gebhart/patrepeval huggingface dataset:
A piezoelectric micro-cantilever bio-sensor using the mass-micro-balancing technique with self-excitation (2005)

A micro biosensor, which can be applied to a lab-on-a-chip (LOC), is developed in order to detect biomaterials such as protein or DNA. The biomaterials are detected by the mass micro-balancing technique, which measures the change of the resonant frequency of the sensor structure. The sensor structure consists of a micro cantilever actuated by piezoelectric PZT film. The PZT film is designed to act as both a sensor and an actuator. The geometry of the micro-cantilever is determined so as to maximize the sensitivity of the sensor, and environmental effects such as added mass effect in liquid are also considered in the design procedure. The microcantilever is 100 /spl mu/m in length, 30 /spl mu/m in width and 5 /spl mu/m in thickness, and the PZT film thickness is 2.5 /spl mu/m. The first resonant frequency of the PZT-micro cantilever is 1.2/spl sim/1.3 MHz. Lastly, the fabricated micro biosensor using the self-exciting PZT-micro cantilever is tested by detecting the insulin-anti insulin binding protein and poly T-sequence DNA.
Genetic analysis of attractin homologs (2007)

Attractin (ATRN) and Attractin-like 1 (ATRNL1) are highly similar type I transmembrane proteins. Atrn null mutant mice have a pleiotropic phenotype including dark fur, juvenile-onset spongiform neurodegeneration, hypomyelination, tremor, and reduced body weight and adiposity, implicating ATRN in numerous biological processes. Bioinformatic analysis indicated that Atrn and Atrnl1 arose from a common ancestral gene early in vertebrate evolution. To investigate the genetics of the ATRN system and explore potential redundancy between Atrn and Atrnl1, we generated and characterized Atrnl1 loss- and gain-of-function mutations in mice. Atrnl1 mutant mice were grossly normal with no alterations of pigmentation, central nervous system pathology or body weight. Atrn null mutant mice carrying a beta-actin promoter-driven Atrnl1 transgene had normal, agouti-banded hairs and significantly delayed onset of spongiform neurodegeneration, indicating that over-expression of ATRNL1 compensates for loss of ATRN. Thus, the two genes are redundant from the perspective of gain-of-function but not loss-of-function mutations.
The primary antimitotic mechanism of action of the synthetic halichondrin E7389 is suppression of microtubule growth (2005)

E7389, which is in phase I and II clinical trials, is a synthetic macrocyclic ketone analogue of the marine sponge natural product halichondrin B. Whereas its mechanism of action has not been fully elucidated, its main target seems to be tubulin and/or the microtubules responsible for the construction and proper function of the mitotic spindle. Like most microtubule-targeted antitumor drugs, it inhibits tumor cell proliferation in association with G(2)-M arrest. It binds to tubulin and inhibits microtubule polymerization. We examined the mechanism of action of E7389 with purified microtubules and in living cells and found that, unlike antimitotic drugs including vinblastine and paclitaxel that suppress both the shortening and growth phases of microtubule dynamic instability, E7389 seems to work by an end-poisoning mechanism that results predominantly in inhibition of microtubule growth, but not shortening, in association with sequestration of tubulin into aggregates. In living MCF7 cells at the concentration that half-maximally blocked cell proliferation and mitosis (1 nmol/L), E7389 did not affect the shortening events of microtubule dynamic instability nor the catastrophe or rescue frequencies, but it significantly suppressed the rate and extent of microtubule growth. Vinblastine, but not E7389, inhibited the dilution-induced microtubule disassembly rate. The results suggest that, at its lowest effective concentrations, E7389 may suppress mitosis by directly binding to microtubule ends as unliganded E7389 or by competition of E7389-induced tubulin aggregates with unliganded soluble tubulin for addition to growing microtubule ends. The result is formation of abnormal mitotic spindles that cannot pass the metaphase/anaphase checkpoint.
Spi a cord stimulation for ischemic heart disease (2000)

An increasing number of patients are suffering from angina pectoris that is chronically refractory to standard anti-ischemic treatment such as pharmacological and surgical strategies. To improve the quality of life of these severely disabled patients, without adversely affecting their prognosis, a number of adjunct therapies are available. One of the most promising appears to be spinal cord stimulation. We will review the literature and discuss the efficacy, safety and mechanisms of neuromodulation as an adjuvant therapy for chronic refractory angina pectoris.
Latanoprost-Dependent Cystoid Macular Edema Following Uncomplicated Cataract Surgery in Pseudoexfoliative Eyes (2010)

