gebhart/patrepeval huggingface dataset:
Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode <i>Heterodera glycines</i> (2021)

The soybean cyst nematode <i>Heterodera glycines</i> is the most economically devastating pathogen of soybean in the United States and threatens to become even more damaging through the selection of virulent nematode populations in the field that can overcome natural resistance mechanisms in soybean cultivars. This pathogen, therefore, demands intense transcriptomic/genomic research inquiries into the biology of its parasitic mechanisms. <i>H. glycines</i> delivers effector proteins that are produced in specialized gland cells into the soybean root to enable infection. The study of effector proteins, thus, is particularly promising when exploring novel management options against this pathogen. Here, we announce the availability of a gland cell-specific RNA-seq resource. These data represent an expression snapshot of gland cell activity during early soybean infection of a virulent and an avirulent <i>H. glycines</i> population, providing a unique and highly valuable resource for scientists examining effector biology and nematode virulence.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Blood pressure (BP) as a biomarker for sorafenib (S), an inhibitor of the vascular endothelial growth factor (VEGF) signaling pathway (2006)

2035 Background: Hypertension is a commonly reported toxicity of agents that inhibit the VEGF signaling pathway (VSP). This new class of cancer therapeutics has broad activity, but optimal dosing methods and integration into established treatment regimens could be enhanced by identification of reliable biomarkers. S, a new treatment for advanced renal cell carcinoma, is an orally available inhibitor of multiple VSP kinases including Raf-1 and VEGFR2. To characterize the chronicity and interindividual variability of BP responses to VSP inhibition we collected serial, standardized measures of BP and concurrent steady-state plasma concentrations ([plasma]) of S, from 30 patients (pts). Methods: Pts with advanced solid tumors, ECOG performance status &lt; 2, and screening BP ≤ 140/90 mmHg on no more than one antihypertensive agent took 400mg S twice daily. Prior to therapy and at 3 time points after steady state [plasma] of drug was achieved, pts underwent 24-hour ambulatory BP monitoring with the SunTech Oscar PowerPack 2 (SunTech Medical, Morrisville, North Carolina). Readings were collected every 15 minutes during daytime hours and every 45 minutes overnight. Results: Unweigthed mean and standard deviations (sd) of systolic (SBP) and diastolic (DBP) 24-hr BP measurements were calculated for each pt. for the sessions pre-therapy and when steady state [plasma] S was reached (between days 6–10 after starting treatment). The differences in mean BPs between the two sessions were compared with (and p values reported for) paired t-tests. Regression analysis of [plasma] of S with either DBP or SBP, or change in DBP or SBP, with main effect and interaction terms for albumin, age, and sex revealed no significant correlation between S [plasma] and BP response. Conclusions: BP elevation is a biomarker for VSP inhibition. The known variability (coefficient of variation = 70%) in total S steady state plasma concentrations did not account for the observed variability in BP response. [Table: see text] [Table: see text]
Abstract LB-306: Long non-coding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma by regulating RNA splicing pathways (2019)

