gebhart/patrepeval huggingface dataset:
Identification of novel oligodendroglioma‐associated candidate tumor suppressor genes in 1p36 and 19q13 using microarray‐based expression profiling (2006)

Loss of heterozygosity (LOH) on chromosomal arms 1p and 19q is the most common genetic alteration in oligodendroglial tumors and associated with response to radio- and chemotherapy as well as favorable prognosis. Using microsatellite analysis, we previously identified the chromosomal regions 1p36.22-p36.31 and 19q13.3, as candidate tumor suppressor gene regions being commonly deleted in these tumors. To identify genes within these regions that are downregulated in oligodendroglial tumors with LOH 1p/19q, we performed cDNA microarray-based RNA expression profiling of 35 gliomas with known allelic status on 1p and 19q, including 7 oligodendrogliomas and 8 diffuse astrocytomas of World Health Organization (WHO) grade II, as well as 14 anaplastic oligodendrogliomas and 6 anaplastic oligoastrocytomas of WHO grade III. The microarrays used for expression profiling carried approximately 7,000 gene-specific cDNAs, with complete coverage of the genes located in 1p36.13-p36.31 and 19q13.2-q13.33. Microarray analysis identified 8 genes from these regions (MGC4399, SRM, ICMT, RPL18, FTL, ZIN, FLJ10781 and DBP), which all showed significantly lower expression in 1p/19q-deleted gliomas when compared to gliomas without 1p/19q losses. Quantitative real-time reverse transcription-PCR analyses were performed for the MGC4399, ICMT and RPL18 genes and confirmed the microarray findings. In addition, we found that the cytosolic phospholipase A2 (PLA2G4C) gene at 19q13.3 demonstrated significantly lower expression in anaplastic oligodendrogliomas (WHO grade III) when compared to well-differentiated oligodendrogliomas (WHO grade II). Taken together, our study provides a set of interesting novel candidate genes that may play important roles in the pathogenesis of oligodendroglial tumors.
Hardware and Software Implementation of an Artificial Pancreas System on a Mobile Device (2017)

In this work, an artificial pancreas (AP) system, implemented on a mobile device is described. The proposed AP platform integrates hardware (insulin pump, glucose monitor, various sensors for vital signs and physical activities) and software (closed-loop control algorithm, sensor fusion, data storage and remote server access) components via smartphone that is running a dedicated Operating System designed for AP systems. Interfacing with this OS and custom application development steps are presented. Closed loop operation is demonstrated with case studies.
The volumetric sources reconstruction method and its applications to geometry reconstruction (2010)

An extension of the Sources Reconstruction Method (SRM) is presented in this contribution. The goal is to extend the methods' capabilities not only for antenna diagnostics but also for profile reconstruction. The idea is to retrieve the induced currents on a conductor surface, so that it will have a correspondence to the body's contour. Multiple incidence angles and frequencies are considered, so that the combination of the reconstructed equivalent currents for each case will improve the method's resolution. A 2D and a 3D application examples based on simulated data are presented.
Extended Interaction Klystrons for terahertz power amplifiers (2010)

Summary form only given. Extended Interaction Klystrons have been demonstrated at frequencies up to 218 GHz CW and 229 GHz pulsed. Modern design, fabrication, and measurement technologies show promise of extending their operation into the THz regime. This paper describes the challenges and some novel approaches to the development of EIKs operating terahertz frequencies, while simultaneously meeting demanding requirements for output power, gain, bandwidth, and efficiency.The main challenges in design include focus and transport of an emittance dominated beam, development of a broadband, high gain circuit, and the minimization of the sensitivity of design to the effects of fabrication and alignment tolerances. The main challenges in fabrication and integration include achieving required component dimensions and alignment within specified tolerances and achieving high quality surface finishes using materials with satisfactory mechanical and thermal properties.
ChemInform Abstract: Palladium‐Catalyzed Arylation of Allylic Benzoates Using Hypervalent Siloxane Derivatives. (2002)

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.
CAG--polyglutamine repeat mutations: independence from gene context (1999)

