gebhart/patrepeval huggingface dataset:
Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4 (2004)

Transcription factors of the auxin response factor (ARF) family have been implicated in auxin-dependent gene regulation, but little is known about the functions of individual ARFs in plants. Here, interaction assays, expression studies and combinations of multiple loss- and gain-of-function mutants were used to assess the roles of two ARFs, NONPHOTOTROPIC HYPOCOTYL 4 (NPH4/ARF7) and MONOPTEROS (MP/ARF5), in Arabidopsis development. Both MP and NPH4 interact strongly and selectively with themselves and with each other, and are expressed in vastly overlapping domains. We show that the regulatory properties of both genes are far more related than suggested by their single mutant phenotypes. NPH4 and MP are capable of controlling both axis formation in the embryo and auxin-dependent cell expansion. Interaction of MP and NPH4 in Arabidopsis plants is indicated by their joint requirement in a number of auxin responses and by synergistic effects associated with the co-overexpression of both genes. Finally, we demonstrate antagonistic interaction between ARF and Aux/IAA gene functions in Arabidopsis development. Overexpression of MP suppresses numerous defects associated with a gain-of-function mutation in BODENLOS (BDL)/IAA12. Together these results provide evidence for the biological relevance of ARF-ARF and ARF-Aux/IAA interaction in Arabidopsis plants and demonstrate that an individual ARF can act in both invariantly programmed pattern formation as well as in conditional responses to external signals.
Formation and characterization of a highly ordered and well-anchored alkylsilane monolayer on mica by self-assembly (1991)

A close-packed, well-ordered monolayer can be formed on a freshly cleaved muscovite mica surface by allowing hydrolyzed octadecyltriethoxysilane to self-assemble from a dilute hydrocarbon solution. The alkyl chains in the monolayer deposited by this method appear to be in a pseudocrystalline environment. Contact angle measurements and Fourier transform infrared spectroscopy indicate that the layer is in all respects equal to a Langmuir-Blodgett monolayer in packing density (almost-equal-to 20 angstrom 2/molecule) and order, but the adhesion of the self-assembled monolayer to the mica surface is much better than that obtainable by any other method of monolayer formation. The self-assembling species, octadecylsilanetriol or low order oligomers, is shown to be surprisingly stable to condensation in dilute solution. The ability to form robust, well-ordered monolayers on mica should open up new possibilities for tailor-made surfaces to be studied in the surface forces apparatus.
Comparing vector space retrieval with the RUBRIC expert system (1988)

RUBRIC is an expert system for full-text information retrieval. The underlying model for RUBRIC's information retrieval process is based upon fuzzy set theory. The RUBRIC developers have compared RUBRIC to the boolean retrieval model, which it subsumes. This study compares RUBRIC to the Vector Space Model for information retrieval, using RUBRIC's own test collection of thirty news articles from the Reuters News Service and their test search for articles which satisfy the information need to find out about "violent acts of terrorism." Results indicate that the vector space model is comparable to RUBRIC for relevant documents, while RUBRIC performs better at retrieving marginally relevant documents.
ChemInform Abstract: Synthesis of 3‐Methyl‐1(2H)‐isoquinolinone Derivatives and Their Biological Activities. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Studies on an (NH4)2Sx-Treated GaAs Surface Using AES, LEELS and RHEED (1989)

Surface properties of (NH 4 ) 2 S x -treated GaAs (100), (111)Ga and (1̄1̄1̄)As planes were studied by means of Auger electron spectroscopy (AES), low-energy electron energy loss spectroscopy (LEELS) and reflection high-energy electron diffraction (RHEED). We found that oxide-free and sulfur-terminated GaAs surfaces produced by the (NH 4 ) 2 S x treatment provided the reduction of interface state density. Furthermore, comparison of various planes revealed that (i) sulfur atoms could combine with both Ga and As and (ii) bonding between Ga and S was stronger than that between As and S.
Epigenetic regulation of CD133 and tumorigenicity of CD133 positive and negative endometrial cancer cells (2010)

These findings support the hypotheses that CD133 expression in endometrial cancer may be epigenetically regulated and that cell fractions enriched for CD133+ cells may well contribute to endometrial cancer tumorigenicity, pathology and recurrence.
Monitoring Huntington’s Disease Progression Through Preclinical and Early Stages (2012)

