gebhart/patrepeval huggingface dataset:
Abstract PL08-01: Differential splicing of oncogenes and tumor suppressor genes between African and Caucasian Americans: Contributing factor in prostate cancer health disparities? (2011)

Abstract There are striking population disparities in prostate cancer (PCa) risk and survival outcome borne out of current health statistics data. This is particularly evident between African Americans (AA) and their Caucasian American (CA) counterparts. Epidemiologic studies have shown that higher mortality and recurrence rates of PCa is still seen in AA men even after adjustment for socioeconomic status, environmental factors and health care access. To test whether differential mRNA splicing may play a role in PCa health disparities, RNA from PCa and patient-matched normal prostate needle biopsies from AAs and CAs was processed and hybridized onto the Affymetrix human Exon 1.0 ST arrays. A 4-way statistical design (10% FDR, &amp;gt;1.5 fold-change) was employed in the following comparisons: AA normal vs. CA normal, AA cancer vs. CA cancer, AA cancer vs. AA normal, and CA cancer vs. CA normal. Our analysis identified &amp;gt;800 genes undergoing differential mRNA splicing between AA and CA cancer specimens. Notably, many of these genes reside within canonical oncogenic signaling pathways. To further delineate the functional consequences of these splice variants, exon-specific and/or exon junction-specific small interfering RNAs (siRNAs) were employed to suppress splice variants for 4 oncogenes (PIK3CD, FGFR3, MET and RASGRP2) in PCa cell lines derived from the AA and CA patient populations. The targeted knockdown of population-specific splice variants appears to have differential effects on cell proliferation and invasive. For example, the splice variant for phosphoinositide-3 kinase delta (PI3KCD) found in AA PCa specimens encodes a more aggressive version of the gene (i.e., leading to greater proliferation and invasion of cancer cells) compared to the variant counterpart found in CA PCa specimens. Taken together, our data suggest that differential mRNA splicing may be critical in PCa health disparities between the AA and CA populations. These findings should advance our knowledge on the molecular mechanisms underlying PCa health disparities, and may facilitate the development of novel strategies for PCa detection, diagnosis, prognosis, and therapy in the AA population. This work was supported by NCI grant 5U01-CA-116937, ACS-IRG-08-091-01 and the Affymetrix Collaborations in Cancer Research Program. Citation Information: Cancer Epidemiol Biomarkers Prev 2011;20(10 Suppl):PL08-01.
Effect of Alismol on Adrenergic Mechanism in Isolated Rabbit Ear Artery (1988)

Effects of alismol, a sesquiterpenoid isolated from the rhyzome of Alisma orientale, on adrenergic mechanisms were examined in the isolated rabbit ear artery. Alismol (10−6 to 10−4 M) inhibited the contraction of isolated rabbit ear artery by electrical stimulation of the perivascular nerves. The inhibition was concentration-dependent; at a concentration of 10−4 M, the inhibition was 90% (n = 8). Treatment with 10−4 M alismol inhibited the increase in 3H-noradrenaline (3H-NAd) release induced by electrical stimulation by 63±6%. Alismol at 10−4 M did not affect the neuronal uptake of 3H-NAd in the artery. Alismol at 10−4 M slightly inhibited contractions induced by exogenously administered NAd. These results demonstrate that alismol inhibits the adrenergic neuro-effector mechanisms in rabbit ear artery, and they suggest that alismol acts primarily on nerve terminals and inhibits their responses to electrical stimulation by interfering with NAd release.
&lt;title&gt;Photonic applications of spatial soliton switches&lt;/title&gt; (1995)

A novel switch is introduced which has the capability of interconnecting 1 input channel to N output channels in a single device, without crosstalk. It is based on the unique properties of spatial solitons which propagate without diffracting in space and create index channels which can be used to guide signals at the same or different frequencies. Angular scanning of the soliton channels is achieved by chirping the phase of the input wavefront. Some properties of the switch and the initial demonstration of soliton scanning in an AlGaAs planar waveguide at 1550 nm are discussed.
Investigation of associations between the pregnane-X receptor gene (NR1I2) and Crohnʼs disease in Canadian children using a gene-wide haplotype-based approach (2008)

Our gene-wide analysis in a pediatric cohort using both the case-control and case-parent designs suggests that the NR1I2 gene is not associated with CD in Canadian children.
Capturing and concentrating adenovirus using magnetic anionic nanobeads (2016)

