gebhart/patrepeval huggingface dataset:
Supplementary Table 2 from Pharmacologic Unmasking of Epigenetically Silenced Genes in Breast Cancer (2023)

Supplementary Table 2 from Pharmacologic Unmasking of Epigenetically Silenced Genes in Breast Cancer
Characterization of low frequency instabilities in a Krypton dusty plasma (2014)

© 2014 IOPThis is an author-created, un-copyedited version of an article accepted for publication/published in Plasma Sources Science and Technology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://dx.doi.org/10.1088/0963-0252/23/6/065009
A Human Monoclonal Antibody Derived from Axillary Lymph Nodes of a Breast Cancer Patient (1989)

A human hybridoma clone (A4-33) was established by fusion of human lymphoblastoid cells, HO-323, with lymphocytes of axillary lymph nodes obtained from a breast cancer patient. This clone has been stable, producing IgM for over 24 months. Enzyme-linked immunosorbent assay (ELISA) showed that monoclonal antibody A4-33 reacted strongly to MCF-7, and weakly to PANC-1 and HT-29, but not to other human malignant cell lines. The reactivity of A4-33 to MCF-7 was markedly reduced by treatment with periodate, but not affected or enhanced by neuraminidase or trypsin. Immunoperoxidase staining of normal human tissue sections showed that A4-33 reacted to acinar and ductal cells of the mammary gland and to ductal epithelial cells of the salivary gland, sweat gland, pancreas and bile duct. With malignant tumor sections, A4-33 reacted to breast cancer, pancreatic cancer and parotid cancer. These results suggested that A4-33 recognized the antigen which commonly exists on ductal epithelial cells of the exocrine gland.
Trial Watch: Toll-like receptor agonists in cancer immunotherapy (2018)

Toll-like receptor (TLR) agonists demonstrate therapeutic promise as immunological adjuvants for anticancer immunotherapy. To date, three TLR agonists have been approved by US regulatory agencies for use in cancer patients. Additionally, the potential of hitherto experimental TLR ligands to mediate clinically useful immunostimulatory effects has been extensively investigated over the past few years. Here, we summarize recent preclinical and clinical advances in the development of TLR agonists for cancer therapy.
Time-reversal acoustic focusing system as a virtual random phased array (2010)

This paper compares the performance of two different systems for dynamic focusing of ultrasonic waves: conventional 2-D phased arrays (PA) and a focusing system based on the principles of time-reversed acoustics (TRA). Focused ultrasound fields obtained in the experiments with the TRA focusing system (TRA FS), which employs a liquid-filled reverberator with 4 piezotransducers attached to its wall, are compared with the focused fields obtained by mathematical simulation of PAs comprised from several tens to several hundreds of elements distributed randomly on the array surface. The experimental and simulated focusing systems had the same aperture and operated at a frequency centered about 600 kHz. Experimental results demonstrated that the TRA FS with a small number of channels can produce complex focused patterns and can steer them with efficiency comparable to that of a PA with hundreds of elements. It is shown that the TRA FS can be realized using an extremely simple means, such as a reverberator made of a water-filled plastic bottle with just a few piezotransducers attached to its walls.
Temporal Genome Expression Profile Analysis During T-cell-Mediated Colitis: Identification of Novel Targets and Pathways (2011)

T cells critically regulate inflammatory bowel disease (IBD), with T-cell-dependent experimental colitis models gaining favor in identifying potential pathogenic mechanisms; yet limited understanding of specific pathogenic molecules or pathways still exists. In this study we sought to identify changes in whole genome expression profiles using the CD4CD45Rbhi T-cell transfer colitis model compared to genome expression differences from Crohn's disease (CD) tissue specimens. Colon tissue was used for histopathological and genome expression profiling analysis at 0, 2, 4, or 6 weeks after adoptive T-cell transfer. We identified 1775 genes that were significantly altered during disease progression, with 361 being progressively downregulated and 341 progressively upregulated. Gene expression changes were validated by quantitative real-time polymerase chain reaction (qRT-PCR), confirming genome expression analysis data. Differentially expressed genes were clearly related to inflammation/immune responses but also strongly associated with metabolic, chemokine signaling, Jak-STAT signaling, and angiogenesis pathways. Ingenuity network analysis revealed 25 unique network associations that were associated with functions such as antigen presentation, cell morphology, cell-to-cell signaling and interaction, as well as nervous system development and function. Moreover, many of these genes and pathways were similarly identified in CD specimens. These findings reveal novel, complex, and dynamic changes in gene expression that may provide useful targets for future therapeutic approaches. (Inflamm Bowel Dis 2012)
Prebiotic‐supplemented partially hydrolysed cow's milk formula for the prevention of eczema in high‐risk infants: a randomized controlled trial (2016)