Cystoid macular edema (CME) following uncomplicated phacoemulcification associated with latanoprost is uncommon. OCT-proven CME associated with latanoprost in 3 eyes with pseudoexfoliation after uncomplicated phacoemulcification was reported. Latanoprost was discontinued whereas topical ketorolac was administered. In all cases, CME resolved completely within the following weeks. In one case the re-administration of latanoprost lead to CME recurrence, which was treated with permanent discontinuation of latanoprost. The correlation between latanoprost and CME and the complete resolution of CME following discontinuation of the drug suggest a causative association between latanoprost and CME.
A tree-trellis based fast search for finding the N Best sentence hypotheses in continuous speech recognition (1990)

In this paper a new, tree-trellis based fast search for finding the <i>N</i> best sentence hypotheses in continuous speech recognition is proposed. The search consists of two parts: a forward, time-synchronous, trellis search and a backward, time asynchronous, tree search. In the first module the well known Viterbi algorithm is used for finding the best hypothesis and for preparing a map of all partial paths scores time synchronously. In the second module a tree search is used to grow partial paths backward and time asynchronously. Each partial path in the backward tree search is rank ordered in a stack by the corresponding full path score, which is computed by adding the partial path score with the best possible score of the remaining path obtained from the trellis path map. In each path growing cycle, the current best partial path, which is at the top of the stack, is extended by one arc (word). The new tree-trellis search is different from the traditional time synchronous Viterbi search in its ability for finding not just the best but the <i>N</i>-best paths of different word content. The new search is also different from the <i>A</i> algorithm, or the stack algorithm, in its capability for providing an exact, full path score estimate of any given partial (i.e., incomplete) path before its completion. When compared with the best candidate Viterbi search, the search complexities for finding the <i>N</i>-best strings are rather low, i.e., only a fraction more computation is needed.
Decentralized structures for parallel Kalman filtering (1988)

Various multisensor network scenarios with signal processing tasks that are amenable to multiprocessor implementation are described. The natural origins of such multitasking are emphasized, and novel parallel structures for state estimation using the Kalman filter are proposed that extend existing results in several directions. In particular, hierarchical network structures are developed that have the property that the optimal global estimate based on all the available information can be reconstructed from estimates computed by local processor nodes solely on the basis of their own local information and transmitted to a central processor. The algorithms potentially yield an approximately linear speedup rate, are reasonably failure-resistant, and are optimized with respect to communication bandwidth and memory requirements at the various processors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
IL-10 Is a Central Regulator of Cyclooxygenase-2 Expression and Prostaglandin Production (2001)

IL-10 is a potent anti-inflammatory and immune regulatory cytokine. IL-10(-/-) mice produce exaggerated amounts of inflammatory cytokines when stimulated with LPS, indicating that endogenous IL-10 is a central regulator of inflammatory cytokine production in vivo. PGs are lipid mediators that are also produced in large amounts during the inflammatory response. To study the role of IL-10 in the regulation of PG production during the acute inflammatory response, we evaluated LPS-induced cyclooxygenase (COX) expression and PG production in wild-type (wt) and IL-10(-/-) mice. LPS-induced PGE(2) production from IL-10(-/-) spleen cells was 5.6-fold greater than that from wt spleen cells. LPS stimulation resulted in the induction of COX-2 mRNA and protein in both wt and IL-10(-/-) spleen cells; however, the magnitude of increase in COX-2 mRNA was 5.5-fold greater in IL-10(-/-) mice as compared with wt mice. COX-1 protein levels were not affected by LPS stimulation in either wt or IL-10(-/-) mice. Neutralization of IFN-gamma, TNF-alpha, or IL-12 markedly decreased the induction of COX-2 in IL-10(-/-) spleen cells, suggesting that increased inflammatory cytokine production mediates much of the COX-2 induction in IL-10(-/-) mice. Treatment of IL-10(-/-) mice with low doses of LPS resulted in a marked induction of COX-2 mRNA in the spleen, whereas wt mice had minimal expression of COX-2 mRNA. These findings indicate that, in addition to IL-10's central role in the regulation of inflammatory cytokines, endogenous IL-10 is an important regulator of PG production in the response to LPS.
Effect of butyrate on the expression of microinjected or transfected genes. (1985)