We recently demonstrated how various enveloped viruses can be efficiently concentrated using magnetic beads coated with an anionic polymer, poly(methyl vinyl ether-maleic anhydrate). However, the exact mechanism of interaction between the virus particles and anionic beads remains unclear. To further investigate whether these magnetic anionic beads specifically bind to the viral envelope, we examined their potential interaction with a nonenveloped virus (adenovirus). The beads were incubated with either adenovirus-infected cell culture medium or nasal aspirates from adenovirus-infected individuals and then separated from the supernatant by applying a magnetic field. After thoroughly washing the beads, adsorption of adenovirus was confirmed by a variety of techniques, including immunochromatography, polymerase chain reaction, Western blotting, and cell culture infection assays. These detection methods positively identified the hexon and penton capsid proteins of adenovirus along with the viral genome on the magnetic beads. Furthermore, various types of adenovirus including Types 5, 6, 11, 19, and 41 were captured using the magnetic bead procedure. Our bead capture method was also found to increase the sensitivity of viral detection. Adenovirus below the detectable limit for immunochromatography was efficiently concentrated using the magnetic bead procedure, allowing the virus to be successfully detected using this methodology. Moreover, these findings clearly demonstrate that a viral envelope is not required for binding to the anionic magnetic beads. Taken together, our results show that this capture procedure increases the sensitivity of detection of adenovirus and would, therefore, be a valuable tool for analyzing both clinical and experimental samples.
When is an outbreak not an outbreak? Fit, divergent strains of Mycobacterium tuberculosis display independent evolution of drug resistance in a large London outbreak (2012)

It appears that this outbreak comprised a heterogeneous collection of closely related strains, which appear to exhibit more variation than would usually be associated with a point source outbreak. These strains appear to have evolved by acquisition of additional antimicrobial resistance mutations while remaining competitive. The acquired resistance and retained competitiveness may be partly responsible for the difficulty in controlling the outbreak.
Case of the Rapidly Growing Uterine Fibroid (2011)

A 47 year old woman with “rapidly growing uterine fibroid”. P.D.M. contacted us because she was told she had a rapidly growing fibroid. She wanted to avoid a hysterectomy, but in her home state of Wyoming was only offered hysterectomy with removal of both ovaries because of the possibility of cancer.
Liquid chromatography coupled to tandem mass spectrometry for the analysis of inositol hexaphosphate after solid-phase extraction (2016)

International audience
Identification of protein components of the microsomal glucose 6-phosphate transporter by photoaffinity labelling (1999)

The glucose-6-phosphatase system catalyses the terminal step of hepatic glucose production from both gluconeogenesis and glycogenolysis and is thus a key regulatory factor of blood glucose homoeostasis. To identify the glucose 6-phosphate transporter T1, we have performed photoaffinity labelling of human and rat liver microsomes by using the specific photoreactive glucose-6-phosphate translocase inhibitors S 0957 and S 1743. Membrane proteins of molecular mass 70, 55, 33 and 31 kDa were labelled in human microsomes by [3H]S 0957, whereas in rat liver microsomes bands at 95, 70, 57, 54, 50, 41, 33 and 31 kDa were detectable. The photoprobe [3H]S 1743 led to the predominant labelling of a 57 kDa and a 50 kDa protein in the rat. Stripping of microsomes with 0.3% CHAPS retains the specific binding of T1 inhibitors; photoaffinity labelling of such CHAPS-treated microsomes resulted in the labelling of membrane proteins of molecular mass 55, 33 and 31 kDa in human liver and 50, 33 and 31 kDa in rat liver. Photoaffinity labelling of human liver tissue samples from a healthy individual and from liver samples of patients with a diagnosed glycogen-storage disease type 1b (GSD type 1b; von Gierke's disease) revealed the absence of the 55 kDa protein from one of the patients with GSD type 1. These findings support the identity of the glucose 6-phosphate transporter T1, with endoplasmic reticulum protein of molecular mass 50 kDa in rat liver and 55 kDa in human liver.
Method to create gradient index in a polymer (2023)