Several neurological disorders have been attributed to the inheritance of long CAG-polyglutamine repeats. Unlike classical mutations, whose deleterious effects are totally dependent on the context of the gene in which they reside, these translated CAG repeat mutations have been shown to cause neurotoxicity and neuronal intranuclear inclusions when expressed outside their natural gene context. We provide a description of mice with different lengths of repeat in the foreign context of the murine Hprt locus, focusing on aspects of the phenotype that provide an insight into the mechanism by which this unusual mutation might cause toxicity.
The orion facility (2004)

ORION will be a user-oriented research facility for understanding the physics and developing the technology for future high-energy particle accelerators, as well as for research in related fields. The facility has as its centerpiece the Next Linear Collider Test Accelerator (NLCTA) at the Stanford Linear Accelerator Center (SLAC). The NLCTA will be modified with the addition of a new, high-brightness photoinjector, its drive laser, an S-band rf power system, a user laser room, a low-energy experimental hall supplied with electron beams up to 60 MeV in energy, and a high-energy hall supplied with beams up to 350 MeV. The facility design and parameters are described here along with highlights from the 2nd ORION Workshop held in February 2003.
Table S2 from Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell–Secreted Cytokines (2023)

&lt;p&gt;Supplementary Table S2: ## Raw count matrix of mini-pool CRISPR screens. ## Normalized gene scores in mini-pool screens.&lt;/p&gt;
COMPARISON OF THE EFFECTS OF CYCLOSPORINE AND ITS METABOLITES ON THE RELEASE OF PROSTACYCLIN AND ENDOTHELIN FROM MESANGIAL CELLS (1992)

CsA-induced alterations in mesangial cell production of potent vasoactive substances may be a contributing factor to the decreased renal blood flow and glomerular thrombosis associated with CsA nephrotoxicity. In this study the toxic effects of several CsA metabolites, previously isolated and characterized by mass spectrometry and nuclear magnetic resonance, were investigated in cultured rabbit mesangial cells. AM4N and AM9 were the most cytotoxic metabolites examined, having potency ratios of 0.28-0.56 with respect to CsA for the inhibition of cell growth and DNA synthesis. In addition the effects of several CsA metabolites were examined on the basal release of prostacyclin and endothelin. A concentration-dependent decrease in prostacyclin production, as measured by release of its stable metabolite, 6-keto-PGF1 alpha, was observed in cells treated with CsA and metabolites. CsA metabolites were equipotent as parent drug resulting in a significant (P less than 0.05) 20-40% reduction in prostacyclin production. The dihydroxylated metabolites of CsA, AM19, and AM1c9 resulted in a significantly (P less than 0.05) increased production of endothelin from the cells. In contrast parent drug resulted in a slight decrease in its production. In general CsA metabolites were found to be significantly less cytotoxic than parent drug in mesangial cells. However, the finding that certain CsA metabolites could alter production of vasoactive substances from these cells suggests that CsA metabolites may directly alter the renal hemodynamics, producing alterations consistent to that observed for CsA-induced renal side effects in vivo.
Single and Dual Channel Noise Reduction (2006)

This chapter contains sections titled: Introduction Linear MMSE Estimators Speech Enhancement in the DFT Domain Optimal Non-linear Estimators Joint Optimum Detection and Estimation of Speech Computation of Likelihood Ratios Estimation of the A Priori Probability of Speech Presence VAD and Noise Estimation Techniques Dual Channel Systems Bibliography
CHARACTERIZATION OF MULTIPLE SCLEROSIS LESIONS AND BRAIN TISSUES WITH Tip DISPERSION IMAGING (1991)

Ramscv, R. M.D.; Lipton, M J. M.D.; Foust, R. J. M.D.; Sepponen, R. E. D.Sc.; Tanttu, J. I. M.Sc. Author Information
A Unifying Parsimony Model of Genome Evolution (2013)

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.
LIFT Study Discontinued (2017)