pHF-OS does not prevent eczema in the first year in high-risk infants. The immunological changes found require confirmation in a separate cohort.
Current Clinical Applications of In Vivo Gene Therapy with AAVs (2020)

Hereditary diseases are caused by mutations in genes, and more than 7,000 rare diseases affect over 30 million Americans. For more than 30 years, hundreds of researchers have maintained that genetic modifications would provide effective treatments for many inherited human diseases, offering durable and possibly curative clinical benefit with a single treatment. This review is limited to gene therapy using adeno-associated virus (AAV) because the gene delivered by this vector does not integrate into the patient genome and has a low immunogenicity. There are now five treatments approved for commercialization and currently available, i.e., Luxturna, Zolgensma, the two chimeric antigen receptor T cell (CAR-T) therapies (Yescarta and Kymriah), and Strimvelis (the gammaretrovirus approved for adenosine deaminase-severe combined immunodeficiency [ADA-SCID] in Europe). Dozens of other treatments are under clinical trials. The review article presents a broad overview of the field of therapy by in vivo gene transfer. We review gene therapy for neuromuscular disorders (spinal muscular atrophy [SMA]; Duchenne muscular dystrophy [DMD]; X-linked myotubular myopathy [XLMTM]; and diseases of the central nervous system, including Alzheimer's disease, Parkinson's disease, Canavan disease, aromatic l-amino acid decarboxylase [AADC] deficiency, and giant axonal neuropathy), ocular disorders (Leber congenital amaurosis, age-related macular degeneration [AMD], choroideremia, achromatopsia, retinitis pigmentosa, and X-linked retinoschisis), the bleeding disorder hemophilia, and lysosomal storage disorders.
Cell-based, bioluminescent assay for monitoring the interaction between PCSK9 and the LDL receptor (2017)

Monitoring the expression of cell-surface receptors, their interaction with extracellular ligands, and their fate upon ligand binding is important for understanding receptor function and developing new therapies. We describe a cell-based method that utilizes bioluminescent protein complementation technology to interrogate binding of a cellular receptor with its extracellular protein ligand, specifically LDL receptor (LDLR) and proprotein convertase subtilisin/kexin type 9 (PCSK9). Purified, full-length tagged PCSK9 is added to assay wells containing cells that stably express LDLR with an extracellular complementary tag. When the tagged PCSK9 binds the receptor, a bright luminescence signal is generated. The interaction is detected at the cell membrane with add-and-read simplicity, no wash steps, and flexibility, allowing data to be collected in endpoint format, kinetically, or with bioluminescent imaging. The assay is flexible, is rapid, and reports accurate biology. It is amenable to 96-well and 384-well formats, and the robustness allows for screening of new drug candidates (<i>Z</i>' = 0.83). The assay reports correct potencies for antibody titrations across a 50%-150% potency range and detects potency changes due to heat stress, suggesting that it may be useful during drug development. This assay technology can be broadly applied when studying other receptors with their extracellular ligands, whether protein or small-molecule binding partners.
Development of photostabilized asymmetrical cyanine dyes forin vivophotoacoustic imaging of tumors (2015)