We have studied the effect of sodium n-butyrate on the expression of specific genes. For this purpose, tk-ts13 cells (a thymidine kinase-deficient mutant originating from Syrian hamster cells) were microinjected or transfected with pC2, a plasmid containing the entire SV40 genome and the herpes simplex virus thymidine kinase gene (HSV-TK), cloned in pBR322. As a measure of the expression of these two genes, one of which is spliced (SV40) and the other one (HSV-TK) which is not, we have taken the protein levels (amount of T antigen for SV40 and incorporation of [3H]thymidine for HSV-TK) and the levels of RNA (by dot blot hybridization). The expression of the microinjected genes was inhibited when tk-ts13 cells were exposed to butyrate, actinomycin D, cycloheximide, and mitomycin C, but not when the cells were treated with insulin or dexamethasone. Further studies showed that a decrease in the percentage of T-positive cells occurs at lower concentrations of butyrate than a decrease in the levels of specific mRNA. In tk-ts13 cells transfected with pC2 and treated with butyrate at a concentration of 3 mM, SV40 mRNA levels are not decreased but the percentage of T-positive cells is decreased 50%. At 5 mM, the amount of T antigen/cell is decreased a further 40%. These results indicate that butyrate may have at least two sites of action, one at the level of mRNA amount and a second at the level of protein amount. In addition, our studies show that the use of microinjected or transfected genes offers certain unique possibilities for studies on the effects of environmental manipulations on gene expression.
Bovine peripheral blood polymorphonuclear neutrophil chemotactic response to Pasteurella haemolytica or zymosan-activated serum. (1982)

The chemotactic influence of Pasteurella haemolytica and of products of its growth was evaluated in vitro, using bovine peripheral blood polymorphonuclear neutrophils (PMN) in an underagarose migration assay system. Pasteurella haemolytica was cultured, quantitated, killed, and lysed by freeze-thawing. The PMN directional migration toward P haemolytica lysate was not significantly (P less than 0.9) different from spontaneous random PMN migration. Also, there was no chemotactic effect of viable 6-hour cultures of P haemolytica when tested in the in vitro underagarose system. Directional migration (1.70 +/- 0.53 mm) of PMN to zymosan-activated pooled bovine serum was observed and determined to be significantly (P less than 0.001) greater than was spontaneous random PMN migration (0.84 +/- 0.21 mm).
Inference from Inadequate and Inaccurate Data, III (1970)

Having measured D numerical properties of a physical object E which requires many more than D parameters for its complete description, we want to estimate P other numerical properties of E . Continuing the discussion in papers I 1 and II, 2 the present paper gives estimates when we believe it likely that we can guess an upper bound M on the Hilbert norm not of h E , the model representing E in some Hilbert space, but of the orthogonal projection of h E onto a sufficiently large subspace. In addition, the present paper simplifies the notation of I, and makes explicit the application of Bayesian subjective probability when there are errors in the data and we want to find the joint probability distribution of more than one prediction.
A Hedonic Model of Prices and Assessments for Single-Family Homes: Does the Assessor Follow the Market or the Market Follow the Assessor? (1975)

Brian J. L. Berry, Robert S. Bednarz, A Hedonic Model of Prices and Assessments for Single-Family Homes: Does the Assessor Follow the Market or the Market Follow the Assessor?, Land Economics, Vol. 51, No. 1 (Feb., 1975), pp. 21-40
Total Degradation of Fenitrothion and Other Organophosphorus Pesticides by Catalytic Oxidation Employing Fe-TAML Peroxide Activators (2006)

A Fe-TAML/H2O2 catalytic oxidation process achieves facile in-solution total degradation of fenitrothion and two other organophosphorus (OP) pesticides. Degradation products have been identified and quantified providing evidence for oxidative hydrolysis, oxidative desulfuration, perhydrolysis, and deep oxidation. Degradation pathways can be selected by pH control to completely obviate all toxic residuals. Aquatic toxicity assays support the environmental compatibility of the degradation process.
Broadband infrared photodetection using a narrow bandgap conjugated polymer (2021)

