gebhart/patrepeval huggingface dataset:
ARHI is the center of allelic deletion on chromosome 1p31 in ovarian and breast cancers (2000)

In our previous work, we had characterized ARHI as an imprinted putative tumor-suppressor gene in ovarian and breast cancers. ARHI is expressed in primary breast and ovarian cell lines but largely absent from the corresponding malignant tumors. Moreover, the non-imprinted functional allele is typically deleted in malignant cells. Since ARHI had been mapped to 1p31, a common deletion site in breast and ovarian cancer and male germ-cell tumors, in this study, we set out to define precisely the physical location of ARHI at 1p31 and to determine if this location lies within the smallest common region of deletion in breast and ovarian cancers. To this end, we first carried out radiation hybrid mapping of ARHI and surrounding markers, followed by a high-resolution study of loss of heterozygosity at 1p31 in 49 ovarian and breast cancers. Combining a radiation hybrid map and a physical map of the region encompassing ARHI, 3 discrete regions of minimal deletion were found at 1p31 in breast and ovarian cancers. ARHI is the most common deletion region at 1p31. Two other less common regions of deletion were found centromeric to this gene. One of them centered on D1S207 and the other one included and was proximal to D1S488. We also confirmed the preferential loss of non-imprinted functional allele in 7 of 9 tumor specimens. These data support the possibility that ARHI is a tumor-suppressor gene and suggest that additional tumor-suppressor genes may lie proximal to ARHI at 1p31. The data obtained from our study should aid in the identification and characterization of genes in this novel imprinted region.
Cardiac Muscle Membrane Stabilization in Myocardial Reperfusion Injury (2019)

The phospholipid bilayer membrane that surrounds each cell in the body represents the first and last line of defense for preserving overall cell viability. In several forms of cardiac and skeletal muscle disease, deficits in the integrity of the muscle membrane play a central role in disease pathogenesis. In Duchenne muscular dystrophy, an inherited and uniformly fatal disease of progressive muscle deterioration, muscle membrane instability is the primary cause of disease, including significant heart disease, for which there is no cure or highly effective treatment. Further, in multiple clinical forms of myocardial ischemia-reperfusion injury, the cardiac sarcolemma is damaged and this plays a key role in disease etiology. In this review, cardiac muscle membrane stability is addressed, with a focus on synthetic block copolymers as a unique chemical-based approach to stabilize damaged muscle membranes. Recent advances using clinically relevant small and large animal models of heart disease are discussed. In addition, mechanistic insights into the copolymer-muscle membrane interface, featuring atomistic, molecular, and physiological structure-function approaches are highlighted. Collectively, muscle membrane instability contributes significantly to morbidity and mortality in prominent acquired and inherited heart diseases. In this context, chemical-based muscle membrane stabilizers provide a novel therapeutic approach for a myriad of heart diseases wherein the integrity of the cardiac muscle membrane is at risk.
Volume Visualization and Volume Rendering Techniques (2000)

There is a wide range of devices and scientific simulation generating volumetric data. Visualizing such data, ranging from regular data sets to scattered data, is a challenging task. This course will give an introduction to the volume rendering transport theory and the involved issues such as interpolation, illumination, classification and others. Different volume rendering techniques will be presented illustrating their fundamental features and differences as well as their limitations. Furthermore, acceleration techniques will be presented including pure software optimizations as well as utilizing special purpose hardware as VolumePro but also dedicated hardware such as polygon graphics subsystems.
Differential expression of the interleukin 5 receptor α isoforms in blood and tissue eosinophils of nasal polyp patients (2009)

The expression of SOL-IL-5Ralpha and TM-IL-5Ralpha differs according to the eosinophil activation state and localization in the body (blood vs tissue) and may therefore be involved in the fine-tuning of the eosinophil homeostasis. Exposure of eosinophils to IL-5 reduces their responsiveness to IL-5 by regulated expression of the IL-5Ralpha isoforms. Since, TM-IL-5Ralpha is down-regulated and SOL-IL-5Ralpha (antagonistic) is upregulated in NP tissue, our findings are important to understand the clinical trials with anti-IL-5 in humans.
Role of NK-1 and NK-2 tachykinin receptor antagonism on the growth of human breast carcinoma cell line MDA-MB-231 (2005)