Huntington's disease (HD) is an autosomal dominant progressive neurodegenerative disorder that typically begins in middle adulthood. The neurodegenerative process that underlies HD, however, likely begins many years before clinical diagnosis. Since genetic testing can identify individuals that will develop HD during this preclinical period, clinical trials aiming to slow disease progression will likely focus on this phase of the illness in an effort to delay disease onset. How to best measure the efficacy of potential disease-modifying therapies in preclinical HD remains a complex challenge. This article will review the clinical and imaging measures that have been assessed as potential markers of disease progression in preclinical and early symptomatic HD.
CD123 (IL-3 Receptor α Chain) Neutralization by a Monoclonal Antibody Selectively Eliminates Human Acute Myeloid Leukemic Stem Cells. (2007)

Abstract Development of effective therapies against acute myeloid leukemia (AML) will likely require elimination of the leukemic stem cell (LSC), which maintains the AML hierarchy. Based on high expression of the IL-3 receptor α chain (CD123) on AML-LSC, we tested a neutralizing antibody against CD123 (7G3) for its in vitro and in vivo effects on AML cells. By flow cytometric analysis, high expression of CD123 on CD34+/38− AML-LSC was confirmed. In vitro, 7G3 inhibited IL-3-induced proliferation in 31/34 primary AML specimens tested. Moreover, exposure of primary AML cells to 7G3 in vitro caused inhibition of IL-3-induced tyrosine phosphorylation and downstream signaling of the IL-3 receptor βc chain in a concentration-dependent fashion. Ex vivo treatment of primary AML cells with 7G3 (10 μg/ml, 2 h) profoundly reduced leukemic engraftment of human CD45+ (huCD45+) cells in non-obese diabetic/severe-combined immunodeficient (NOD/SCID) mice in 9/10 evaluable samples (mean ± SEM, 89.7 ±1.9% inhibition relative to IgG2a control, P=0.013), establishing that the AML-LSC was targeted. The overall survival of engrafted mice was significantly improved (median survival of control IgG2a-treated group 11.5 weeks versus 24 weeks for the 7G3-treated group, n = 10 per group, P=0.019). Moreover, ex vivo 7G3 treatment reduced the short-term homing efficiency of AML cells to the bone marrow by 65% compared with IgG2a control-treated cells, measured at 24 h post inoculation. In contrast, ex vivo exposure to 7G3 had minor, if any, effects on the engraftment of normal bone marrow cells (23.5 ±8.9% inhibition relative to IgG2a control, n=5). Direct delivery of 7G3-treated AML cells into the bone marrow by intra-femoral injection did not completely restore engraftment, suggesting a specific biological role of 7G3 in inhibiting homing, lodgement and proliferation of AML-LSC. Despite some sample to sample heterogeneity, thrice-weekly administration of 7G3 to NOD/SCID mice with pre-established AML consistently reduced AML dissemination to peripheral blood, spleen and liver, and reduced infiltration of a single AML sample in the bone marrow. 7G3 treatment was also associated with down-regulation of CD123 expression on AML cells in vivo. AML cells harvested from 7G3-treated mice were unable to repopulate secondary recipient mice, with engraftment reduced to 5.7 ±4.1% (n=7) huCD45+ cells in the femoral bone marrow compared with 26.8 ±6.6% in IgG2a-treated controls (n=9, P=0.024), indicating that CD123 neutralization targeted AML-LSC self-renewal ability, specifically reducing the proportion of AML-LSC. These results suggest that blocking CD123 inhibits homing, lodgement and proliferation of AML-LSC in the bone marrow microenvironment and prevents subsequent organ infiltration, and support additional investigations into 7G3 and its potential as a novel therapy for AML.
Frequency dependence of magnetic resonance spin-lattice relaxation of protons in biological materials. (1984)