Early prediction of therapeutic outcome is important in determining whether the ongoing therapy is beneficial. In addition to anatomical response determined using the Response Evaluation Criteria in Solid Tumors (RECIST) criteria, recent studies have indicated that change in tumor glucose use on or after treatment correlates with histopathologic tumor regression and patient outcomes. This Perspective discusses the use of (18)F-fluorodeoxyglucose-positron emission tomography (FDG-PET) for pharmacodynamic evaluation in a very early phase of treatment to predict clinical outcomes in patients with advanced non-small-cell lung cancer. We conducted a study to assess whether early metabolic response determined using FDG-PET correlated with clinical outcomes in patients treated with gefitinib or those treated with carboplatin plus paclitaxel (CP). Early metabolic response to gefitinib, but not CP, correlated with the late metabolic response, anatomical response, progression-free survival, and even overall survival. A rapid effect of molecular targeted agents might not be aptly evaluated using the conventional criteria, eg, RECIST, in a very early phase of treatment before volumetric shrinkage of the tumor. Based on the findings of several studies, and on the findings from our study, use of FDG-PET might enable prediction of clinical outcomes at a very early stage of treatment, especially in patients treated with molecular targeted agents with rapid clinical efficacy.
Microwave Ablation in Primary Lung Malignancies (2019)

Lung cancer is the leading cause of cancer-related mortality worldwide. Eighty-five percent of cases correspond to non-small cell lung cancer (NSCLC) and pivotal nonsurgical options for early-stage disease include percutaneous ablation and stereotactic body radiation therapy (SBRT). Microwave Ablation (MWA) is a locoregional treatment option that has many advantages over radiofrequency ablation and has been able to overcome the limitations of this technique in the treatment of early-stage NSCLC. In this review article, we highlight the current evidence supporting the use of MWA in patients with early-stage NSCLC and discuss the technical considerations of the procedure, including optimal patient selection and planning strategies, as well as the potential complications and reported outcomes. Finally, we mention future trends involving ablation in NSCLC, including its role in combination with SBRT in central tumors, management of post-SBRT local recurrence, and its potential as an adjuvant treatment option for patients with resistance to systemic therapy or in combination with checkpoint inhibitors.
Preparation of Polyvinyl Alcohol/Xylan Blending Films with 1,2,3,4‐Butane Tetracarboxylic Acid as a New Plasticizer (2014)

Miscible, biodegradable polyvinyl alcohol (PVA)/xylan blending films were firstly prepared in the range of the PVA/xylan weight ratio from 1 : 2 to 3 : 1 by casting method using 1,2,3,4‐butane tetracarboxylic acid (BTCA) as a new plasticizer. The properties of blending films as functions of PVA/xylan weight ratio and BTCA amount were discussed. XRD and FT‐IR were applied to characterize the blending films. Experimental results indicated that tensile strength (TS) and elongation at break (EAB) of blending films decreased along with the decrease of the PVA/xylan weight ratio. Both of TS and EAB firstly increased and then decreased as the amount of BTCA was increased. More importantly, blending films were biodegraded almost by 41% with an addition of 10% BTCA in blending films within 30 days in soil. For all hydroxyl functionalized polymers (xylan and PVA), their molecular interactions and miscibility with BTCA endowed blending films with the biocompatibility and biodegradability. Therefore, these blending films are environmentally friendly materials which could be applied as biodegradable plastics for food packaging and agricultural applications.
Kardiovaskuläre Verträglichkeit von Dapagliflozin bei Patienten mit Typ-2-Diabetes-mellitus (T2DM) und unterschiedlichen Ausprägungen des kardiovaskulären Risikos (2016)

