gebhart/patrepeval huggingface dataset:
Maize VP1 complements Arabidopsisabi3 and confers a novel ABA/auxin interaction in roots (2001)

The maize Vp1 gene and abi3 gene of Arabidopsis are believed to be orthologs based on similarities of the mutant phenotypes and amino acid sequence conservation. Here we show that expression of VP1 driven by the 35S promoter can partially complement abi3-6, a deletion mutant allele of abi3. The visible phenotype of seed produced from VP1 expression in the abi3 mutant background is nearly indistinguishable from wild type. VP1 fully restores abscisic acid (ABA) sensitivity of abi3 during seed germination and suppresses the early flowering phenotype of abi3. The temporal regulation of C1-beta-glucuronidase (GUS) and chlorophyll a/b binding protein (cab3)-GUS reporter genes in developing seeds of 35S-VP1 lines were similar to wild type. On the other hand, two qualitative differences are observed between the 35S-VP1 line and wild type. The levels of CRC and C1-GUS expression are markedly lower in the seeds of 35S-VP1 lines than in wild type suggesting incomplete complementation of gene activation functions. Similar to ectopic expression of ABI3 (Parcy et al., 1994), ectopic expression of VP1 in vegetative tissue enhances ABA inhibition of root growth. In addition, 35S-VP1 confers strong ABA inducible expression of the normally seed-specific cruciferin C (CRC) gene in leaves. In contrast, ectopic ABA induction of C1-GUS is restricted to a localized region of the root elongation zone. The ABA-dependent C1-GUS expression expanded to a broader area in the root tissues treated with exogenous application of auxin. Interestingly, auxin-induced lateral root formation is completely suppressed by ABA in 35S-VP1 plants but not in wild type. These results indicate VP1 mediates a novel interaction between ABA and auxin signaling that results in developmental arrest and altered patterns of gene expression.
Quantitative Assessment of Whole-Body Tumor Burden in Adult Patients with Neurofibromatosis (2012)

WBMRI provides a comprehensive phenotype of neurofibromatosis patients, identifies distinct anatomic subgroups, and provides the basis for investigating molecular biomarkers that correlate with unique disease manifestations.
Exciton diffusion and dissociation in a poly(p-phenylenevinylene)/C60 heterojunction photovoltaic cell (1996)

We report measurements of the photovoltaic response of two-layer photocells formed with layers of the conjugated polymer poly(phenylenevinylene), PPV and fullerene, C60, formed between indium-tin oxide and aluminum electrodes. Peak quantum efficiencies of up to ∼9% (electrons collected per incident photon) were measured under short-circuit conditions. We model the photovoltaic response as arising from excitons photogenerated in the PPV layer which are able to diffuse to the interface with the C60 layer where they are ionized. We obtain a value for the exciton diffusion range of 7±1 nm, both from the spectral response and from the absolute efficiency. We demonstrate that the branching ratio for the creation of singlet excitons from absorbed photons is close to unity.
New Methods of Preparative Organic Chemistry IV. Cyclization of Dialdehydes with Nitromethane (1964)

Abstract Condensation of nitromethane with suitable diadehydes in alkaline medium provides a general method of cyclization, in which the methyl group of the nitromethane is incorporated into the ring. This method leads to 5‐, 6‐, and 7‐membered rings and is equally applicable to aliphatic, aromatic, and sugar dialdehydes. For example, glyoxal is converted into 1,4‐dideoxy‐1,4‐dinitro‐neo‐inositol, and glutaraldehyde into trans‐2‐nitrocyclohexane‐1,3‐diol, while the corresponding cyclization of xylo‐trihydroxyglutaraldehyde leads to deoxy‐nitroinositols having the scyllo, myo‐1, and muco‐3 configurations.‐In the case of aromatic dialdehydes, the cyclization is accompanied by elimination of water. Thus, phthalaldehyde, naphthalene‐2,3‐dicarboxaldehyde, and homophthalaldehyde yield, respectively, 2‐nitroindenol, 2‐nitrobenzindenol, and 2‐nitronaphthalene. ‐Application of the method to sugar dialdehydes (aldehydic diglycol derivatives of monosaccharides formed by periodate oxidation) constitutes an excellent synthesis of 3‐amino sugars, since 3‐deoxy‐3‐nitropyranoses are formed smoothly on cyclization, and the corresponding 3‐amino derivatives are obtained by hydrogenation. Thus, the reaction sequence: periodate oxidation → cyclization with nitromethane → hydrogenation, leads in the case of α‐and β‐ D ‐pentosides to 3‐amino‐3‐deoxy‐ D ‐and‐ L ‐pentosides, respectively, with ribo, xylo, and arabino configurations. α‐ D ‐hexosides give derivatives with gluco, manno, and galacto configurations. 3‐Amino‐3,6‐dideoxyglucosides of the D ‐and L ‐series are obtained from 6‐deoxy‐ D ‐or‐ L ‐hexosides, respectively, and 3‐aminohexosans with gulo, ido, and altro configurations are obtained from 1,6‐anhydro sugars. Cyclization of the dialdehydes obtained from sedoheptulose and methyl 4,6‐O‐ethylidene‐α‐ D ‐glucoside by periodate oxidation, leads to 3‐nitro and, after hydrogenation, to 3‐amino derivatives of 3‐deoxyheptopyranoses.
Sequential and Cooperative Sensing for Multi-Channel Cognitive Radios (2010)