Photoacoustic imaging (PAI) contributes to tumor diagnosis through the use of PAI probes that effectively accumulate in tumors. Previously, we developed a symmetrical cyanine dye, IC7-1-Bu, which showed high potential as a PAI probe because of its high tumor targeting ability and sufficient in vivo PA signal. However, IC7-1-Bu lacks photostability for multiple laser irradiations, so we developed stabilized PAI probes using IC7-1-Bu as a lead compound. We focused on the effect of singlet oxygen (1O2) generated by excited PAI probes on probe degeneration. We introduced a triplet-state quencher (TSQ) moiety into IC7-1-Bu to quench 1O2 generation and designed three IC-n-T derivatives with different linker lengths (n indicates linker length). The IC-n-T derivatives emitted in vitro PA signals that were comparable to IC7-1-Bu and significantly reduced 1O2 generation while showing improved photostability against multiple irradiations. Of the three derivatives evaluated, IC-5-T accumulated in tumors effectively to allow clear PAI of tumors in vivo. Furthermore, the photostability of IC-5-T was 1.5-fold higher than that of IC7-1-Bu in in vivo sequential PAI. These results suggest that IC-5-T is a potential PAI probe for in vivo sequential tumor imaging.
Ribosome Stall intheermALeader: a Barricade to5'-to-3' Nucleolytic Cleavage oftheermATranscript (1989)

Erythromycin-induced mRNA stabilization was tested inthree constructions inwhichtheermA transcript was elongated bymakinginsertions attheermAtranscription start. Whereas mRNA downstream oftheleader peptide isstabilized byerythromycin, mRNA upstream isnot.Inthepresenceoferythromycin, specific mRNA decayintermediates inboththeextended ermAgenesandthewild-type ermAgene were detected byboth Northern blotting andSinuclease mapping. The5'endsoftheintermediates map tothesequencesthat encode eachofthetwoermnA leader peptides, suggesting that theintermediates areproduced bystalled erythromycinboundribosomes acting asbarricades todegradation by5'-to-3' RNases. Inaddition, whereas erythromycin was foundpreviously tostabilize ermAtranscripts onlyphysically, an ernC-cat-86 hybrid transcript was stabilized bothphysically andfunctionally byerythromycin. Thestability ofprocaryotic mRNAsvaries widely, leading todifferential rates ofgeneexpression (for reviews, see references 4and7).Several enzymes that canparticipate in thedegradation ofmRNAshavebeenidentified, andvarious sequence determinants andstructural features oftranscripts havebeenshowntoinfluence therates ofdecay ofspecific transcripts. Ourstudies havefocused onantibiotic-induced stabilization oftranscripts oftheermfamily ofgenesfrom Staphylococcus aureus. Theermfamily ofgenesspecifies rRNAmethylases that confer resistance tomacrolide, lincosamide, andstreptogramin B antibiotics byreducing theaffinity between these antibiotics andribosomes. Expression ofthemethylase is induced bynanomolar concentrations ofthemacrolide antibiotic erythromycin (28). Genetic andbiochemical studies of S.aureusgeneermC,amodelsystem forerythromycininduced antibiotic resistance, havedemonstrated thatsynthesis ofrRNAmethylase isposttranscriptionally controlled
Cavitation Microjets as a Contributory Mechanism for Renal Calculi Disintegration in Eswl (1988)

The rarefaction shock wave produced by an extracorporeal shockwave lithotripter can result in liquid failure at numerous discrete sites near the second focus. When the liquid fails, vapor-filled cavities can grow to relatively large sizes and subsequently collapse with enormous violence. This phenomenon, called acoustic cavitation, has been shown to cause severe erosion in materials exposed to cavitation fields. It is proposed in this paper that ESWL devices generate acoustic cavitation in vivo and that the high speed liquid microjets produced during cavitation bubble collapse play an important role in renal calculi disintegration.
Understanding the evolution of nuclear waste repositories by performing appropriate experiments – selected investigations at Mont Terri rock laboratory (2019)