Soft tissue sarcomas (STS) are malignant tumors from diverse mesenchymal tissues. About 40% STS patients develop fatal lung metastasis with a median survival of 15 months. The mechanisms driving the development of lung metastasis in sarcoma patients are poorly understood. Therefore, our lab has developed a genetically engineered mouse model (GEMM) of high-grade primary STS with conditional mutations in Kras and Trp53 (KP) where 40% of mice tumors develop lung metastasis. This KP model recapitulates human patients with Undifferentiated Pleomorphic Sarcoma (UPS), one of the most common subtypes of STS diagnosed in adults. RNA sequencing (RNA-Seq) was performed on paired primary and lung metastases in KP mouse sarcomas and determined that the expression of the long non-coding RNA (lncRNA) Neat1 is increased in lung metastases compared to paired primary tumors. Real time PCR (qPCR) in 22 paired KP mouse primary sarcomas and lung metastases further confirmed that Neat1 is significantly upregulated in some lung metastases. In addition, RNA-Seq and qPCR data from 10 pairs of human primary sarcomas and matched lung metastases also showed that NEAT1 levels are increased in lung metastases. Furthermore, NEAT1 RNA in situ hybridization (ISH) on tissue microarrays (TMAs) of human primary UPS and lung metastases determined that the expression of NEAT1 is upregulated in lung metastases. Next, CRISPR/Cas9 technology was applied to delete Neat1 in primary mouse sarcoma cells and loss of expression of Neat1 was confirmed by qPCR and northern blot in knockout (KO) clones. In addition, loss of Neat1 significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. Furthermore, RNA pull down assay with mass spectrometry analysis determined Neat1 interacting proteins, such as Khsrp, were mainly involved in RNA splicing pathways which was also shown to be dysregulated in lung metastases and Neat1 KO cells. Finally, CRISPR/Cas9 mediated knockout of Khsrp significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. Overall, these results suggest that upregulation of Neat1 promotes lung metastasis of soft tissue sarcoma through regulating RNA splicing pathways and NEAT1 is a potential target to prevent or treat lung metastasis in sarcoma patients.Citation Format: Jianguo Huang, Eric Xu, Mohit Sachdeva, Timothy Robinson, Xiaodi Qin, Dadong Zhang, Kouros Owzar, Nalan Gokgoz, Andrew Seto, Irene Andrulis, Jay Wunder, Tomoyo Okada, Simuel Singer, Alexander Lazar, Brian Rubin, David G. Kirsch. Long non-coding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma by regulating RNA splicing pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-306.
Immunoquantification and enzyme kinetics of alpha-L-iduronidase in cultured fibroblasts from normal controls and mucopolysaccharidosis type I patients. (1992)

alpha-L-Iduronidase activity is deficient in mucopolysaccharidosis type I (MPS I; Hurler syndrome, Scheie syndrome) patients and results in the disruption of the sequential degradation of the glycosaminoglycans dermatan sulfate and heparan sulfate. A monoclonal antibody-based immunoquantification assay has been developed for alpha-L-iduronidase, which enables the detection of at least 16 pg alpha-L-iduronidase protein. Cultured human skin fibroblasts from 12 normal controls contained 17-54 ng alpha-L-iduronidase protein/mg extracted cell protein. Fibroblasts from 23 MPS I patients were assayed for alpha-L-iduronidase protein content. Fibroblast extracts from one MPS I patient contained at least six times the level of alpha-L-iduronidase protein for normal controls--but contained no associated enzyme activity--and is proposed to represent a mutation affecting the active site of the enzyme. Fibroblast extracts from 11 MPS I patients contained 0.05-2.03 ng alpha-L-iduronidase protein/mg extracted cell protein, whereas immunodetectable protein could not be detected in the other 11 patients. Four fibroblast extracts with no immunodetectable alpha-L-iduronidase protein had residual alpha-L-iduronidase activity, suggesting that the mutant alpha-L-iduronidase in cultured cells from these MPS I patients has been modified to mask or remove the epitopes detected by two monoclonal antibodies used in the quantification assay. Both the absence of immunoreactivity in a mild MPS I patient and high protein level in a severe MPS I patient present limitations to the use of immunoquantification analysis as a sole measure of patient phenotype. Enzyme kinetic analysis of alpha-L-iduronidase from MPS I fibroblasts revealed a number of patients with either abnormal substrate binding or catalytic activity.(ABSTRACT TRUNCATED AT 250 WORDS)
Fluorescence Spectroscopy (2016)