Fragestellung: T2DM-Patienten haben ein erhöhtes Risiko für kardiovaskuläre Erkrankungen. Der SGLT-2 Inhibitor Dapagliflozin (DAPA) verringert Blutglukosespiegel, außerdem kommt es zur Reduktion von Körpergewicht und Blutdruck. In einer Metaanalyse lag die Eintrittswahrscheinlichkeit pro 100 Expositionsjahre für den primären kombinierten Endpunkt (kardiovaskulärer [KV] Tod, Myokardinfarkt [MI], Schlaganfall oder Hospitalisierung aufgrund von instabiler Angina pectoris) bei 1,62 für DAPA vs. 2,06 für Kontrolle (HR 0,79). Hier wurden die Effekte bei Patientensubgruppen mit unterschiedlich ausgeprägten KV-Erkrankungen genauer charakterisiert, fokussierend auf schwerwiegende unerwünschte KV-Ereignisse (MACE; Kompositendpunkt aus KV Tod, MI oder Schlaganfall).
Wound Center Without Walls: The New Model of Providing Care During the COVID-19 Pandemic. (2020)

The COVID-19 pandemic poses a major challenge in delivering care to wound patients. Due to multiple comorbidities, wound patients are at an increased risk for the most extreme complications of COVID-19 and providers must focus on reducing their exposure risk. The Federal, State, and local governments, as well as payers, have urged hospitals and providers to reduce utilization of nonessential health services, but they also have given more flexibility to shift the site of necessary care to lower risk environments. Providers must be prepared for disruption from this pandemic mode of health care for the next 18 months, at minimum. The wound provider must accept the new normal during the pandemic by adapting their care to meet the safety needs of the patient and the public. The Wound Center Without Walls is a strategy to untether wound care from a physical location and aggressively triage and provide care to patients with wounds across the spectrum of the health system utilizing technology and community-centered care.
Alkyne versus Allene Activation in Platinum‐ and Gold‐Catalyzed Cycloisomerization of Hydroxylated 1,5‐Allenynes (2007)

Chemo- and stereoselective transformations of 3-hydroxy-1,5-allenynes 1 into a variety of new and potentially useful cyclic compounds have been achieved. Substrates bearing a silyl group at the alkyne moiety undergo purely thermal or Lewis acid catalyzed Alder-ene type transformations into 2-methylene-3-vinylcyclopent-3-enol derivatives 2. When heated in the presence of a catalytic amount of PtCl(2) or PtCl(4), these incipient cyclopentenols could be further transformed into 3-vinylcyclopent-2-enones 3. On the other hand, alkyl-substituted 3-hydroxy-1,5-allenynes proved to be stable under refluxing conditions. Nevertheless, PtCl(2) and PtCl(4) could selectively activate the alkyne moiety of these substrates toward intramolecular nucleophilic attack of the internal allene double bond to yield unprecedented 6-methylenebicyclo[3.1.0]hexan-3-one derivatives 4. With gold-based catalysts, provided that the reaction is carried out in dichloromethane, both Au(I) and Au(III) complexes selectively activate the allene fragment of the substrates toward intramolecular nucleophilic attack of the hydroxyl group to yield 2-ethynyl-3,6-dihydro-2H-pyrans 5. Compounds of type 4 can also be formed with Au(I) and Au(III) complexes if the reaction is carried out in toluene. The reactivity of these new compounds has been partially investigated, and polycyclic ketones were obtained after oxidation under mild conditions or gold-catalyzed cycloisomerization.
Don't trust the datasheet: a validation of commercial G alpha i/o primary antibodies for Western blotting (2019)