Novel photo-writable and thermally switchable polymeric materials exhibit a refractive index change of .DELTA.n.gtoreq.1.0 when exposed to UV light or heat. For example, lithography can be used to convert a non-conjugated precursor polymer to a conjugated polymer having a higher index-of-refraction. Further, two-photon lithography can be used to pattern high-spatial frequency structures.
Cellulose Nanofibrils as Assay Substrates for Cellulases and Lytic Polysaccharide Monooxygenases (2020)

A facile method for preparing colloidal cellulose nanofibrils (CNFs) from potato tubers is presented comprising alkaline treatment to remove noncellulosic polysaccharides, followed by hypochlorite oxidation and homogenization. The CNF consisted of ∼94% cellulose, and carboxyl groups on the surface of CNF prevented their agglomeration. Aqueous suspensions of CNF had up to two times higher optical transparency than phosphoric acid swollen cellulose (PASC). The motivation for preparing CNF was to use it as a substrate for probing cellulose-degrading enzymes. It was shown that a lytic polysaccharide monooxygenase (LPMO) is active on CNF under formation of the same products as with other cellulose substrates. Moreover, CNF responded to cellulase treatment in a similar way to microcrystalline cellulose (Avicel), while PASC was rapidly broken down. Thus, a new assay substrate for these enzymes is presented with a unique combination of naturelike fibrillar structures and high optical transparency, which opens up for new types of analyses.
Synthesis of organo-mineral nanohybrid material: Phenoxyacetate anions in the lamella of Mg-Al-layered double hydroxide (2006)

An organo-mineral nanohybrid material in which the organic moiety is interleaved inside the inorganic lamella was prepared by using phenoxyacetate anions as a guest in the Mg-Al-layered double hydroxide lamella (as an inorganic host) by the self-assembly technique, anion exchange and the reconstruction methods. The powder XRD patterns of the resulted materials show that the basal spacing of the Mg-AI-layered double hydroxide with carbonate as the counter anions expanded from 7.7 ? to around 16.6 ? in the nanohybrid materials. IR studies show that the absorption bands of the resulting materials correspond to the characteristic functional groups of the host and the guest structures. When the two results are taken together, the expansion can be attributed to the intercalation of the phenoxyacetic acid in the inorganic interlamella for the formation of the nanohybrid material. The intercalation of phenoxyacetate anions was also confirmed by thermogravimetric analysis (TG).
New realistic approach of the kinetics in fast labelling procedures (1987)

Abstract A real kinetic approach of fast labelling reactions is obtained by introducing a corrected reaction time τ which takes into account the temperature rise process of the reaction solution. τ is obtained by transformation of transient temperature data to isothermal conditions at a preset temperature. Experimental data obtained for 123 I‐radioiodination of ortho‐iodohippuric acid fit completely with the theory.
Long-term oxidation performance of ingot-produced Fe<sub>3</sub>Al alloys (1999)

AbstractThe oxidation performance of ingot-produced Fe-28at.%Al-(2–5)%Cr alloys with minor oxygen-active element additions was examined in long-term exposures at 1,000–1,300°C. As expected for alumina-forming alloys, additions of Zr, Y and Hf improved the oxidation behavior of these alloys. At the lower end of the temperature range, these alloys performed similarly to other iron-base alumina-formers. However, at higher temperatures, scale spallation was increased and significant deformation of the substrate was observed. This type of scale spallation was not observed on other alumina-formers. Oxidation data were used to predict times to breakaway for this temperature range.Keywords: ODS FeCrAlFe3Al alloysoxidation performancereactive element additionslifetime prediction
Submicron thermal imaging of quantum dot lasers on GaAs and Si substrates (2006)

We map a laserpsilas internal temperature structure for the first time, identifying separate heat sources due to contact heating and nonradiative recombination and using this technique to compare degradation mechanisms for GaAs-based and Si-based lasers.
Budd-Chiari Syndrome: Long term success via hepatic decompression using transjugular intrahepatic porto-systemic shunt (2010)

Our results confirm the role of TIPS in the management of patients with acute, subacute and chronic BCS. The limited number of patients with OLT does not allow to draw a meaningful conclusion. However, the underlying disease may generate major complications, a reason why OLT should be limited to patients who cannot be managed by TIPS.
Cholinergic neuronal signals attenuate inflammasome activation through inhibiting mitochondrial stress (P1264) (2013)