Abstract. Any site selection process for a final repository for high-level and heat producing radioactive waste is a national challenge and has to take into account, among others, regional geological settings. In Germany, the site selection has to restart from zero, and all potential host rocks have to be considered equal, including argillaceous rocks. Therefore, the Federal Institute for Geosciences and Natural Resources (BGR) performs appropriate experiments in the Swiss Mont Terri rock laboratory, which is located in the Jurassic Opalinus Clay. In this paper, activities and results from actual and still ongoing experiments, with participation of BGR, are presented exemplarily. All experiments aim for a contribution to understand particular aspects regarding the behaviour of underground facilities, BGR's focus lies mainly on aspects of the early lifetime of a repository, namely the construction, post-closure transient, and partly post-closure equilibrium phases. It is obvious that for a full understanding of the evolution of a final repository, knowledge and experience of many different groups, their studies and results covering all aspects, have to be included. In this paper, we can only emphasise a few representative examples on geophysical and geotechnical in-situ site investigations, geotechnical mine-by monitoring, laboratory investigations, and modelling aspects. The combined interpretation of these results enhance interpretations and is a prerequisite for a comprehensive understanding of a repository.
Contribution of surface energy and roughness to the wettability of polyamide 6 and polypropylene film in the plasma-induced process (2015)

Plasma-induced etching and chemical vapor coating processes are well-known technologies that modify the wetting properties of polymeric surfaces by engineering the surface roughness and surface energy. The contributing effect of plasma treatment for O 2 etching and hexamethyldisiloxane (HMDSO) vapor coating on the wetting properties was investigated for polyamide 6 (PA6) and polypropylene (PP) substrates. The surface energy components of PA6 and PP were analyzed by the Owens–Wendt model, and were associated with the wettability of water and diiodomethane. With the introduction of roughness by the O 2 etching process without HMDSO coating, the wettability of PA6 substrate was enhanced while that of PP was deteriorated when they were observed after 20 days aging. When the surface was etched for 7 min or longer with the subsequent coating with HMDSO, both PA6 and PP lost hydrophilic property, giving water contact angle of 180°. The wettability was examined for the varied treatment conditions and as a function of average nano-pillar length. This study helps better understand the interactions between the surface energy and roughness of polymeric materials, and their influence on surface wettability.
Table S5 from Anti-Inflammatory Drugs Remodel the Tumor Immune Environment to Enhance Immune Checkpoint Blockade Efficacy (2023)

&lt;p&gt;Table S5&lt;/p&gt;
Targeting CK2 overexpression and hyperactivation as a novel therapeutic tool in chronic lymphocytic leukemia (2010)

Expression of protein kinase CK2 is frequently deregulated in cancer and mounting evidence implicates CK2 in tumorigenesis. Here, we show that CK2 is overexpressed and hyperactivated in chronic lymphocytic leukemia (CLL). Inhibition of CK2 induces apoptosis of CLL cells without significantly affecting normal B and T lymphocytes. Importantly, this effect is not reversed by coculture with OP9 stromal cells, which are otherwise capable of rescuing CLL cells from in vitro spontaneous apoptosis. CLL cell death upon CK2 inhibition is mediated by inactivation of PKC, a PI3K downstream target, and correlates with increased PTEN activity, indicating that CK2 promotes CLL cell survival at least in part via PI3K-dependent signaling. Although CK2 antagonists induce significant apoptosis of CLL cells in all patient samples analyzed, sensitivity to CK2 blockade positively correlates with the percentage of CLL cells in the peripheral blood, β2 microglobulin serum levels and clinical stage. These data suggest that subsets of patients with aggressive and advanced stage disease may especially benefit from therapeutic strategies targeting CK2 function. Overall, our study indicates that CK2 plays a critical role in CLL cell survival, laying the groundwork for the inclusion of CK2 inhibitors into future therapeutic strategies.
Response to Esteve-Gassent et al.: flaB sequences obtained from Texas PCR products are identical to the positive control strain Borrelia burgdorferi B31 (2015)

Feria-Arroyo et al. had reported previously that, based on PCR analysis, 45% of Ixodes scapularis ticks collected in Texas and Mexico were infected with the Lyme disease spirochete Borrelia burgdorferi (Parasit. Vectors 2014, 7:199). However, our analyses of their initial data (Parasit. Vectors 2014, 7:467) and a recent response by Esteve-Gassent et al. (Parasit. Vectors 2015, 8:129) provide evidence that the positive PCR results obtained from both ribosomal RNA intergenic sequences and the flagellin gene flaB are highly likely due to contamination by the B. burgdorferi B31 positive control strain.
1A1-O08 An Experimental Study of Power Assist Systems with Adjustable Stiffness Devices in Periodic Motions (2007)