The frequency dependence of spin-lattice (T1) relaxation times of protons in tissues and other macromolecular solutions was investigated. This dependence can be principally assigned to reduced mobility of water molecules "hydrated" on the surface of macromolecular structures. The T1 relaxation time of "hydration water" was found to increase linearly with frequency in the range from 5 to 100 MHz (T1 = 1.83 f + 25.0). It is assumed that the remainder of water in the tissue has a relaxation rate that is independent of frequency, as is characteristic of bulk tap water. Variations occur in the fraction of water hydrated or bound from one organ to the next. As the observed relaxation rate is a weighted average of the two rates as described by the fast exchange model, the above empirical relationship can be used to take a tissue T1 relaxation time measured at one frequency and then calculate the tissue T1 relaxation time that would be expected at another frequency. Good agreements were obtained between such calculated tissue T1 values and the T1 values actually measured at the second frequency. Variations between the calculated and measured T1 values in some classes of tissues indicate that there are also less important secondary factors such as lipid content.
DOMINANT SUPPRESSORS OF A MUSCLE MUTANT DEFINE AN ESSENTIAL GENE OF CAENORHABDITIS ELEGANS (1982)

The sup-11 1 locus of C. elegans was defined by rare dominant suppressors of unc-93(e1500) III, a mutation that affects muscle structure. All ten of these dominant suppressors have a recessive "scrawny" phenotype. Two additional classes of sup-11 alleles were identified. One class, null alleles, was obtained by reversion of the dominant suppressor activity. These null alleles are recessive embryonic lethals, indicating that sup-11 is an essential gene. Members of the second class, rare semidominant revertants of the "scrawny" phenotype, are partial suppressors of unc-93(e1500). The genetic properties of the dominant suppressor mutations suggest that they are rare missense mutations that confer a novel activity to the sup-11 protein. We consider some of the ways that sup-11 alleles might suppress unc-93(e1500), including the possibilities that the altered sup-11 proteins restore function to a protein complex or are modified products of a gene that is a member of an unc-93 gene family.
Force-controllable ankle foot orthosis (AFO) to assist drop foot gait (2002)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, February 2003.
The extracellular domain of HER2/neu is a potential immunogen for active specific immunotherapy of breast cancer. (1990)

The proto-oncogene HER2/neu encodes a protein tyrosine kinase (p185HER2) that is homologous to the human epidermal growth factor receptor. Amplification and/or overexpression of HER2/neu occurs in multiple human malignancies and appears to be integrally involved in progression of some breast and ovarian cancers. Because of this fact, HER2/neu is an intriguing target for specific cancer therapeutic strategies. One such strategy is active specific immunotherapy, in which the immune system is targeted at specific antigens expressed by tumor cells. We have employed a transfected cell line that secretes the extracellular domain of p185HER2 as a source of HER2-derived immunogen in a guinea pig model. The immunized animals developed a cellular immune response, as monitored by delayed-type hypersensitivity, and antisera derived from immunized animals specifically inhibited the in vitro growth of human breast tumor cells overexpressing p185HER2. These data provide support for an immunotherapeutic approach to cancers characterized by overexpression of the HER2/neu proto-oncogene.
Replicated database recovery using multicast communication (2002)

Database replication with update-anywhere capability and one-copy serializability has long been thought impractical. Protocols have been proposed for replicated databases that take advantage of atomic broadcast systems to simplify message passing and conflict resolution. The paper presents global recovery algorithms to handle site failures when such protocols are used.
Dexamethasone inhibits the hexose monophosphate shunt in activated rat peritoneal macrophages by reducing hexokinase-dependent sugar uptake (1991)