Effective spectrum sensing is a critical prerequisite for multi-channel cognitive radio (CR) networks, where multiple spectrum bands are sensed to identify transmission opportunities, while preventing interference to the primary users. The present paper develops sequential spectrum sensing algorithms which explicitly take into account the sensing time overhead, and optimize a performance metric capturing the effective average data rate of CR transmitters. A constrained dynamic programming problem is formulated to obtain the policy that chooses the best time to stop taking measurements and the best set of channels to access for data transmission, while adhering to hard “collision” constraints imposed to protect primary links. Given the associated Lagrange multipliers, the optimal access policy is obtained in closed form, and the subsequent problem reduces to an optimal stopping problem. A basis expansion-based sub-optimal strategy is employed to mitigate the prohibitive computational complexity of the optimal stopping policy. A novel on-line implementation based on the recursive least-squares (RLS) algorithm along with a stochastic dual update procedure is then developed to obviate the lengthy training phase of the batch scheme. Cooperative sequential sensing generalizations are also provided with either raw or quantized measurements collected at a central processing unit. The numerical results presented verify the efficacy of the proposed algorithms.
Patient's experience (2004)

It's not often that I'm ill and I had no intention of saying anything, but Bill brought it up for me because I wouldn't.1 Nineteen years ago I'd gone to my previous GP with bad stomach pains, and he just told me that it was an ulcer, so I always put it down to an ulcer. We sometimes had the odd glass of wine together in the evening, but not every evening, so it wasn't alcohol causing my pain. My Nan had skin problems, and I've dealt with cystitis before, so it didn't seem worth mentioning.

I never really thought I was …
Specific humoral and cellular immunity induced by Trypanosoma cruzi DNA immunization in a canine model (2013)

Chagas disease has a high incidence in Mexico and other Latin American countries. Because one of the most important known methods of prevention is vector control, which has been effective only in certain areas of South America, the development of a vaccine to protect people at risk has been proposed. In this study, we assessed the cellular and humoral immune response generated following immunization with pBCSP and pBCSSP4 plasmids containing the genes encoding a trans-sialidase protein (present in all three forms of T. cruzi) and an amastigote specific glycoprotein, respectively, in a canine model. Thirty-five beagle dogs were divided randomly into 5 groups (n=7) and were immunized twice intramuscularly with 500 μg of pBCSSP4, pBCSP, pBk-CMV (empty plasmid) or saline solution. Fifteen days after the last immunization the 4 groups were infected intraperitoneally with 500,000 metacyclic trypomastigotes. The fifth group was unimmunized/infected. The parasitaemia in the immunized/infected dogs was for a shorter period (14 vs. 29 days) and the parasite load was lower. The concentration of IgG1 (0.612±0.019 O.D.) and IgG2 (1.167±0.097 O.D.) subclasses was measured (absorbance) 15 days after the last immunization with both recombinant plasmids, the majority of which were IgG2. The treatment of parasites using the serum from dogs immunized with pBCSP and pBCSSP4 plasmids produced 54% (±11.8) and 68% (±21.4) complement-mediated lysis, respectively. At 12 h post immunization, an increase in cytokines was not observed; however, vaccination with pBCSSP4 significantly increased the levels of IFN-γ and IL-10 at 9 months post-infection. The recombinant plasmid immunization stimulated the spleen cell proliferation showing a positive stimulatory index above 2.0. In conclusion, immunization using both genes effectively induces a humoral and cellular immune response.
Emerging Photoluminescence in Monolayer MoS2 (2010)