Abstract The mammalian immune system and the nervous system coevolved under the influence of cellular and environmental stress. Immunity is highly linked with mitochondrial stress, which importantly regulates the activation inflammasome, a key component of innate immunity. Here we show that cholinergic neuronal signals attenuate inflammasome activation by inhibiting mitochondrial stress. Cholinergic receptor agonists or vagus nerve stimulation significantly inhibited the inflammasome activation and mitochondrial stress; whereas genetic deletion of alpha 7 nicotinic acetylcholine receptor (a7 nAchR) significantly enhanced the inflammasome activation and mitochondrial stress. Immunohistochemical analysis revealed that a7 is localized in the mitochondria. We also found that extracellular acetylcholine rapidly influxes into macrophage cytoplasm upon ATP stimulation in a P2X7 receptor-dependent manner. Importantly, acetylcholine significantly attenuated calcium or hydrogen oxide-induced mitochondrial damage and the subsequent mitochondrial DNA release. Together, these findings unravel a novel neurotransmitter-mediated signaling pathway, in which acetylcholine translocates into cytoplasm of immune cells during inflammation, and inhibits inflammasome activation by preserving mitochondrial membrane integrity.
C—H Bond Activation by Iridium and Rhodium Complexes: Catalytic Hydrogen—Deuterium Exchange and C—C Bond-Forming Reactions (2004)

The metal-mediated activation of carbon-hydrogen bonds has the potential of leading to important fundamental insights, as well as to advances in large-scale industrial and synthetic organic chemical processes. Our initial finding of C-H oxidative addition reactions in low-valent iridium (I) complexes was followed by a more recent discovery and exploration of C-H activation processes at Ir (III) centers. This paper reviews recent studies of the Ir (III) reaction that include work directed toward elucidation of its reaction mechanism and the development of catalytic hydrogen/deuterium exchange reactions. The article also discusses collaborative studies of rhodium (I)-catalyzed reactions that provide a method for adding complexity to a range of carbo- and heterocyclic arene compounds with structures analogous to those found in physiologically active organic compounds.
One consensual depression diagnosis tool to serve many countries: a challenge! A RAND/UCLA methodology (2018)

The SLR extracted 7 tools. Two instruments were considered sufficiently effective and reliable for use: the Hospital Anxiety and Depression Scale and the Hopkins Symptoms Checklist-25 (HSCL-25). After testing face-to-face, HSCL-25 was selected. A multicultural consensus on one diagnostic tool for depression was obtained for the HSCL-25. This tool will provide the opportunity to select homogeneous populations for European collaborative research in daily practice.
Results of an ongoing open-label, phase II study of carfilzomib in patients with relapsed and/or refractory multiple myeloma (R/R MM). (2010)

8000 Background: Carfilzomib (CFZ) is a highly selective proteasome inhibitor with single-agent activity in patients (pts) with R/R MM. Methods: In this ongoing study of single-agent CFZ in R/R MM, pts were stratified based on prior exposure to BTZ and CFZ dose level (Table). CFZ IV was administered on days 1, 2, 8, 9, 15, and 16 every 28 d for up to 12 cycles. Study endpoints included overall response rate (ORR), defined as ≥ partial response (PR), duration of response (DOR), and safety. Results: The BTZ-treated cohort included 35 pts (14 refractory to most recent treatment). For BTZ-naive pts, cohort 1 included 59 pts and cohort 2 included 20 pts. Pts received a mean of 5 cycles of CFZ (range 1–12). Thirty-three BTZ-treated pts were evaluable with an ORR of 18%. For BTZ-naive pts, 54 pts in cohort 1 and 19 pts in cohort 2 were evaluable with ORRs of 46% and 53%, respectively. Median DOR (≥MR) was ≥8.8 months (mo). Treatment groups and patient responses are shown in the Table. In the combined pt population, the most common adverse events (AEs) included fatigue (66%), nausea (49%), dyspnea (40%), anemia (34%), diarrhea (32%) and were primarily ≤ Gr 2 in severity. The most common ≥ Gr 3 AEs were anemia, thrombocytopenia, and neutropenia (10% each). Febrile neutropenia and treatment-emergent peripheral neuropathy (PN) were uncommon. Of 23 pts who completed the 12 cycle protocol, 7 chose to continue CFZ therapy on an extended treatment protocol. Updated results for all cohorts will be presented. Conclusions: Single-agent CFZ is active in pts with R/R MM. AEs were generally mild and thereby durable disease control was obtained with continued dosing. Severe PN is rare and does not limit therapy. BTZ-treated N=35 BTZ-naive Cohort 1 N=54 Cohort 2 N=19 CFZ administration 20 mg/m2 20 mg/m2 20 mg/m2 cycle 1, 27 mg/m2 cycle 2+ Best response CR 1 1 0 VGPR 1 5 1 PR 4 19 9 MR 4 8 0 SD 13 12 6 Median DOR (≥MR) 9.0 mo 8.8 mo TBD Median TTP 5.3 mo 7.6 mo TBD Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Onyx Bristol-Myers Squibb, Celgene, Centocor Ortho Biotech, Exelixis, Genzyme, Millennium, Onyx Pharmaceuticals Onyx Bristol-Myers Squibb, Celgene, Centocor Ortho Biotech, Exelixis, Johnson & Johnson, Merck, Millennium, Onyx Celgene, Merck, Millennium, Novartis, Onyx
Denoising Autoencoder Trained on Simulation-Derived Structures for Noise Reduction in Chromatin Scanning Transmission Electron Microscopy (2023)