Dexamethasone decreases 2-D-deoxyglucose (2-dGlc) uptake and accumulation into rat peritoneal macrophages in vitro in a concentration- and time-dependent manner (Ki for 1 microM-dexamethasone after a 2 h exposure = 0.71 +/- 0.21 microM; Ki for 0.1 microM-dexamethasone after exposure for 4 h = 0.10 +/- 0.06 microM). The inhibition of 2-dGlc uptake is consistent with a decrease in the coupling between endofacial hexokinase activity and the sugar transporter. The evidence for this is: (1) the Km for zero-trans 2-dGlc uptake in quiescent macrophages was increased by dexamethasone, but there was no significant effect on the Vmax.; (2) dexamethasone increased the rate of exit of sugar from cells preloaded with 2-dGlc; (3). the free sugar accumulation within the cytosol of the cells above the external solution concentration was significantly decreased by dexamethasone. These effects of dexamethasone on 2-dGlc transport were antagonized by simultaneous exposure to the steroid RU 38486 (Ki = 0.04 +/- 0.01 microM; 4 h incubation). Although dexamethasone inhibited zero-trans uptake, the maximum rate of infinite-trans exchange uptake of 2-dGlc into cells preloaded with 3-O-methyl-D-glucose (40 mM) was unaltered by dexamethasone or RU 38486, indicating that the dexamethasone-dependent decrease in zero-trans uptake was not due to a change in the number of transporters in the plasma membrane. Dexamethasone also inhibited the phorbol myristate acetate-induced stimulation of hexose monophosphate shunt (HMPS) activity, and this was reversed by RU 38486. Cytochalasin B, the potent sugar-transport inhibitor, inhibited HMPS activity and 2-d[2,6-3H]Glc uptake equally, indicating a single site of action. By contrast, dexamethasone showed differential inhibition of HMPS activity and 2-d[2,6-3H]Glc uptake, suggesting that it not only acts by decreasing the coupling between hexokinase and sugar transport, but also at one or more additional points.
Requirement of Sox2-mediated signaling for differentiation of early Xenopus neuroectoderm (2000)

From early stages of development, Sox2-class transcription factors (Sox1, Sox2 and Sox3) are expressed in neural tissues and sensory epithelia. In this report, we show that Sox2 function is required for neural differentiation of early Xenopus ectoderm. Microinjection of dominant-negative forms of Sox2 (dnSox2) mRNA inhibits neural differentiation of animal caps caused by attenuation of BMP signals. Expression of dnSox2 in developing embryos suppresses expression of N-CAM and regional neural markers. We have analyzed temporal requirement of Sox2-mediated signaling by using an inducible dnSox2 construct fused to the ligand-binding domain of the glucocorticoid receptor. Attenuation of Sox2 function both from the late blastula stage and from the late gastrula stage onwards causes an inhibition of neural differentiation in animal caps and in whole embryos. Additionally, dnSox2-injected cells that fail to differentiate into neural tissues are not able to adopt epidermal cell fate. These data suggest that Sox2-class genes are essential for early neuroectoderm cells to consolidate their neural identity during secondary steps of neural differentiation.
Structural Basis and Catalytic Mechanism for the Dual Functional Endo-β-N-Acetylglucosaminidase A (2009)

Endo-beta-N-acetylglucosaminidases (ENGases) are dual specificity enzymes with an ability to catalyze hydrolysis and transglycosylation reactions. Recently, these enzymes have become the focus of intense research because of their potential for synthesis of glycopeptides. We have determined the 3D structures of an ENGase from Arthrobacter protophormiae (Endo-A) in 3 forms, one in native form, one in complex with Man(3)GlcNAc-thiazoline and another in complex with GlcNAc-Asn. The carbohydrate moiety sits above the TIM-barrel in a cleft region surrounded by aromatic residues. The conserved essential catalytic residues - E173, N171 and Y205 are within hydrogen bonding distance of the substrate. W216 and W244 regulate access to the active site during transglycosylation by serving as "gate-keepers". Interestingly, Y299F mutation resulted in a 3 fold increase in the transglycosylation activity. The structure provides insights into the catalytic mechanism of GH85 family of glycoside hydrolases at molecular level and could assist rational engineering of ENGases.
Efficient cladding pumping of an Er3+ fibre (1995)

We report for the first time efficient operation of a cladding pumped Er3+ fibre configured in both fibre laser and fibre amplifier form. The fibre was of a double clad design compatible with beamshaped 980nm broadstripe pump lasers An efficiency in excess of 40% has been achieved
Word Representations: A Simple and General Method for Semi-Supervised Learning (2010)

If we take an existing supervised NLP system, a simple and general way to improve accuracy is to use unsupervised word representations as extra word features. We evaluate Brown clusters, Collobert and Weston (2008) embeddings, and HLBL (Mnih &amp;amp; Hinton, 2009) embeddings of words on both NER and chunking. We use near state-of-the-art supervised baselines, and find that each of the three word representations improves the accuracy of these baselines. We find further improvements by combining different word representations. You can download our word features, for off-the-shelf use in existing NLP systems, as well as our code, here:
Fluorometric detection of HIV-1 genome through use of an internal control, inosine-substituted primers, and microtiter plate format (1996)