Fluorescence spectroscopy is unique in its combination of sensitivity with experimental versatility. The advent of relatively affordable, robust, yet sophisticated, benchtop fluorimeters in conjunction with the vast and growing number of commercially available fluorescent probes have contributed to the accessibility and popularity of fluorescence spectroscopy. It has become one of the most important analytical techniques for the in vitro study of biomolecules and in vivo cellular imaging, providing spatial and temporal information. This chapter discusses the majority of techniques commonly used in the study of biomolecules. The quintessential fluorescence-based technique is steady-state fluorescence spectroscopy. In contrast to steady-state fluorescence spectroscopy, time-resolved fluorescence analysis can facilitate the simultaneous analysis of multiple emissive states with overlapping spectral bands, each with its own fluorescence decay, by deconvolution of a sample's multiexponential decay curve. Steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy, and fluorescence anisotropy are typically concerned with monitoring a single fluorescent probe.
Immunoblastic lymphadenopathy associated with methyldopa therapy. A case report (1978)

The case of a 71-year-old woman who developed generalized weakness, lymphadenopathy, and a skin rash during methyldopa therapy is described. The prompt disappearance of symptoms following the discontinuation of the drug implicates it in the initial triggering of the abnormal lymphoid proliferation. Shortly thereafter, florid immunoblastic lymphadenopathy developed, and the patient subsequently responded to corticosteroid therapy. The frequent occurrence of immunoblastic lymphadenopathy during or shortly after the administration of various therapeutic medications is emphasized. The nature of the disorder and its differential diagnosis are discussed.
Supplemental Table 6 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER&lt;sup&gt;+&lt;/sup&gt; Metastatic Breast Cancer (2023)

&lt;p&gt;Evolutionary status data&lt;/p&gt;
An Immuno-PF2D-MS/MS Proteomic Approach for Bacterial Antigenic Characterization:  To <i>Bacillus</i> and Beyond (2007)

We are confronted daily to unknown microorganisms that have yet to be characterized, detected, and/or analyzed. We propose, in this study, a multidimensional strategy using polyclonal antibodies, consisting of a novel proteomic tool, the ProteomeLab PF2D, coupled to immunological techniques and mass spectrometry (i-PF2D-MS/MS). To evaluate this strategy, we have applied it to Bacillus subtilis, considered here as our unknown bacterial model.
Quantitative Phosphoproteomic and Metabolomic Analyses Reveal GmMYB173 Optimizes Flavonoid Metabolism in Soybean under Salt Stress (2018)

Salinity causes osmotic stress to crops and limits their productivity. To understand the mechanism underlying soybean salt tolerance, proteomics approach was used to identify phosphoproteins altered by NaCl treatment. Results revealed that 412 of the 4698 quantitatively analyzed phosphopeptides were significantly up-regulated on salt treatment, including a phosphopeptide covering the serine 59 in the transcription factor GmMYB173. Our data showed that GmMYB173 is one of the three MYB proteins differentially phosphorylated on salt treatment, and a substrate of the casein kinase-II. MYB recognition sites exist in the promoter of flavonoid synthase gene GmCHS5 and one was found to mediate its recognition by GmMYB173, an event facilitated by phosphorylation. Because GmCHS5 catalyzes the synthesis of chalcone, flavonoids derived from chalcone were monitored using metabolomics approach. Results revealed that 24 flavonoids of 6745 metabolites were significantly up-regulated after salt treatment. We further compared the salt tolerance and flavonoid accumulation in soybean transgenic roots expressing the <sup>35</sup>S promoter driven cds and <i>RNAi</i> constructs of <i>GmMYB173</i> and <i>GmCHS5</i>, as well as phospho-mimic (<i>GmMYB173<sub>S59D</sub></i> ) and phospho-ablative (<i>GmMYB173<sub>S59A</sub></i> ) mutants of <i>GmMYB173</i> Overexpression of <i>GmMYB173<sub>S59D</sub></i> and <i>GmCHS5</i> resulted in the highest increase in salt tolerance and accumulation of cyaniding-3-arabinoside chloride, a dihydroxy B-ring flavonoid. The dihydroxy B-ring flavonoids are more effective as anti-oxidative agents when compared with monohydroxy B-ring flavonoids, such as formononetin. Hence the salt-triggered phosphorylation of GmMYB173, subsequent increase in its affinity to GmCHS5 promoter and the elevated transcription of GmCHS5 likely contribute to soybean salt tolerance by enhancing the accumulation of dihydroxy B-ring flavonoids.
MAB21L4 regulates the TGF-β-induced expression of target genes in epidermal keratinocytes (2021)

