gebhart/patrepeval huggingface dataset:
Recent Developments in One‐Dimensional Inorganic Nanostructures for Photodetectors (2010)

Abstract With large surface‐to‐volume ratios and Debye length comparable to their small sizes, one‐dimensional inorganic nanostructures have extensively been investigated and widely used to fabricate high‐performance nano­scale electronic and optoelectronic devices. This feature article reviews the state‐of‐the‐art research activities that focus on the one‐dimensional inorganic nanostructures and their photodetector applications. It begins with a survey of one‐dimensional inorganic nanostructures and the fundamentals of photodetectors. Some remarkable photoresponse characteristics are then presented, which are organized into sections covering several kinds of important nanostructures, such as ZnO, V 2 O 5 , ZnS, In 2 Se 3 , InSe, CdS, CdSe, ZnSe, Sb 2 Se 3 , ZrS 2 , Ag 2 S, and Zn x Cd 1‐ x Se. Each section describes the corresponding photodetective properties in detail. Finally, the article concludes with some perspectives and outlook on the future developments in the field.
Phosphorothioate Oligodeoxynucleotides Bind to Basic Fibroblast Growth Factor, Inhibit Its Binding to Cell Surface Receptors, and Remove It from Low Affinity Binding Sites on Extracellular Matrix (1995)

We studied the interactions of phosphorothioate oligodeoxynucleotides and heparin-binding growth factors. By means of a gel mobility shift assay, we demonstrated that phosphodiester and phosphorothioate homopolymers bound to basic fibroblast growth factor (bFGF). Binding of a probe phosphodiester oligodeoxynucleotide could also be shown for other proteins of the FGF family, including acidic fibroblast growth factor (aFGF), Kaposi's growth factor (FGF-4) as well as for the bFGF-related vascular endothelial growth factor, VEGF. No binding to epidermal growth factor (EGF) was observed. In addition, using a radioreceptor assay, we have shown that phosphorothioate homopolymers of cytidine and thymidine blocked binding of not only 125I-bFGF, but also of 125I-PDGF to NIH 3T3 cells, whereas phosphodiester oligodeoxynucleotides were ineffective. The extent of blockade of binding was dependent on the chain length of the phosphorothioate oligodeoxynucleotide. Furthermore, we have examined the effects of 18-mer phosphorothioate oligodeoxynucleotides of different sequences on 125I-bFGF binding to low and high affinity sites on both NIH 3T3 fibroblasts and DU-145 prostate cancer cells. Despite the fact that we have observed inhibition of bFGF binding by the 18-mer phosphorothioate oligodeoxynucleotides for both the high and low affinity classes of bFGF receptor, the inhibition was sequence-selective only for the high affinity receptors. We have also demonstrated that phosphorothioate homopolymers of cytidine and thymidine release bFGF bound to low affinity receptors in extracellular matrix (ECM). Finally, the most potent phosphorothioate oligodeoxynucleotides used in these experiments (e.g. SdC28) were inhibitors of bFGF-induced DNA synthesis in NIH 3T3 cells.
Human Xeno-Autoantibodies against a Non-Human Sialic Acid Serve as Novel Serum Biomarkers and Immunotherapeutics in Cancer (2011)

Human carcinomas can metabolically incorporate and present the dietary non-human sialic acid Neu5Gc, which differs from the human sialic acid N-acetylneuraminic acid (Neu5Ac) by 1 oxygen atom. Tumor-associated Neu5Gc can interact with low levels of circulating anti-Neu5Gc antibodies, thereby facilitating tumor progression via chronic inflammation in a human-like Neu5Gc-deficient mouse model. Here we show that human anti-Neu5Gc antibodies can be affinity-purified in substantial amounts from clinically approved intravenous IgG (IVIG) and used at higher concentrations to suppress growth of the same Neu5Gc-expressing tumors. Hypothesizing that this polyclonal spectrum of human anti-Neu5Gc antibodies also includes potential cancer biomarkers, we then characterize them in cancer and noncancer patients' sera, using a novel sialoglycan microarray presenting multiple Neu5Gc-glycans and control Neu5Ac-glycans. Antibodies against Neu5Gcα2-6GalNAcα1-O-Ser/Thr (GcSTn) were found to be more prominent in patients with carcinomas than with other diseases. This unusual epitope arises from dietary Neu5Gc incorporation into the carcinoma marker Sialyl-Tn, and is the first example of such a novel mechanism for biomarker generation. Finally, human serum or purified antibodies rich in anti-GcSTn-reactivity kill GcSTn-expressing human tumors via complement-dependent cytotoxicity or antibody-dependent cellular cytotoxicity. Such xeno-autoantibodies and xeno-autoantigens have potential for novel diagnostics, prognostics, and therapeutics in human carcinomas.
Effect of CL-316,243, a thermogenic beta 3-agonist, on energy balance and brown and white adipose tissues in rats (1994)

