OTUs was increased from 0.005 to 0.1. A network of the communities in external and internal parts of the sponge illustrated the co-variation of some unique microbes in certain parts of the sponge, suggesting that the universal primers are useful in simultaneous detection of prokaryotic and eukaryotic microbial communities.
The persisting (P) cell: histamine content, regulation by a T cell-derived factor, origin from a bone marrow precursor, and relationship to mast cells. (1981)

Histamine was detected at levels of 100 ng/10(6) cells in the metachromatic granules of the persisting (P) cell, which appears in cultures of murine lymphoid or bone marrow cells and is capable of long-term growth in vitro in the presence of a T cell-derived growth factor. This factor, which we termed P-cell stimulating factor, was distinct from t-cell growth factor and had an apparent molecular weight of 25,000-30,000. P cells did not originate from Thy.1-positive cells nor was the thymus necessary for the development of their precursors. Moreover, P cells grew directly from colonies generated in agar cultures of bone marrow cells, the nature of the colonies indicating that P cells shared a common precursor with hemopoietic cells. Mutant Wf/Wf mice, although deficient in certain mast cells, possessed P-cell precursors. It is hypothesized that P cells are related to a specialized subset of mast cells, derived from a bone marrow progenitor but regulated by activated T cells.
The emerging role of iron, zinc, copper, magnesium and selenium and oxidative stress in health and diseases (2005)

From Volume 20 (2006), this title is published by Society of Integrated Sciences (International Medart, PO Box 37, 814 99 Bratislava 1, Slovak Republic, E-mail: publisher@nel.edu, Fax: +41 13553207).
Gesture recognition via pose classification (2002)

This paper describes a modular approach to gesture recognition. The complex task of gesture recognition from image sequences was decomposed by first identifying the hand pose in individual frames. The pose information was then incorporated with hand motion to recognize gestures. Independent recognition modules were devised for different subtasks. A radial basis function (RBF) neural network was trained to recognize static hand poses. Inputs to the RBF network were feature vectors extracted from segmented 2D binary images of the hand. The pose recognition results of using Zernike moments and Fourier descriptors as the feature vectors were compared, and it was found that Fourier descriptors were superior in terms of computational speed. Combined outputs from a set of recurrent neural networks (RNN) and hidden Markov model (HMM) chains were used to recognize gestures from the temporal sequence of pose classifier outputs. The combined classifier achieved a recognition rate of 86.8%. In addition, we illustrate that the inclusion of an intermediate pose classification stage is advantageous for recognition and training speed.
Localized and directed lateral growth of carbon nanotubes from a porous template (2002)

We report on the growth of laterally oriented carbon nanotubes with both positional and directional control. The growth was done by chemical vapor deposition from Fe/Mo catalyst embedded inside a porous silicon medium which was formed electrochemically on the vertical faces of etched posts on a silicon substrate. A solution containing the catalyst was allowed to diffuse into the porous medium only in lithographically defined areas. Nanotubes grew only in the patterned areas with a preferred orientation normal to the edges of the etched posts.
Ionic Conductivity of LiTi2(PO4)3 Mixed with Lithium Salts (1990)

Abstract LiTi2(PO4)3-lithium salt systems have been investigated in order to obtain a high lithium ion conductor. The salts acted as binder for sintering. The porosity decreased considerably and the conductivity of the pellets increased by the binder utilization. The maximum conductivity was 3 × 10−4 S·cm−1 for the LiTi2(PO4)3–0.2Li3BO3 system. The mixed binder was found to exist as a glassy or a thin coating second phase.
Sphere decoding for retransmission diversity in MIMO flat-fading channels (2004)

We define an ARQ protocol for MIMO flat-fading channels which varies the bit-to-symbol mapping per retransmission. We begin by defining a model for distinctly mapped transmissions through MIMO channels, and the effect this mapping diversity has on a sphere decoder receiver. Varying the symbol mapping complicates the sphere decoding process, particularly for the enumeration of candidate solutions within the sphere. A technique that promises quick candidate enumeration is suggested, borrowing concepts from existing closest point search schemes. The value of mapping diversity, in reducing BER and reducing computational complexity, is analyzed.
Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA (2002)

Pyrrolysine is a lysine derivative encoded by the UAG codon in methylamine methyltransferase genes of Methanosarcina barkeri. Near a methyltransferase gene cluster is the pylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon. The adjacent pylS gene encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with lysine but is not closely related to known lysyl-tRNA synthetases. Homologs of pylS and pylT are found in a Gram-positive bacterium. Charging a tRNA(CUA) with lysine is a likely first step in translating UAG amber codons as pyrrolysine in certain methanogens. Our results indicate that pyrrolysine is the 22nd genetically encoded natural amino acid.
Construction of Plant Expression Vector of Fusion Gene Ubiquitin and Signal Peptide Sequence of Pathogenesis-related Protein 1a (2006)

The fusion protein of ubiquitin had been used to enhance output of exterior protein.Signal peptide sequence can convey extraneous protein to a specifical position of cell.Ubiquitin and signal peptide sequence of pathogenesis-related protein 1a(PRS) were recombined together by TP-PCR in the research based on pBin438 of the efficient strongly plant expression vector.The fusion gene was constructed on expression vector pBLG(named pBLG-UP).The experiment would lay a foundation for accumulating protein effectively in the plant.
Bone Disease in Thalassemia: A Frequent and Still Unresolved Problem (2008)

Adults with beta thalassemia major frequently have low BMD, fractures, and bone pain. The purpose of this study was to determine the prevalence of low BMD, fractures, and bone pain in all thalassemia syndromes in childhood, adolescence, and adulthood, associations of BMD with fractures and bone pain, and etiology of bone disease in thalassemia. Patients of all thalassemia syndromes in the Thalassemia Clinical Research Network, > or =6 yr of age, with no preexisting medical condition affecting bone mass or requiring steroids, participated. We measured spine and femur BMD and whole body BMC by DXA and assessed vertebral abnormalities by morphometric X-ray absorptiometry (MXA). Medical history by interview and review of medical records, physical examinations, and blood and urine collections were performed. Three hundred sixty-one subjects, 49% male, with a mean age of 23.2 yr (range, 6.1-75 yr), were studied. Spine and femur BMD Z-scores < -2 occurred in 46% and 25% of participants, respectively. Greater age, lower weight, hypogonadism, and increased bone turnover were strong independent predictors of low bone mass regardless of thalassemia syndrome. Peak bone mass was suboptimal. Thirty-six percent of patients had a history of fractures, and 34% reported bone pain. BMD was negatively associated with fractures but not with bone pain. Nine percent of participants had uniformly decreased height of several vertebrae by MXA, which was associated with the use of iron chelator deferoxamine before 6 yr of age. In patients with thalassemia, low BMD and fractures occur frequently and independently of the particular syndrome. Peak bone mass is suboptimal. Low BMD is associated with hypogonadism, increased bone turnover, and an increased risk for fractures.