Smad proteins transduce signals downstream of transforming growth factor-β (TGF-β) and are one of the factors that regulate the expression of genes related to diseases affecting the skin. In the present study, we identified MAB21L4, also known as male abnormal 21 like 4 or C2orf54, as the most up-regulated targets of TGF-β and Smad3 in differentiated human progenitor epidermal keratinocytes using chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq). We found that TGF-β induced expression of the barrier protein involucrin (encoded by the IVL gene). Transcriptional activity of the IVL promoter induced by TGF-β was inhibited by MAB21L4 siRNAs. Further analysis revealed that MAB21L4 siRNAs also down-regulated the expression of several target genes of TGF-β. MAB21L4 protein was located mainly in the cytosol, where it was physically bound to Smad3 and a transcriptional corepressor c-Ski. siRNAs for MAB21L4 did not inhibit the binding of Smad3 to their target genomic regions but down-regulated the acetylation of histone H3 lys 27 (H3K27ac), an active histone mark, near the Smad3 binding regions. These findings suggest that TGF-β-induced MAB21L4 up-regulates the gene expression induced by TGF-β, possibly through the inhibition of c-Ski via physical interaction in the cytosol.
ChemInform Abstract: Syntheses and Biological Properties of Novel Aza‐podophyllotoxin Analogues Possessing Pronounced Antitumor Activity. (1995)

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.
Advanced Head-Up Display System for Closed Circuit Rebreathers (2019)

U.S. Navy Special Warfare (NSW) and Explosive Ordnance Disposal (EOD) Divers perform critical underwater missions while diving Closed Circuit Rebreather Underwater Breathing Apparatus (CCR-UBAs). Military CCR-UBAs are typically back-worn, electronically controlled, mixed gas diving systems with the oxygen in the diver's breathing gas mix monitored and controlled via a battery-powered electronic module. Two separate electronic visual displays monitor the status of the rebreather with oxygen and diluent bottle pressures monitored on two separate analog pressure gauges. The electronic visual displays are comprised of a primary display module (PDM) and a secondary display module (SDM). The PDM connects to the CCR-UBA electronics module via a cable and is a simple series of red and green light emitting diodes (LEDs) that alert the diver to any equipment malfunctions or warnings. The PDM attaches to the dive mask on the upper right or left side, or to the regulator slightly below the diver's normal field of vision. The SDM is an alphanumeric liquid crystal display (LCD) handset that displays detailed data on oxygen sensor voltages, and batteries' status. It connects to the CCR-UBA electronics module via a separate cable. Depth is monitored on a separate depth gauge. During dive missions in high turbidity and zero visibility conditions (which is very common in military dive missions), the diver is unable to see the critical information on the SDM, oxygen and diluent gauges, and the depth gauge. Under a project funded by the Combating Terrorism Technical Support Office (CTTSO), the Naval Surface Warfare Center-Panama City Division (NSWCPCD) developed two (2) concept prototype systems that fully integrate the critical CCR-UBA display data into a single head-up display capability, clearly visible by the NSW/EOD diver even in high turbidity and zero visibility conditions. The paper will describe the different design approaches taken for the two different prototype systems developed, use of additive manufacturing/3D printing to design and build the prototypes, the unique optical system design, and results of design reference mission testing by military divers.
ChemInform Abstract: Core‐Modified Smaragdyrins: First Examples of Stable Meso‐Substituted Expanded Corrole. (1999)

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.
Quantum State Engineering with Continuous-Variable Post-Selective Thresholding (2005)

We present a scheme to conditionally engineer an optical quantum system via post-selection. This scheme yields high-fidelity squeezed single photon and superposition of coherent states, from input single and two photon Fock states respectively. The input Fock state is interacted with an ancilla squeezed vacuum state using a beam-splitter. We transform the quantum system by post-selecting on the continuous-observable measurement outcome of the ancilla state. We experimentally demonstrate the principles of this scheme using displaced coherent states and measure experimentally fidelities that are only achievable using quantum resources.
A visibility optimization study for grating-based X-ray Phase Contrast Imaging (2012)