The objective was to assess the effect of a new, highly selective beta 3-adrenergic agonist, CL-316,243 (CL) (J. D. Bloom, M. D. Dutia, B. D. Johnson, A. Wissner, M. G. Burns, E. E. Largis, J. A. Dolan, and T. H. Claus., J. Med. Chem. 35: 3081, 1992), on energy balance and brown and white adipose tissues (BAT and WAT, respectively) in young rats eating a high-fat diet to induce obesity. Chronic treatment with CL increased body temperature and 24-h energy expenditure, mainly by increasing resting metabolic rate. Food intake was not altered but carcass fat was reduced. Interscapular BAT was markedly hypertrophied, with three- to fourfold increases in the content of uncoupling protein (UCP) and cytochrome oxidase. Quantitative immunoelectron microscopy of interscapular BAT of CL-treated rats showed smaller mitochondria with an unchanged total amount of UCP per mitochondrion. The relative frequency of the four major cell types in BAT (mature brown adipocytes, preadipocytes, interstitial cells, endothelial cells) was not altered. The CL-induced hypertrophy differed from that induced by chronic stimulation by endogenous norepinephrine (as in cold-adaptation) in absence of hyperplasia (there was a slightly reduced DNA content), absence of an increase in the thyroxine (T4) 5'-deiodinase activity, and absence of a selective increase in UCP concentration. WAT depots weighed less and had fewer cells (lower DNA content) in the CL-treated rats. Some multilocular adipocytes appeared in these normally almost exclusively unilocular WAT depots (mesenteric, inguinal, epididymal, retroperitoneal). We conclude that CL not only promotes BAT mitochondrial proliferation and thermogenesis and overall energy expenditure and leanness, but also retards the development of WAT hyperplasia during the early stage of diet-induced obesity.
Traveling Salesman Should not be Greedy: Domination Analysis of Greedy-Type Heuristics for the TSP (2001)

&lt;p&gt;Computational experiments show that the greedy algorithm (GR)&lt;br /&gt;and the nearest neighbor algorithm (NN), popular choices for tour &lt;br /&gt;construction heuristics, work at acceptable level for the Euclidean TSP,&lt;br /&gt;but produce very poor results for the general Symmetric and Asymmetric&lt;br /&gt; TSP (STSP and ATSP). We prove that for every n &gt;= 2 there&lt;br /&gt;is an instance of ATSP (STSP) on n vertices for which GR finds the&lt;br /&gt;worst tour. The same result holds for NN. We also analyze the repetitive&lt;br /&gt; NN (RNN) that starts NN from every vertex and chooses the best&lt;br /&gt;tour obtained. We prove that, for the ATSP, RNN always produces&lt;br /&gt;a tour, which is not worse than at least n/2 − 1 other tours, but for&lt;br /&gt;some instance it finds a tour, which is not worse than at most n − 2&lt;br /&gt;other tours, n &gt;= 4. We also show that, for some instance of the STSP&lt;br /&gt;on n &gt;= 4 vertices, RNN produces a tour not worse than at most 2^(n−3) tours. These results are in sharp contrast to earlier results by G. Gutin and A. Yeo, and A. Punnen and S. Kabadi, who proved that, for the ATSP, there are tour construction heuristics, including some popular ones, that always build a tour not worse than at least (n − 2)! tours.&lt;/p&gt;&lt;p&gt;Keywords: TSP, domination analysis, greedy algorithm, nearest&lt;br /&gt;neighbor algorithm&lt;/p&gt;
Optical multimode frequency-domain reflectometer (1994)

A multimode laser can instantaneously generate a carrier frequency of significantly wide band. The proposed systems, composed of a free-running multimode laser diode, an optical spectrometer, and a computing system for fast Fourier transformation, can easily provide the potential for ultrahigh resolution of the order of 10 microm without scanning frequencies as in frequency-domain reflectometers of either the continuously or the stepwise-swept variety.
Structures of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability near the Active Center (2011)