We demonstrate that neurokinin A (NKA) and substance P (SP) play a role in the proliferation of the estrogen receptor-negative (ER-) cell line MDA-MB-231, a human breast carcinoma expressing both NK-1 and NK-2 receptors. In vitro experiments showed that the specific receptor antagonists MEN 11,467 (NK-1) and nepadutant (MEN 11,420; NK-2) inhibited tumor cell proliferation, and blocked the stimulatory effect of SP and NKA. Anti-tumoral activity of NK-1 and NK-2 receptor antagonists was demonstrated in nude mice, measuring growth inhibition of MDA-MB-231 tumor cells xenografted s.c. and by using the hollow-fiber assay. In both systems a significant inhibition was found when compounds were administered at 5 mg/kg i.v. every day for 2 weeks. Results obtained from both these models suggest that the in vivo activity of NK-1 and NK-2 antagonists may be a result of a cytostatic effect rather than a cytotoxic effect. Our results suggest that the control of breast carcinoma (ER-) growth by tachykinin receptor antagonists may become a new form of targeted therapy for these human tumors.
Efficacy and Safety of Treatment With an Anti-M2e Monoclonal Antibody in Experimental Human Influenza (2014)

These data indicate that TCN-032 may provide immediate immunity and therapeutic benefit in influenza A infection, with no apparent emergence of resistant virus. TCN-032 was safe with no evidence of immune exacerbation based on serum cytokine expression. Clinicaltrials.gov registry number. NCT01719874.
Transcriptional derepression of the Saccharomyces cerevisiae HSP26 gene during heat shock. (1990)

hsp26, the small heat shock protein of Saccharomyces cerevisiae, accumulates in response to heat and other types of stress. It also accumulates during the normal course of development, as cells enter stationary phase growth or begin to sporulate (S. Kurtz, J. Rossi, L. Petko, and S. Lindquist, Science 231:1154-1157, 1986). Analysis of deletion and insertion mutations demonstrated that transcriptional control plays a critical role in regulating HSP26 expression. The HSP26 promoter was found to be complex and appears to contain repressing elements as well as activating elements. Several upstream deletion mutations resulted in strong constitutive expression of HSP26. Furthermore, upstream sequences from the HSP26 gene repressed the constitutive expression of a heterologous heat shock gene. We propose that basal repression and heat-induced depression of transcription play major roles in regulating the expression of HSP26. None of the recombinant constructs that we analyzed separated cis-regulatory sequences responsible for heat shock regulation from those responsible for developmental regulation of HSP26. Depression of HSP26 transcription may be the general mechanism of HSP26 induction in yeast cells. This regulatory scheme is very different from that described for the regulation of most other heat shock genes.
ChemInform Abstract: Photochemistry and Single‐Crystal Polarized Absorption Spectroscopy of (η4‐Cyclooctatetraene)tricarbonyliron. (1986)

Abstract The wavelength‐dependent CO and ole‐ ?n photosubstitution quantum yields for the title complex with P(OMe)3 in cyclohexane are studied.
Coichicine Interferes with L-Selectin and Leukocyte Function-Associated Antigen-i Expression on Human I Lymphocytes a nd Inhibits I Cell (1996)

Colchicine, which inhibits cell microtubule assembly by preventing polymerization of tubulin monomers, inhibits cell-mediated immune responses and pro- motes long-term survival of major histocompatibility complex-incompatible renal allograffs in rats. Here we evaluated the effect of blocking cell microtubule assembly by colchicine on T cell and endothelial cell adhesion receptors involved in transducing signals for T cell activation. By using immunofluorescence flow cytometry analysis, evidence is presented that colchicine, in a dose-dependent fashion, downregu-
Methyl 2,4-anhydro-5-azido-5,6-dideoxy-L-altronate (2004)

The title compound, C7H11N3O4, was prepared from l-rhamnose as a conformationally restricted dipeptide isostere containing an oxetane ring. Its crystal structure was determined to confirm the synthetic product.
Fructus sophorae attenuates secretion of proinflammatory mediators and cytokines through the modulation of NF-κB and MAPK signaling pathways in LPS-stimulated RAW 264.7 macrophages (2016)