Novel physical phenomena can emerge in low-dimensional nanomaterials. Bulk MoS(2), a prototypical metal dichalcogenide, is an indirect bandgap semiconductor with negligible photoluminescence. When the MoS(2) crystal is thinned to monolayer, however, a strong photoluminescence emerges, indicating an indirect to direct bandgap transition in this d-electron system. This observation shows that quantum confinement in layered d-electron materials like MoS(2) provides new opportunities for engineering the electronic structure of matter at the nanoscale.
Single multiplex assay to identify simultaneously enteropathogenic, enteroaggregative, enterotoxigenic, enteroinvasive and Shiga toxin-producingEscherichia colistrains in Brazilian children (2007)

A multiplex PCR to differentiate typical and atypical enteropathogenic Escherichia coli (EPEC), enteroaggregative E. coli (EAEC), enterotoxigenic (ETEC), enteroinvasive E. coli (EIEC) and Shiga toxin-producing E. coli (STEC) strains was developed and evaluated. The targets selected for each group were eae and bfpA for EPEC, aggR for EAEC, elt and est for ETEC, ipaH for EIEC and stx for STEC isolates. This PCR was specific and sensitive for rapid detection of target isolates in stools. Among 79 children with acute diarrhea, this technique identified 13 (16.4%) with atypical EPEC, four (5%) with EAEC, three (3.8%) with typical EPEC, one (1.3%) with ETEC and one (1.3%) with EIEC.
Choice of normal ovarian control influences determination of differentially expressed genes in ovarian cancer expression profiling studies. (2003)

These results suggest that the selection of a normal control to compare with epithelial ovarian cancer samples in microarray studies strongly influences the genes that are identified as differentially expressed and complicates comparison with studies using a different normal control.
Toll-Like Receptor 4 or 2 Agonists Decrease Allergic Inflammation (2004)

Toll-like receptors (TLRs) recognize highly conserved microbial molecular patterns, such as found in endotoxin. This study tested whether TLR4 and TLR2 stimulation in vivo would modulate subsequent adaptive (allergic) immune responses. We analyzed the effects of pulmonary administration of a TLR4 agonist, lipid A (LpA), and two TLR2 agonists, peptidoglycan (Ppg) and PamCys, in a murine model of allergic inflammation. The TLR agonists were administered during allergen sensitization or challenge. Both TLR agonists decreased the allergen-induced pulmonary recruitment of eosinophils when administered at sensitization or challenge. When given before sensitization, the TLR4 and TLR2 agonists decreased additional allergen-induced parameters of inflammation (pulmonary eosinophilia, bronchoalveolar lavage IL-13, total serum IgE, and airway hyperresponsiveness). Interestingly, TLR4 and TLR2 agonists decreased the number of CD4+ cells in the lung. Also, at the site of local allergen stimulation, the draining thoracic lymph nodes, allergen-induced lymphocyte proliferation, and IL-13 secretion were decreased by administration of LpA and Ppg. These data provide a distinct example of the modulation of adaptive (allergic) responses by non-antigen-dependent stimuli. Our findings also demonstrate that both TLR4 and TLR2 agonists decrease allergic responses, supporting the concept that exposure to bacterial components under defined conditions may protect against allergic disease.
Synthesis, Biological, and Antitumor Activity of a Highly Potent 6-Substituted Pyrrolo[2,3-d]pyrimidine Thienoyl Antifolate Inhibitor with Proton-Coupled Folate Transporter and Folate Receptor Selectivity over the Reduced Folate Carrier That Inhibits β-Glycinamide Ribonucleotide Formyltransferase (2011)

2-Amino-4-oxo-6-substituted pyrrolo[2,3-d]pyrimidine antifolates with a thienoyl side chain (compounds 1-3, respectively) were synthesized for comparison with compound 4, the previous lead compound of this series. Conversion of hydroxyl acetylen-thiophene carboxylic esters to thiophenyl-α-bromomethylketones and condensation with 2,4-diamino-6-hydroxypyrimidine afforded the 6-substituted pyrrolo[2,3-d]pyrimidine compounds of type 18 and 19. Coupling with l-glutamate diethyl ester, followed by saponification, afforded 1-3. Compound 3 selectively inhibited the proliferation of cells expressing folate receptors (FRs) α or β, or the proton-coupled folate transporter (PCFT), including KB and IGROV1 human tumor cells, much more potently than 4. Compound 3 was more inhibitory than 4 toward β-glycinamide ribonucleotide formyltransferase (GARFTase). Both 3 and 4 depleted cellular ATP pools. In SCID mice with IGROV1 tumors, 3 was more efficacious than 4. Collectively, our results show potent antitumor activity for 3 in vitro and in vivo, associated with its selective membrane transport by FRs and PCFT over RFC and inhibition of GARFTase, clearly establishing the 3-atom bridge as superior to the 1-, 2-, and 4-atom bridge lengths for the activity of this series.
Phosphatidylinositol 3-kinase facilitates bile acid-induced Ca2+responses in pancreatic acinar cells (2006)