An X-ray phase contrast grating interferometer consists of three gratings in the beam line to generate interference patterns and acquire phase shift information if an object is placed into the beam. These gratings have a pitch of a few micrometers and therefore very accurate alignment is needed to acquire phase information reliably. In this work we have investigated different setup parameters and environmental influences on the detected signal quality by Six Sigma methods. We have used this information to optimize our setup and established a semi-automatic alignment procedure to reproduce a stable signal quality.
Synthesis of superficially modified Ce<sub>1−x</sub>(Zr + Y)<sub>x</sub>O<sub>2−δ </sub> solid solutions and thermogravimetric analysis of their performance in the catalytic soot combustion (2020)

Abstract In this work, solid solutions of general formula Ce 1−x (Zr + Y)xO 2− δ were chemically synthesized through the so-called citrate-EDTA complexing method, wherein the doping cations Zr and Y were substituted in the ceria lattice with an equimolar amount of 0.05 ≤ x ≤ = 0.25. The ternary oxides were heat-treated, and those that showed the best textural properties were superficially impregnated with Fe 2 O 3 particles by the thermal decomposition method using a metalorganic precursor. The X-ray diffraction results suggest that co-doping with Zr 4+ and Y 3+ promotes a slight distortion of the CeO 2 cubic cell. Nevertheless, the fluorite cubic structure of the oxides remains stable after being exposed to heat treatments. Furthermore, using scanning electron microscopy and Raman techniques, the presence of deposited Fe 2 O 3 and the formation of extrinsic vacancies in the materials could be corroborated. Finally, the oxides’ catalytic evaluation in the soot oxidation reaction was carried out using the thermogravimetry technique. The ternary oxide with cerium molar content equal to 0.9 and impregnated with Fe 2 O 3 presented excellent catalytic behavior for soot oxidation. T 10 , T 50 , and T 90 temperatures were 310, 383, and 416 °C, respectively.
Acclimation of photosynthesis and respiration to elevated atmospheric CO<sub>2</sub> in two Scrub Oaks (2002)

Abstract For two species of oak, we determined whether increasing atmospheric CO 2 concentration ( C a ) would decrease leaf mitochondrial respiration (R) directly, or indirectly owing to their growth in elevated C a , or both. In particular, we tested whether acclimatory decreases in leaf‐Rubisco content in elevated C a would decrease R associated with its maintenance. This hypothesis was tested in summer 2000 on sun and shade leaves of Quercus myrtifolia Willd. and Quercus geminata Small. We also measured R on five occasions between summer 1999 and 2000 on leaves of Q. myrtifolia . The oaks were grown in the field for 4 years, in either current ambient or elevated (current ambient + 350 µmol mol −1 ) C a , in open‐top chambers (OTCs). For Q. myrtifolia , an increase in C a from 360 to 710 µmol mol −1 had no direct effect on R at any time during the year. In April 1999, R in young Q. myrtifolia leaves was significantly higher in elevated C a —the only evidence for an indirect effect of growth in elevated C a . Leaf R was significantly correlated with leaf nitrogen (N) concentration for the sun and shade leaves of both the species of oak. Acclimation of photosynthesis in elevated C a significantly reduced maximum RuBP‐saturated carboxylation capacity ( V c max ) for both the sun and shade leaves of only Q. geminata . However, we estimated that only 11–12% of total leaf N was invested in Rubisco; consequently, acclimation in this plant resulted in a small effect on N and an insignificant effect on R. In this study measurements of respiration and photosynthesis were made on material removed from the field; this procedure had no effect on gas exchange properties. The findings of this study were applicable to R expressed either per unit leaf area or unit dry weight, and did not support the hypothesis that elevated C a decreases R directly, or indirectly owing to acclimatory decreases in Rubisco content.