This study investigated the inhibitory effects and underlying mechanisms of fructus sophorae, the dried ripe fruit of Styphnolobium japonicum (L.) Schott, on the production of proinflammatory molecules in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. The results indicated that pretreatment with noncytotoxic concentrations of fructus sophorae extract (FSE) significantly inhibited the release of the proinflammatory mediators nitric oxide (NO) and prostaglandin E(2), which were associated with the downregulation of both mRNA and protein for inducible NO synthase and cyclooxygenase-2, respectively, in LPS-challenged RAW 264.7 cells. FSE also blocked the LPS-induced expression of the proinflammatory cytokines interleukin (IL)-6 and IL-1β. Furthermore, the results showed that FSE efficiently attenuated the LPS-induced nuclear translocation of nuclear factor-kappa B (NF-κB) and phosphorylation of the mitogen-activated protein kinases (MAPKs) extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) but not p38 MAPK. These results suggest that FSE exhibits anti-inflammatory activity by inhibiting proinflammatory mediators and cytokines through the inactivation of NF-κB, ERK and JNK, and it may offer therapeutic potential for treating inflammatory diseases accompanied with macrophage activation.
Genomic Alterations in Primary Gastric Adenocarcinomas Correlate with Clinicopathological Characteristics and Survival (2004)

Microarray CGH has revealed several chromosomal regions that have not been described before in gastric cancer at this frequency and resolution, such as amplification of at 7q21-q22 and 12q14.1-q21.1, as well gains at 1q32.3, 7p11.2, and losses at 13q13.1. Interestingly, gain of 1q32.3 and loss of 18q22.1 are associated with a bad prognosis indicating that these regions could harbour gene(s) that may determine aggressive tumour behaviour and poor clinical outcome.
Preclinical Safety and Efficacy Assessments for Novel Femtosecond Lasers in Corneal Refractive Surgery (2022)

Preclinical safety requirements and test methods have been standardized over time to guide medical device developers in the path needed to manufacture safe devices and achieve regulatory approval. Today, femtosecond lasers are commonly used in cataract and refractive surgeries. Currently, an industry standard to guide developers in preclinical testing of ophthalmic lasers does not exist. Consequently, the data presented in regulatory submissions may vary between manufacturers, making the regulatory review process more ambiguous. Here, the authors present a comprehensive discussion of preclinical test methods applied to the evaluation of an ophthalmic laser. We include in vitro and ex vivo models, as well as an in vivo rabbit model subject to corneal refractive treatments, for consideration in a preclinical safety evaluation plan. Scientific rationale to support the ocular endpoints of evaluation in the rabbit model to demonstrate safety is also presented and discussed.
Time-resolved fluorescence measurement based on spectroscopy and DSP techniques for Bi/Er codoped fibre characterisation (2014)

We propose a novel method of combining time-resolved / spectroscopic and DSP techniques for fluorescence lifetime measurement. The lifetime of Bi/Er codoped fibre is determined with good accuracy over a range of emission wavelengths.
Distributed algorithms for optimization problems with equality constraints (2013)

In this paper we introduce two discrete-time, distributed optimization algorithms executed by a set of agents whose interactions are subject to a communication graph. The algorithms can be applied to optimization problems where the cost function is expressed as a sum of functions, and where each function is associated to an agent. In addition, the agents can have equality constraints as well. The algorithms are not consensus-based and can be applied to non-convex optimization problems with equality constraints. We demonstrate that the first distributed algorithm results naturally from applying a first order method to solve the first order necessary conditions for a lifted optimization problem with equality constraints; the solution of our original problem is embedded in the solution of this lifted optimization problem. Using an augmented Lagrangian idea, we derive a second distributed algorithm that requires weaker conditions for local convergence compared to the first algorithm. For both algorithms we address the local convergence properties.
Design of New Ligands for the Palladium‐Catalyzed Arylation of α‐Branched Secondary Amines (2015)

In Pd-catalyzed C-N cross-coupling reactions, α-branched secondary amines are difficult coupling partners and the desired products are often produced in low yields. In order to provide a robust method for accessing N-aryl α-branched tertiary amines, new catalysts have been designed to suppress undesired side reactions often encountered when these amine nucleophiles are used. These advances enabled the arylation of a wide array of sterically encumbered amines, highlighting the importance of rational ligand design in facilitating challenging Pd-catalyzed cross-coupling reactions.
Camera-Augmented Non-Contact Vital Sign Monitoring in Real Time (2022)