Primary antibodies are an integral part of Western blotting but validation of the specificity and sensitivity of antibodies by suppliers is extremely lacking. Multiple examples of this are evident in the G alpha i/o family of proteins. G alpha proteins are important signal transducing molecules for both endogenous cellular function and drug action that are divided into four families: Gs, Gi/o, Gq/11, and G12/13. These four families of proteins interact with the nearly 1000 G protein coupled receptors (GPCRs) in the human body, the largest and most diverse group of receptors. Because of the diversity of these receptors, around one third of all drugs on the market target GPCRs, which, in part, utilize different G alpha subunit proteins to evoke their downstream signaling and physiological responses. Therefore, it is important that researchers have tools; e.g., selective antibodies, that can clearly define how G alpha proteins produce their effects associated with a receptor and its ligand. Multiple commercially available G alpha protein antibodies have been employed for relative G protein quantification, but they have not been adequately verified for both their specificity and sensitivity. In this study, BL‐21 DE3 RIL competent cells were used to express and purify five protein members of the Gi/o family of G alpha proteins. Gi1, Gi2, Gi3, Go, and Gz proteins were purified using an AKTA FPLC system and a histidine trap purification column. Western blots using these proteins and multiple Gi/o primary antibodies from different vendors were used to determine the specificity of the antibodies for their advertised protein. Our results showed antibodies that were successful in binding specifically to their target and antibodies that either did not bind to the protein of interest or expressed binding to multiple members of the Gi/o family despite claims that it was selective in targeting a single protein. After determination of specificity, purified proteins were used in a 1:2 dilution series to determine the linear range of detection for each antibody that was deemed specific for a single protein. This linear range was then used for determination of sensitivity and absolute quantitation of Gi/o proteins in Sprague‐Dawley rat brain tissue, specifically punches from the paraventricular nucleus and cortex. Together, the results of these studies indicate that certain antibodies, which are available from commercial vendors for use in Western blot assays, may not be selective for a specific Gi/o subunit protein as advertised. Thus, it is essential that investigators be sure to verify that their antibody is selective and specific for their target protein in their own hands, to ensure that the use of the antibody in subsequent studies is valid. Support or Funding Information NIH 5P30GM106392 to DK and R01GM097350 to SK This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Oligomerization of vinyl monomers 18. Stereochemistry of anionic oligomerization of 4‐vinylpyridine (1985)

Abstract Oligomers of 4‐vinylpyridine were prepared by reaction in vacuo of 4‐vinylpyridine with lithio‐4‐ethylpyridine at −78°C, followed by reaction with CH 3 I( 13 CH 3 I) or CH 3 OH. The stereochemistry was studied by NMR and GC. Methylation and the addition of 4‐vinylpyridine occurred in a stereochemically nonselective manner. The data also indicated that in contrast to the oligomerization of 2‐vinylpyridine the stereoisomeric meso and racemic 4‐pyridyl carbanions propagated with equal reaction rates. The stereochemistry was readily explained by an absence of coordination of the Li ion by the nitrogen of the penultimate pyridine ring observed in the corresponding oligomerization of 2‐vinylpyridine.
A DUAL REFLECTOR FEED SYSTEM FOR A SUB-MM HOLOGRAM CATR (2002)

Manufacturing of large holograms for compact antenna test ranges can be facilitated with a modified hologram illumination. The relative quiet-zone size of the CATR can also be increased, which allows testing of larger telescope antennas with a fixed-sized hologram. The modified hologram illumination can be realized with a dual reflector feed system. In this paper, a simple ray tracing based synthesis technique for designing the dual shaped hyperbolic reflector feed system is described. Simulation results of a design example at 310 GHz are presented. The required accuracies in the reflector system assembly are also discussed.
Photodynamic Effects of Antioxidant Substituted Porphyrin Photosensitizers on Gram-positive and -negative Bacteria¶ (2003)

Photodynamic treatment of the gram-negative bacteria Escherichia coli B and Acinetobacter baumannii and the gram-positive bacterium Staphylococcus aureus was performed using two newly devised and synthesized antioxidant carrier photosensitizers (antioxidant carrier sensitizers-2 [ACS-2] and antioxidant carrier sensitizers-3 [ACS-3]), which are butyl hydroxy toluene and propyl gallate substituted haematoporphyrins, respectively. It was found that ACS-2 is less reactive than other photosensitizers previously used for the same purpose, whereas ACS-3 is very effective against the multidrug-resistant bacterium A. baumannii, causing its complete eradication at a low fluence (approximately 7.5 J/cm2) of blue light (407-420 nm) and a low concentration (10 microM). At a higher fluence (approximately 37.5 J/cm2) complete eradication of E. coli B can be obtained under the same conditions. Furthermore, X-ray microanalysis and ultrastructural changes indicate that ACS-3, especially in the case of photodynamic treatment of A. baumannii, interferes with membrane functions and causes the inactivation of the bacterium. ACS-3 may be suggested as a specific photosensitization agent for photoinactivation of gram-negative bacteria.