Bile acids are known to induce Ca(2+) signals in pancreatic acinar cells. We have recently shown that phosphatidylinositol 3-kinase (PI3K) regulates changes in free cytosolic Ca(2+) concentration ([Ca(2+)](i)) elicited by CCK by inhibiting sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA). The present study sought to determine whether PI3K regulates bile acid-induced [Ca(2+)](i) responses. In pancreatic acinar cells, pharmacological inhibition of PI3K with LY-294002 or wortmannin inhibited [Ca(2+)](i) responses to taurolithocholic acid 3-sulfate (TLC-S) and taurochenodeoxycholate (TCDC). Furthermore, genetic deletion of the PI3K gamma-isoform also decreased [Ca(2+)](i) responses to bile acids. Depletion of CCK-sensitive intracellular Ca(2+) pools or application of caffeine inhibited bile acid-induced [Ca(2+)](i) signals, indicating that bile acids release Ca(2+) from agonist-sensitive endoplasmic reticulum (ER) stores via an inositol (1,4,5)-trisphosphate-dependent mechanism. PI3K inhibitors increased the amount of Ca(2+) in intracellular stores during the exposure of acinar cells to bile acids, suggesting that PI3K negatively regulates SERCA-dependent Ca(2+) reloading into the ER. Bile acids inhibited Ca(2+) reloading into ER in permeabilized acinar cells. This effect was augmented by phosphatidylinositol (3,4,5)-trisphosphate (PIP(3)), suggesting that both bile acids and PI3K act synergistically to inhibit SERCA. Furthermore, inhibition of PI3K by LY-294002 completely inhibited trypsinogen activation caused by the bile acid TLC-S. Our results indicate that PI3K and its product, PIP(3), facilitate bile acid-induced [Ca(2+)](i) responses in pancreatic acinar cells through inhibition of SERCA-dependent Ca(2+) reloading into the ER and that bile acid-induced trypsinogen activation is mediated by PI3K. The findings have important implications for the mechanism of acute pancreatitis since [Ca(2+)](i) increases and trypsinogen activation mediate key pathological processes in this disorder.
Prognostic Score Including Gene Mutations in Chronic Myelomonocytic Leukemia (2013)

A new prognostic score including ASXL1 status, age, hemoglobin, WBC, and platelet counts defines three groups of CMML patients with distinct outcomes. Based on concordance analysis, this score appears more discriminative than those based solely on clinical parameters.
A Wireless Sensor Network Solution for Precision Agriculture Based on Zigbee Technology (2012)

The article has been retracted due to the investigation of complaints received against it. The Editorial Board found that substantial portions of the text quite like the one published in other journal. The problem is under investigation. This paper published in Vol.4 No.1, 2012, has been removed from this site temporally.
Pharmacological purging of minimal residual disease from peripheral blood stem cell collections of acute myeloblastic leukemia patients: preclinical studies. (1997)