Photodetection spanning the short-, mid-, and long-wave infrared (SWIR-LWIR) underpins modern science and technology. Devices using state-of-the-art narrow bandgap semiconductors require complex manufacturing, high costs, and cooling requirements that remain prohibitive for many applications. We report high-performance infrared photodetection from a donor-acceptor conjugated polymer with broadband SWIR-LWIR operation. Electronic correlations within the π-conjugated backbone promote a high-spin ground state, narrow bandgap, long-wavelength absorption, and intrinsic electrical conductivity. These previously unobserved attributes enabled the fabrication of a thin-film photoconductive detector from solution, which demonstrates specific detectivities greater than 2.10 × 10<sup>9</sup> Jones. These room temperature detectivities closely approach those of cooled epitaxial devices. This work provides a fundamentally new platform for broadly applicable, low-cost, ambient temperature infrared optoelectronics.
CB2 cannabinoid receptors as an emerging target for demyelinating diseases: from neuroimmune interactions to cell replacement strategies (2007)

Amongst the various demyelinating diseases that affect the central nervous system, those induced by an inflammatory response stand out because of their epidemiological relevance. The best known inflammatory-induced demyelinating disease is multiple sclerosis, but the immune response is a common pathogenic mechanism in many other less common pathologies (e.g., acute disseminated encephalomyelitis and acute necrotizing haemorrhagic encephalomyelitis). In all such cases, modulation of the immune response seems to be a logical therapeutic approach. Cannabinoids are well known immunomodulatory molecules that act through CB1 and CB2 receptors. While activation of CB1 receptors has a psychotropic effect, activation of CB2 receptors alone does not. Therefore, to bypass the ethical problems that could result from the treatment of inflammation with psychotropic molecules, considerable effort is being made to study the potential therapeutic value of activating CB2 receptors. In this review we examine the current knowledge and understanding of the utility of cannabinoids as therapeutic molecules for inflammatory-mediated demyelinating pathologies. Moreover, we discuss how CB2 receptor activation is related to the modulation of immunopathogenic states.
NMR Characterization of Fourth-Generation PAMAM Dendrimers in the Presence and Absence of Palladium Dendrimer-Encapsulated Nanoparticles (2008)

High-resolution solution NMR spectroscopy has been used to characterize the structure of Pd dendrimer-encapsulated nanoparticles (DENs), consisting of approximately 55-atom nanoparticles encapsulated within fourth-generation, hydroxyl-terminated poly(amidoamine) PAMAM dendrimers (G4-OH). Detailed analysis of 1D and 2D NMR spectra of dendrimers with (G4-OH(Pd(55))) and without (G4-OH) nanoparticles unambiguously demonstrate that single nanoparticles are encapsulated within individual dendrimers. This conclusion is based on the following results. First, the NMR data show that signals arising from the innermost methylenes of G4-OH(Pd(55)) are more highly influenced by the presence of the Pd nanoparticles than are the terminal functional groups. This means that DENs are encapsulated within dendrimers rather than being adsorbed to their surface, as would be the case for aggregates consisting of multiple dendrimers and nanoparticles. Second, extraction of DENs from within their dendrimer hosts results in an increase in the NMR intensity associated with the interior methylenes, which corroborates the previous point. Third, NMR pulse-field gradient spin-echo experiments demonstrate that G4-OH and G4-OH(Pd(55)) have identical hydrodynamic radii, and this finding excludes the presence of dendrimer/nanoparticle aggregates.
Response of MSTd Neurons to Simulated 3D Orientation of Rotating Planes (2002)

We studied whether the dorsal division of the medial superior temporal area (MSTd) in the macaque has activity related to structure-from-motion (SFM) processing. As the simplest form of three-dimensional (3D) structure, we chose a planar stimulus and examined the relation between the neural responses and the simulated 3D orientation of the plane defined by motion cues. We recorded from 114 MSTd neurons while monkeys were performing a visual fixation task. These neurons responded to a basic set of optic flow patterns such as translation, expansion/contraction, and rotation. Responses of these neurons to rotating plane stimuli were examined to see whether the MSTd neurons exhibited selectivity to the tilt and slant that characterize the 3D orientation of the plane. We found that most MSTd neurons tested (97 of 114) responded to the plane stimuli, and many neurons (65 of 97) exhibited selectivity to tilt and/or slant. Of 97 neurons, 18% (17/97) were selective only to tilt, 24% (23/97) only to slant, and 26% (25/97) to both. Control experiments rejected the possibility that the selectivity could be explained solely by the sensitivity to local stimulus components such as local translation, local speed, and local speed gradients. These results suggest that MSTd neurons are sensitive to stimulus features specific to the perceived 3D orientation of the rotating plane stimuli and suggest that area MSTd is involved in SFM processing.
Role of the microbiota in inflammatory bowel diseases (2011)