Formation of N-terminal pyroglutamate (pGlu or pE) from glutaminyl or glutamyl precursors is catalyzed by glutaminyl cyclases (QC). As the formation of pGlu-amyloid has been linked with Alzheimer's disease, inhibitors of QCs are currently the subject of intense development. Here, we report three crystal structures of N-glycosylated mammalian QC from humans (hQC) and mice (mQC). Whereas the overall structures of the enzymes are similar to those reported previously, two surface loops in the neighborhood of the active center exhibit conformational variability. Furthermore, two conserved cysteine residues form a disulfide bond at the base of the active center that was not present in previous reports of hQC structure. Site-directed mutagenesis suggests a structure-stabilizing role of the disulfide bond. At the entrance to the active center, the conserved tryptophan residue, W(207), which displayed multiple orientations in previous structure, shows a single conformation in both glycosylated human and murine QCs. Although mutagenesis of W(207) into leucine or glutamine altered substrate conversion significantly, the binding constants of inhibitors such as the highly potent PQ50 (PBD150) were minimally affected. The crystal structure of PQ50 bound to the active center of murine QC reveals principal binding determinants provided by the catalytic zinc ion and a hydrophobic funnel. This study presents a first comparison of two mammalian QCs containing typical, conserved post-translational modifications.
Adult somatic cell nuclear transfer is used to preserve the last surviving cow of the Enderby Island cattle breed (1999)

To preserve the female genetics of an endangered breed of cattle, adapted to sub-Antarctic conditions, adult somatic cell nuclear transfer was used to clone the last surviving Enderby Island cow from mural granulosa cells. Embryos reconstructed with metaphase II cytoplasts and quiescent cells were either activated and fused simultaneously (AFS) at 24 or 30 hours post maturation (hpm) or alternatively, fused 4-6 h before activation at 26-30 hpm (FBA). A significantly higher proportion of fused embryos developed in vitro to grade 1-3 blastocysts on Day 7 with FBA (39.8+/-2.8%) compared to AFS with activation either at 24 hpm (10.6+/-3.9%, P<0.01) or at 30 hpm (18.6+/-4.1%, P<0.01). Following the transfer of 74 embryos from the FBA treatment over two experiments, survival rates on Days 30, 55, 85, 150 and 190 of pregnancy were 38%, 30%, 23%, 16% and 15%, respectively. Of 22 embryos transferred in the first experiment, two calves were born alive with one calf surviving. DNA analyses confirmed that the calves were genetically identical to the Enderby Island cow. Additional pregnancies are currently ongoing. These data show that embryo development is increased by prolonged exposure of quiescent somatic cell nuclei to oocyte cytoplasm before artificial activation, possibly facilitating nuclear reprogramming. The successful demonstration of somatic cell nuclear transfer in animal conservation extends the applications of the technology beyond the main agricultural and biomedical interests.
Efficacy of the Novel Camptothecin Gimatecan against Orthotopic and Metastatic Human Tumor Xenograft Models (2004)

In all tumor systems investigated, including orthotopic tumor growth models and lung metastases, the oral administration of gimatecan showed a therapeutic benefit in terms of survival increase. The good oral availability allowed a prolonged daily treatment regimen, which seems the most promising to exploit the therapeutic potential of the drug.
Mechanism of tumor dormancy (2015)

Tumor dormancy is a phase of occurrence and progress of cancer. In recent years, with the further study of circulating tumor cells, disseminated tumor cells and cancer stem cells, it is found that they are closely related to the tumor dormancy. Moreover, tumor microenvironment is another important factor in tumor dormancy.


Key words: 
Neoplasms; Dormancy period; Tumor microenvironment
Alterations of Na+Currents in Myocytes From Epicardial Border Zone of the Infarcted Heart (1997)