We describe a PCR-based fluorometric assay for the detection of the HIV-1 genome. This technique consists of a reverse hybridization with oligonucleotide probes covalently coated onto a microtiter plate as a solid support. Several improvements to the PCR amplification and detection steps gave greater sensitivity and specificity for HIV-1 screening and resulted in a convenient and rapid technique. False-positive results were avoided by using uracyl DNA glycosylase. False-negative results from the presence of PCR inhibitors were detected by coamplifying an internal control with the viral sequence. False-negative results from viral genome variability were limited by using two pairs of primers and by incorporating inosine at the primer positions corresponding to viral polymorphic nucleotides. Furthermore, the hybridization buffer and enzymatic reaction were optimized to increase the assay's sensitivity. The sensitivity and specificity of the fluorometric detection were similar to those of radioisotopic oligonucleotide solution hybridization; however, hands-on time was reduced, and the use of radioactivity was eliminated. We have used this technique routinely on 115 samples and obtained 100% specificity and high sensitivity (only one false-negative result) according to viral culture and (or) serological status of the patients.
Oncolytic Newcastle Disease Virus for Cancer Therapy: Old Challenges and New Directions (2012)

Newcastle disease virus (NDV) is an avian paramyxovirus, which has been demonstrated to possess significant oncolytic activity against mammalian cancers. This review summarizes the research leading to the elucidation of the mechanisms of NDV-mediated oncolysis, as well as the development of novel oncolytic agents through the use of genetic engineering. Clinical trials utilizing NDV strains and NDV-based autologous tumor cell vaccines will expand our knowledge of these novel anticancer strategies and will ultimately result in the successful use of the virus in the clinical setting.
Thermodynamic and molecular determinants of sterol solubilities in bile salt micelles (1987)

We examined, by reverse-phase high performance liquid chromatography (HPLC), the hydrophilic-hydrophobic balance of cholesterol and 12 non-cholesterol sterols and related this property to their equilibrium micellar solubilities in sodium taurocholate and sodium glycodeoxycholate solutions. Sterols investigated exhibited structural variations in the polar function (3 alpha-OH, 3 beta-OH, 3 beta-SH), nuclear double bonds (none, delta 5, or delta 7), side chain length (C27, C28, C29) and side chain double bonds (none, delta 22, or delta 24). In general, a sterol's hydrophilic-hydrophobic balance became progressively more hydrophobic (as exemplified by increasing HPLC retention values, k') with additions of side chain methyl (C28) and ethyl (C29) groups and with 3 beta-SH substitution of the 3-OH polar function. Side chain delta 22 and especially delta 24 double bonds rendered the sterols appreciably more hydrophilic, whereas a single nuclear double bond had little influence. Sterol solubilities (24 degrees C, 0.15 M Na+) were uniformly greater in 50 mM solutions of sodium glycodeoxycholate (range 0.15 to 2.5 mM) than in equimolar solutions of the more hydrophilic bile salt, sodium taurocholate (range 0.07 to 0.67 mM). For each bile salt system, a strong inverse correlation existed between micellar solubilities of sterols and their HPLC k' values, indicating that more hydrophilic sterols had greater micellar solubilities than the more hydrophobic ones. Based upon the aqueous monomeric solubilities of cholesterol (C27) and beta-sitosterol (C29) at 24 degrees C, we derived free energy changes associated with micellar binding and found that solubilization of both sterols was more energetically favored in glycodeoxycholate solutions. Although cholesterol exhibited a higher binding affinity than beta-sitosterol in glycodeoxycholate micelles, solubilization of beta-sitosterol in taurocholate micelles was more energetically favored than cholesterol by -0.6 kcal/mol. Based upon these results we offer a thermodynamic explanation for the greater micellar solubilities of more hydrophilic sterols and suggest that the high affinity, but low capacity, of a typical phytosterol for binding to trihydroxy bile salt micelles may provide a physical-chemical basis for its inhibition of intestinal cholesterol absorption.
Designable visual markers (2009)

Visual markers are graphic symbols designed to be easily recognised by machines. They are traditionally used to track goods, but there is increasing interest in their application to mobile HCI. By scanning a visual marker through a camera phone users can retrieve localised information and access mobile services.