Scanning transmission electron microscopy tomography with ChromEM staining (ChromSTEM), has allowed for the three-dimensional study of genome organization. By leveraging convolutional neural networks and molecular dynamics simulations, we have developed a denoising autoencoder (DAE) capable of postprocessing experimental ChromSTEM images to provide nucleosome-level resolution. Our DAE is trained on synthetic images generated from simulations of the chromatin fiber using the 1-cylinder per nucleosome (1CPN) model of chromatin. We find that our DAE is capable of removing noise commonly found in high-angle annular dark field (HAADF) STEM experiments and is able to learn structural features driven by the physics of chromatin folding. The DAE outperforms other well-known denoising algorithms without degradation of structural features and permits the resolution of α-tetrahedron tetranucleosome motifs that induce local chromatin compaction and mediate DNA accessibility. Notably, we find no evidence for the 30 nm fiber, which has been suggested to serve as the higher-order structure of the chromatin fiber. This approach provides high-resolution STEM images that allow for the resolution of single nucleosomes and organized domains within chromatin dense regions comprising of folding motifs that modulate the accessibility of DNA to external biological machinery.
Detection of Antibody to Hepatitis C Virus in Prospectively Followed Transfusion Recipients with Acute and Chronic Non-A, Non-B Hepatitis (1990)

ALTER, H. J.; PURCELL, R. H.; SHIH, J. W.; MELPOLLER, J. C.; HOUGHTON, I. M.; CHOO, Q. -L.; KUS, G. K. Author Information
Comparative studies of galactose-6-mustard and L-phenylalanine mustard on cell growth and cell cycle kinetics in vitro (1992)

The effect of galactose-6-mustard (G-6-M) on cell growth and cell cycle kinetics was studied in murine P388 leukemia and Chinese hamster ovary (CHO) cells in vitro and compared with the effect of L-phenylalanine mustard (L-PAM). The IC50 values of G-6-M for the P388 and CHO cells were 10 and 100 microM, respectively. No difference of the IC50 value of L-PAM (2 microM) between the two cell lines was found. The effect of G-6-M and L-PAM on cell kinetics was similar for the two cell lines at IC50 doses. The relative cell outflow from the G2 stage was inhibited to a higher extent than the relative cell outflow from the S phase. The relative cell outflow from the G1 stage was only partly inhibited. These results are discussed in relation to growth conditions, differences in DNA repair capacity, and cellular uptake of G-6-M between P388 and CHO cells.
Щодо питання доцільності та перспектив створення єдиного слідчого органу в Україні крізь призму нового Кримінального процесуального кодексу (2013)

The article draws attention to the fact that, ispositions of the Criminal procedural code of Ukraine in view of their influence on standards of the Criminal code of Ukraine, determining separated rules of criminal responsibility realization under the current Criminal Legislation were analyzed. It is shown that the corresponding inconsistence of showed branches of law leads to difficulties appearing at the practical activities of criminal proceedings involved bodies and persons in particular at rectitude of standards interpretation, one-upmanship rules usage etc. Showed specific examples that take place in practice. Conclusions concerning advised application of provisions of Criminal Code and Criminal Procedural Code in practice are drew and recommendations are gave.