This study develops a camera-guided frequency-modulated continuous-wave (FMCW) radar to monitor vital signs. A red-green-blue-depth (RGB-D) camera estimates the human torso landmarks and a processing unit constantly adapts the radar beams to the direction of the subjects. To constantly optimize the regions of interest for monitoring respiratory rate (RR) and heart rate (HR), a novel method, coined “singular value-based point detection (SVPD),” is designed. Vital sign extraction is then followed as the last step. Experiments are conducted for the cases of single-subject (10 subjects, 31 scenarios, and 1550 repetitions) and dual-subject monitoring (6 subjects, 6 scenarios, and 90 repetitions). Average (RR, HR) accuracies of (97.68%, 85.88%), (90.02%, 86.05%), (96.71%, 89.50%), and (97.52%, 86.71%) are achieved for the range of distances (0.5-2.5 m), azimuth angles (0°–30°), elevation angles (−30°–+30°), and incident angles (−30°–+30°), respectively. The higher chest and upper abdomen are determined as the optimal regions for RR and HR estimation respectively, with average accuracies of 98.31% and 86.93%. Finally, the capability of dual-subject monitoring at various inter-subject distances (range of 20–70 cm) is confirmed with average accuracies of 92.26% and 73.23% for RR and HR respectively.
Biologic Characterization of Chicken-Derived H6N2 Low Pathogenic Avian Influenza Viruses in Chickens and Ducks (2010)

Low pathogenic avian influenza H6N2 viruses were biologically characterized by infecting chickens and ducks in order to compare adaptation of these viruses in these species. We examined the clinical signs, virus shedding, and immune response to infection in 4-wk-old white leghorn chickens and in 2-wk-old Pekin ducks. Five H6N2 viruses isolated between 2000 and 2004 from chickens in California, and one H6N2 virus isolated from chickens in New York in 1998, were given intrachoanally at a dose of 1 x 10(6) 50% embryo infectious dose per bird. Oral-pharyngeal and cloacal swabs were taken at 2, 4, and 7 days postinoculation (PI) and tested by real-time reverse-transcriptase polymerase chain reaction for presence of virus. Serum was collected at 7, 14, and 21 days PI and examined for avian influenza virus antibodies by commercial enzyme-linked immunosorbent assay (ELISA) and hemagglutination inhibition (HI) testing. Virus shedding for all of the viruses was detected in the oral-pharyngeal swabs from chickens at 2 and 4 days PI, but only three of the five viruses were detected at 7 days PI. Only two viruses were detected in the cloacal swabs from the chickens. Virus shedding for four of the five viruses was detected in the oral-pharyngeal cavity of the ducks, and fecal shedding was detected for three of the viruses (including the virus not shed by the oral-pharyngeal route) in ducks at 4 and 7 days PI. All other fecal swabs from the ducks were negative. Fewer ducks shed virus compared to chickens. Both the chickens and the ducks developed antibodies, as evidenced by HI and ELISA titers. The data indicate that the H6N2 viruses can infect both chickens and ducks, but based on the number of birds shedding virus and on histopathology, the viruses appear to be more adapted to chickens. Virus shedding, which could go unnoticed in the absence of clinical signs in commercial chickens, can lead to transmission of the virus among poultry. However, the viruses isolated in 2004 did not appear to replicate or cause more disease than earlier virus isolates.
Deep Tomographic Image Reconstruction: Yesterday, Today, and Tomorrow—Editorial for the 2nd Special Issue “Machine Learning for Image Reconstruction” (2021)

As a follow-up to the first IEEE Transactions on Medical Imaging (TMI) special issue on the theme of deep tomographic reconstruction, the second special issue is assembled to reflect the status and momentum of this rapidly emerging field. In this editorial, we provide a brief background illustrating the motivation for the development of network-based, data-driven, and learning-oriented reconstruction methods, summarize the included papers, and report our verification of the shared deep learning codes. Finally, we discuss several important research topics to facilitate further investigation and collaboration.
An Asymmetric Synthesis of Fully Functionalized B Ring System of Taxol (1995)

Abstract Optically active 7-t-butyldimethylsiloxy-4,8-dibenzyloxy-6,6-dimethyl-5-p-methoxybenzyloxy-2-cycloocten-1-one (1) was synthesized from 3,7-dibenzyloxy-4,8-di-t-butyldimethylsiloxy-5,5-dimethyl-6-p-methoxybenzyloxy-2-octanone (2) by way of intramolecular Reformatsky-type reaction using SmI2.
Supplementary Methods from ERK and p38 MAPK Activities Determine Sensitivity to PI3K/mTOR Inhibition via Regulation of MYC and YAP (2023)

&lt;p&gt;Description of additional methods and procedures used in the study.&lt;/p&gt;
A Novel Y-Shaped, S–O–N–O–S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease (2023)