Studying the role of the human microbiome as it relates to human health status has revolutionized our view of microbial community contributions to a large number of diseases, particularly chronic inflammatory disorders. The lower gastrointestinal (GI) tract houses trillions of microbial cells representing a large diversity of species in relatively well-defined phylogenetic ratios that are associated with maintenance of key aspects of host physiology and immune homeostasis. It is not surprising, therefore, that many GI inflammatory diseases, including inflammatory bowel disease (IBD), are associated with substantial changes in the composition of these microbial assemblages, either as a cause or consequence of host inflammatory response. Here we review current knowledge in the emerging field of human microbiome research as it relates to IBD, specifically focusing on Crohn's disease (CD) and ulcerative colitis (UC). We discuss bacteriotherapeutic efforts to restore GI microbial assemblage integrity via probiotic supplementation of IBD patients, and speculate on future directions for the field.
Pan-cancer analysis of ROS1 genomic aberrations (2015)

The ROS proto-oncogene 1 (ROS1) encodes the ROS1 receptor kinase. ROS1 rearrangements are known to be oncogenic in glioblastoma, non–small-cell lung carcinoma (NSCLC) and cholangiocarcinoma. The clinical relevance of ROS1 genomic aberrations in other human cancers is largely unexamined. Here, we performed a pan-cancer analysis of ROS1 genomic aberrations across 20 cancer sites by interrogating the whole-exome sequencing data of the Cancer Genome Atlas (TCGA) via the cBioportal (www.cbioportal.org). We found that ROS1 point mutations occur at a noticeable average frequency of 4.09%, while ROS1 gene rearrangement is uncommon, except for lung cancer. As ROS1 is potentially druggable by small molecule kinase inhibitors, it remains to be determined if any of these ROS1 mutations are associated with potential clinical benefits in patients. In our study, ROS1 gene amplification was noted in a small subset of patient tumors. For reasons unclear, ROS1 gene copy loss was found to be common in some cancer types. We also found that ROS1 mutations extend over the entire gene with three emerging hotspot mutation sites (R245I, P1539S and E2308) and several other recurrent clusters that frequently occur at the interdomain 2, 3, 4 regions, kinase and C’-terminal kinase domains by domain mapping. Similar mutation pattern (except for the C’-terminal kinase domain) was found in ROS1-mutated cancer cell lines from the Cell Line Encyclopedia (CCLE) and the NCI-60 panel. Lastly, we summarized all published ROS1 mutants related to tumorigenesis and secondary mutations of drug resistance in order to facilitate our understanding of the potential contributions or impacts of these pan-cancer ROS1 mutation spectra in multiple cancer types.
Diphtheria toxin entry into cells is facilitated by low pH. (1980)

At neutral pH, NH4Cl and chloroquine protected cells against diphtheria toxin. A brief exposure of the cells to low pH (4.5-5.5) at 37 degrees completely abolished this protection. When, to cells preincubated with diphtheria toxin and NH4Cl, neutralizing amounts of anti-diphtheria toxin were added before the pH was lowered, the toxic effect was considerably reduced, but it was not completely abolished. A much stronger toxic effect was seen when antibodies were added immediately after incubation at low pH. Upon a short incubation with diphtheria toxin at low pH, the rate of protein synthesis in the cells decreased much faster than when the normal pH was maintained. The data suggest that, at low pH, diphtheria toxin (or its A fragment) penetrates directly through the surface membrane of the cell. The possibility is discussed that, when the medium has a neutral pH, the entry of diphtheria toxin involves adsorptive endocytosis and reduction of the pH in the vesicles possibly by fusion with lysosomes. Low pH did not facilitate the entry of the closely related toxins abrin, ricin, and modeccin.