Previously, we have shown abnormalities in Vmax and in the recovery of Vmax in myocytes dispersed from the epicardial border zone (EBZ) of the 5-day infarcted canine heart (myocytes from the EBZ [IZs]). Thus, we sought to determine the characteristics of the whole-cell Na+ current (INa) in IsZs and compare them with the INa of cells from noninfarcted hearts (myocytes from noninfarcted epicardium [NZs]). INa was recorded using patch-clamp techniques under conditions that eliminated contaminating currents and controlled INa for measurement (19 degrees C, 5 mmol/L [Na+]zero). Peak INa density (at -25 mV) was significantly reduced in IZs (4.9 +/- 0.44 pA/pF, n = 36) versus NZs (12.8 +/- 0.55 pA/pF, n = 54; P < .001), yet the half-maximal activation voltage (V0.5), time course of decay, and time to peak INa were no different. However, in IZs, V0.5 of the availability curve (I/Imax curve) was shifted significantly in the hyperpolarizing direction (-80.2 +/- 0.48 mV in NZs [n = 45] versus -83.9 +/- 0.59 mV in IZs [n = 27], P < .01). Inactivation of INa directly from a depolarized prepotential (-60 mV) was significantly accelerated in IZs versus NZs (fast and slow time constants [T1 and T2, respectively] were as follows: NZs [n = 28], T1 = 71.5 +/- 5.6 ms and T2 = 243.7 +/- 17.1 ms; IZs [n = 21], T1 = 36.3 +/- 2.4 ms and T2 = 153 +/- 11.3 ms; P < .001). Recovery of INa from inactivation was dependent on the holding potential (VH) in both cell types but was significantly slower in IZs. At (VH) = -90 mV, INa recovery had a lag in 18 (82%) of 22 IZs (with a 17.6 +/- 1.5-ms lag) versus 2 (9%) of 22 NZs (with 5.9- and 8.7-ms lags); at VH = -100 mV, T1 = 60.9 +/- 2.6 ms and T2 = 352.8 +/- 28.1 ms in NZs (n = 41) versus T1 = 76.3 +/- 4.8 ms and T2 = 464.4 +/- 47.2 ms in IZs (n = 26) (P < .002 and P < .03, respectively); at VH = -110 mV, T1 = 33.4 +/- 1.8 ms and T2 = 293.5 +/- 33.6 ms in NZs (n = 21) versus T1 = 44.3 +/- 2.9 ms and T2 = 388.4 +/- 38 ms in IZs (n = 18) (P < .002 and P < .07, respectively). In sum, INa is reduced, and its kinetics are altered in IZs. These changes may underlie the altered excitability and postrepolarization refractoriness of the ventricular fibers of the EBZ, thus contributing to reentrant arrhythmias in the infarcted heart.
Prefractionation techniques in proteome analysis (2003)

The present review deals with a number of prefractionation protocols in preparation for two-dimensional map analysis, both in the fields of chromatography and in the field of electrophoresis. In the first case, Fountoulaki's groups has reported just about any chromatographic procedure useful as a prefractionation step, including affinity, ion-exchange, and reversed-phase resins. As a result of the various enrichment steps, several hundred new species, previously undetected in unfractionated samples, could be revealed for the first time. Electrophoretic prefractionation protocols include all those electrokinetic methodologies which are performed in free solution, essentially all relying on isoelectric focusing steps. The devices here reviewed include multichamber apparatus, such as the multicompartment electrolyzer with Immobiline membranes, Off-Gel electrophoresis in a multicup device and the Rotofor, an instrument also based on a multichamber system but exploiting the conventional technique of carrier-ampholyte-focusing. Other instruments of interest are the Octopus, a continuous-flow device for isoelectric focusing in a upward flowing liquid curtain, and the Gradiflow, where different pI cuts are obtained by a multistep passage through two compartments buffered at different pH values. It is felt that this panoply of methods could offer a strong step forward in "mining below the tip of the iceberg" for detecting the "unseen proteome".
Training and search algorithms for an interactive wordspotting system (1992)

Algorithms for a speaker-dependent wordspotting system based on hidden Markov models (HMMs) are described. The system allows a user to specify keywords dynamically and to train the associated HMMs via a single repetition of a keyword. Nonkeyword speech is modeled using an HMM trained from a prerecorded sample of continuous speech. The wordspotter is intended for interactive applications, such as the editing of voice mail or mixed-media documents, and for keyword indexing in audio or video recordings. The forward-backward search algorithm used in the wordspotter is compared with the Viterbi decoder on the basis of speed and accuracy. In addition, an algorithm for speaker adaptation is described which allows indexing by a user into another talker's speech.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recognizing textual entailment: Rational, evaluation and approaches (2009)

Abstract The goal of identifying textual entailment – whether one piece of text can be plausibly inferred from another – has emerged in recent years as a generic core problem in natural language understanding. Work in this area has been largely driven by the PASCAL Recognizing Textual Entailment (RTE) challenges, which are a series of annual competitive meetings. The current work exhibits strong ties to some earlier lines of research, particularly automatic acquisition of paraphrases and lexical semantic relationships and unsupervised inference in applications such as question answering, information extraction and summarization. It has also opened the way to newer lines of research on more involved inference methods, on knowledge representations needed to support this natural language understanding challenge and on the use of learning methods in this context. RTE has fostered an active and growing community of researchers focused on the problem of applied entailment. This special issue of the JNLE provides an opportunity to showcase some of the most important work in this emerging area.
Two-step activation of paper batteries for high power generation: design and fabrication of biofluid- and water-activated paper batteries (2006)