As the COVID-19 pathogen, SARS-CoV-2 relies on its main protease (M<sup>Pro</sup>) for pathogenesis and replication. During crystallographic analyses of M<sup>Pro</sup> crystals that were exposed to the air, a uniquely Y-shaped, S-O-N-O-S-bridged post-translational cross-link that connects three residues C22, C44, and K61 at their side chains was frequently observed. As a novel covalent modification, this cross-link serves potentially as a redox switch to regulate the catalytic activity of M<sup>Pro</sup>, a demonstrated drug target of COVID-19. The formation of this linkage leads to a much more open active site that can potentially be targeted for the development of novel SARS-CoV-2 antivirals. The structural rearrangement of M<sup>Pro</sup> by this cross-link indicates that small molecules that lock M<sup>Pro</sup> in the cross-linked form can potentially be used with other active-site-targeting molecules such as paxlovid for synergistic effects in inhibiting SARS-CoV-2 viral replication.
Computational Studies of Lithium Manganese and Nickel-Manganese Oxide Spinel Surfaces (2015)

LiMn 2 O 4 is ideal as a high-capacity Li-ion battery cathode material by virtue of its low toxicity, low cost, and the high natural abundance of Mn. However, this material suffers from Mn dissolution problem that not only induces capacity fade, but can also poison the anode. Several approaches have been devised to mitigate Mn dissolution, including doping, coatings, and even particle shape control. Previous studies have shown that the electrochemical performance and cycling stability of these materials depend not only on the composition, but on the particle morphology as well. Simulations of the structure of low index surfaces of the spinel-structured LiMn 2 O 4 and its derivatives, such as the high voltage LiNi 0.5 Mn 1.5 O 4 spinel have been performed within the GGA+U approximation, and ab-initio molecular dynamics. New insights resulting from this work, including interactions with electrolytes, will be presented. This work was supported as part of the Center for Electrochemical Energy Science, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.
Crystal structure analyses of two TMA silicates with ordered defects: RUB-20, a layered zeolite precursor, and RUB-22, a microporous framework silicate (2015)

Abstract Synthesis experiments in the simple system TMAOH/SiO 2 /H 2 O led at 160°C to the crystallization of two new tetramethylammonium (TMA) silicates, RUB-20 and RUB-22. The common feature of the two silicates is the presence of ordered defects within the silicate network, necessary to compensate the charge of the occluded TMA cation. RUB-20, [(CH 3 ) 4 N] 1.7 [Si 18 O 35 (OH) 4 ], is a layered material with a 0 = 10.493(2) Å, b 0 = 13.988(2) Å, c 0 = 7.411(1) Å, β = 97.80(2)° and space group P 2 1 / m . It consists of ferrierite type ( fer ) silicate layers which possess a significant amount of defects. These defects apply only to one particular Si–O–Si bridge which is hydrolyzed to about 50% to form two additional Si–OH/Si–O - groups which point to the interlayer region of the structure. These silanol groups together with the regular terminal silanol groups of neighbouring fer layers form a system of hydrogen bonds which binds the layers together. In addition, weak ionic bonds exist between the negatively charged silicate layers and the intercalated TMA cations. RUB-22 is a zeolite-like silicate possessing a microporous framework with double-cages, housing the TMA cations. The Rietveld structure analysis revealed a pseudo monoclinic unit cell with a 0 = 13.6626(2) Å, b 0 = 13.2400(2) Å, c 0 = 12.3009(2) Å, α = 90.003(3)°, β = 112.700(1)°, γ = 90.005(3) and space group <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>C</m:mi> <m:mover> <m:mn>1</m:mn> <m:mo>¯</m:mo> </m:mover> <m:mo>.</m:mo> </m:mrow> </m:math> $C\bar 1.$ RUB-22, [(CH 3 ) 4 N] 4 [Si 32 O 60 (OH) 12 ], possesses an interrupted silica framework of the same topology as RUB-10, [(CH 3 ) 4 N] 4 [Si 32 B 4 O 72 ] (zeolite framework type RUT ), however, with the difference that defects replace the [BO4]-tetrahedra. The defects can be regarded as “hydroxyl nests” surrounding a vacancy □(OH-Si) 3 ( - O-Si) instead of B(-O-Si) 4 groups. Heating the as made materials at 600°C led in the case of RUB-20 to a highly disordered zeolite of the CDO type and in the case of RUB-22 to a distorted and defective RUT -type material.