In this paper we describe an experimental model for ex vivo purging of contaminating tumor cells from peripheral blood stem cell (PBSC) collections obtained from patients with acute myeloblastic leukemia (AML). We studied the combination of the alkylating agent nitrogen mustard (NM; concentrations ranging from 0.25 to 1.25 microg/mL) and etoposide (VP-16; constant dose of 20 microg/mL), and the conventional cyclophosphamide (Cy)-derivative mafosfamide (concentrations: 20-175 microg/mL).1) To compare the toxicity of the purging protocols on bone marrow (BM) and circulating trilineage precursors collected from normal donors after priming with granulocyte colony-stimulating factor (G-CSF) or after complete remission (CR) consolidation chemotherapy and G-CSF (leukemic patients); 2) to demonstrate the survival of very primitive hematopoietic progenitors (LTC-IC) in the peripheral blood (PB) and the BM after pharmacological treatment; and 3) to evaluate the antineoplastic efficacy of purging protocols on PBSC collections using 3 well-established leukemic cell lines. Our results demonstrated that the toxicity on BM and PB progenitor cells could be correlated with the complete killing of committed granulocyte-macrophage colony-forming units (CFU-GMs) and erythroid precursors (BFU-Es), a condition reached at the concentration of 1.5 microg/mL of NM (in addition to 20 microg/mL of VP-16) and 175 microg/mL of mafosfamide. Notably, early and late megakaryocyte progenitor cells (CFU-MKs and BFU-MKs, respectively) showed higher sensitivity to NM/VP-16, but not to mafosfamide, than did CFU-GMs and BFU-Es. The dose of NM capable of inhibiting 95% of CFU-MKs and BFU-MKs (ID95) was 0.75 microg/mL. After incubation with the same dose of NM, the recovery of CFU-GMs and BFU-Es was 20 +/- 8% SD and 25 +/- 10% SD, respectively (p < 0.05). Long-term liquid cultures showed the recovery of primitive hematopoietic cells after incubation with the highest concentrations of NM/VP-16 and mafosfamide, with no significant differences between PB and BM samples. Under the same experimental conditions, we observed a more than 5-log reduction of contaminating leukemic cell lines (i.e., K-562, KG-1, and HL-60). In conclusion, we demonstrated that NM/VP-16 and mafosfamide purging agents are capable of killing leukemic cell lines that contaminate leukapheresis products from patients with AML, whereas an acceptable proportion of primitive LTC-IC is spared. Moreover, despite the different kinetic and functional profile of mobilized and steady-state BM progenitors, we did not observe any difference in toxicity of antineoplastic agents on hematopoietic cells at different levels of differentiation. These data suggest that pharmacological strategies developed for eliminating minimal residual disease (MRD) from BM autografts can be effectively and safely applied to circulating stem cell harvests.
Effects of Surface Roughness on Hydrogen Gas Sensing Properties of Single Pd Nanowires (2011)

We report on the effects of surface roughness resulting from an ion milling technique on the hydrogen gas sensing performance of a single Pd nanowire grown by electrodeposition into nanochannels in anodized aluminum oxide templates. A combination of electron beam lithography and a lift-off process was utilized to fabricate four-terminal devices based on individual Pd nanowires. These results are the first demonstration of the effect of ion milling on the response time in a single Pd nanowire used as a hydrogen sensor. The response time of the single Pd nanowire surface-treated by ion milling was 20 times faster than that of a sample without surface treatment. The faster response time was due to the surface roughness effects of the surface treatment, an increase in the surface-to-volume ratio of the ion-milled nanowire.
Site-Specific Incorporation of p-Propargyloxyphenylalanine in a Cell-Free Environment for Direct Protein−Protein Click Conjugation (2010)

The tyrosine analog p-propargyloxyphenylalanine (pPa), like tyrosine, has limited water solubility. It has been postulated that this limited solubility has contributed to reduced cellular uptake of pPa and thus reduced in vivo incorporation of pPa into proteins. Using a cell-free protein synthesis system (CFPS) to circumvent cellular uptake, pPa has been incorporated site-specifically into proteins with high specificity at yields up to 27 times greater than the highest previously reported yield. The alkyne group present on proteins incorporated with pPa provides a reactive residue for site-specific bioconjugation with the copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition (CuAAC). Previously, incorporation of another CuAAC-compatible unnatural amino acid p-azido-l-phenylalanine (pAz) was demonstrated with CFPS. However, incorporation of pPa may be preferred over pAz due to the instability of the pAz's aryl-azido moiety upon UV or near-UV light exposure. Also, the ability to incorporate site-specifically both reactants of the CuAAC (the alkyne group of pPa and the azido group of pAz) into proteins enables direct site-specific conjugation of heterologous proteins. We have demonstrated (for the first time to our knowledge) a one-step, linker-less, site-specific, direct protein-to-protein conjugation using CuAAC and unnatural amino acids.
High-quality GaAs Schottky diodes fabricated by strained layer epitaxy (1985)

High-quality GaAs Schottky diodes have been fabricated using a strained layer to improve the material quality. The epitaxial layer has been isoelectronically doped with In with a concentration of 4×1019 cm−3. The diodes fabricated on these layers show a reverse current of 100 pA–200 pA up to 50 V reverse-bias voltage at room temperature. The Schottky contact area was 7500 μm2 and the doping concentration 1×1016 cm−3. An excellent, reproducible ideality factor of 1.02 has been obtained over seven decades of forward current. Results of Schottky diodes fabricated on isoelectronically doped layers in comparison to conventionally fabricated devices are reported.