Two-step activation of paper batteries has been successfully demonstrated to provide quick activation and to supply high power to credit card-sized biosystems on a plastic chip. A stack of a magnesium layer (an anode), a fluid guide (absorbent paper), a highly doped filter paper with copper chloride (a cathode) and a copper layer as a current collector is laminated between two transparent plastic films into a high power biofluid- and water-activated battery. The battery is activated by two-step activation: (1) after placing a drop of biofluid/water-based solution on the fluid inlet, the surface tension first drives the fluid to soak the fluid guide; (2) the fluid in the fluid guide then penetrates into the heavily doped filter paper with copper chloride to start the battery reaction. The fabricated half credit card-sized battery was activated by saliva, urine and tap water and delivered a maximum voltage of 1.56 V within 10 s after activation and a maximum power of 15.6 mW. When 10 kΩ and 1 KΩ loads are used, the service time with water, urine and saliva is measured as more than 2 h. An in-series battery of 3 V has been successfully tested to power two LEDs (light emitting diodes) and an electric driving circuit. As such, this high power paper battery could be integrated with on-demand credit card-sized biosystems such as healthcare test kits, biochips, lab-on-a-chip, DNA chips, protein chips or even test chips for water quality checking or chemical checking.
MEIOTIC AND MITOTIC BEHAVIOR OF DICENTRIC CHROMOSOMES IN SACCHAROMYCES CEREVISIAE (1984)

Meiotic recombination between a circular and a linear chromosome in Saccharomyces cerevisiae has been investigated. The circle was a haploid-viable derivative of chromosome III constructed by joining regions near the two chromosome ends via a recombinant DNA construction: (HMR/MAT-URA3-pBR322-MAT/HML) and was also deleted for MAL2 (which therefore uniquely marks a linear chromosome III). Recombination along chromosome III was measured for eight intervals spanning the entire length of the circular derivative. Only 25% of all tetrads from a ring/rod diploid contained four viable spores. These proved to be cases in which there was either no recombination along chromosome III or in which there were two-strand double crossovers or higher order crossovers that would not produce a dicentric chromosome.--At least half of the tetrads with three viable spores included one Ura+ Mal+ spore that was genetically highly unstable. The Ura+ Mal+ spore colonies gave rise to as many as seven genetically distinct, stable ("healed") derivatives, some of which had lost either URA3 or MAL2. Analysis of markers on chromosome III suggests that dicentric chromosomes frequently do not break during meiosis but are inherited intact into a haploid spore. In mitosis, however, the dicentric chromosome is frequently broken, giving rise to a variety of genetically distinct derivatives. We have also shown that dicentric ring chromosomes exhibit similar behavior: at least half the time they are not broken during meiosis but are broken and healed during mitosis.--The ring/rod diploid can also be used to determine the frequency of sister chromatid exchange (SCE) along an entire yeast ring chromosome. We estimate that an unequal number of SCE events occurs in approximately 15% of all cells undergoing meiosis. In contrast, the mitotic instability (and presumably SCE events) of a ring chromosome is low, occurring at a rate of about 1.2 X 10(-3) per cell division.
MatchNet: Unifying feature and metric learning for patch-based matching (2015)

Motivated by recent successes on learning feature representations and on learning feature comparison functions, we propose a unified approach to combining both for training a patch matching system. Our system, dubbed Match-Net, consists of a deep convolutional network that extracts features from patches and a network of three fully connected layers that computes a similarity between the extracted features. To ensure experimental repeatability, we train MatchNet on standard datasets and employ an input sampler to augment the training set with synthetic exemplar pairs that reduce overfitting. Once trained, we achieve better computational efficiency during matching by disassembling MatchNet and separately applying the feature computation and similarity networks in two sequential stages. We perform a comprehensive set of experiments on standard datasets to carefully study the contributions of each aspect of MatchNet, with direct comparisons to established methods. Our results confirm that our unified approach improves accuracy over previous state-of-the-art results on patch matching datasets, while reducing the storage requirement for descriptors. We make pre-trained MatchNet publicly available.