This paper describes an experimental study of power assist systems proposed by the authors. This power assist systems utilize mechanical elastic elements and optimize stiffness of the elastic elements in order to reduce torque of actuators while generating operator's periodical motions. These systems realize amplification of its operator's torque and optimization of the stiffness simultaneously. However, we haven't carried out experiments using power assist systems which consist of mechanical devices with stiffness adjustability. Therefore, we made an experimental system which has an adjustable stiffness device. The stiffness of the elastic element installed in the experimental system could be adjusted from 1.8[Nm/rad] to 6.6[Nm/rad] within 0.7 seconds. As a result of the experiment, we confirmed that the power assist system can amplify operator's torque and optimize its stiffness. In addition, we experimentally investigated that the elastic element reduced the actuator's torque.
String analysis for x86 binaries (2005)

Information about string values at key points in a program can help program understanding, reverse engineering, and forensics. We present a static-analysis technique for recovering possible string values in an executable program, when no debug information or source code is available. The result of our analysis is a regular language that describes a superset of the string values possible at a given program point. We also impart some of the lessons learned in the process of implementing our analysis as a tool for recovering C-style strings in x86 executables.
Estimation of the Optimal Surrogate Based on a Randomized Trial (2018)

A common scientific problem is to determine a surrogate outcome for a long-term outcome so that future randomized studies can restrict themselves to only collecting the surrogate outcome. We consider the setting that we observe n independent and identically distributed observations of a random variable consisting of baseline covariates, a treatment, a vector of candidate surrogate outcomes at an intermediate time point, and the final outcome of interest at a final time point. We assume the treatment is randomized, conditional on the baseline covariates. The goal is to use these data to learn a most-promising surrogate for use in future trials for inference about a mean contrast treatment effect on the final outcome. We define an optimal surrogate for the current study as the function of the data generating distribution collected by the intermediate time point that satisfies the Prentice definition of a valid surrogate endpoint and that optimally predicts the final outcome: this optimal surrogate is an unknown parameter. We show that this optimal surrogate is a conditional mean and present super-learner and targeted super-learner based estimators, whose predicted outcomes are used as the surrogate in applications. We demonstrate a number of desirable properties of this optimal surrogate and its estimators, and study the methodology in simulations and an application to dengue vaccine efficacy trials.
Synthesis of myo-inositol 1,4-bisphosphate-5-phosphorothioate (1989)

Synthesis of myo-insoitol 1,4,5-triphosphate and myo-inositol 1,4,-bisphosphate-5-phosphorothioate, a phosphatase-resistant analogue of a biological second messenger, have been accomplished using a novel combination of PIII and PV chemistry and a new deprotection method for the 2,2,2-trichloroethyl group.
Plant‐dependent active biological containment system for recombinant rhizobacteria (2003)

This work describes the construction of the rhizobacterium Pseudomonas putida strain CS-4, which contains an active biological containment (ABC) system that ensures bacterial suicide in the absence of proline. Maize plants exudate proline, which allows CS-4 to colonize the rhizosphere at a similar level to that of the wild-type strain. However, when the plants are removed, the CS-4 population decreased in bulk soil at a higher rate than the wild-type strain.
Low-Elevation Ionosphere Spatial Anomalies Discovered from the 20 November 2003 Storm (2011)

This paper presents data from low-elevation satellites on 20 November 2003 in the Ohio region, the area of the largest validated gradients seen to date. As viewed by&#13;\nmultiple CORS stations in central and northeastern Ohio, SVN 26 came into view around 2030 UT on this day, rose to an elevation angle of about 15 degrees just after 2100 UT, and set between 2135 and 2200 UT. This observation window is very close to the time that peak ionosphere gradients were observed at those stations on higher-elevation satellites. An ionosphere gradient of about 300 mm/km was discovered on SVN 26 between CORS stations KNTN and SIDN at 2050 UT, when SVN 26 was at about 12.6° elevation relative to these two sites. Thirty minutes later, at 2120 UT, a gradient of about 360&#13;\nmm/km was discovered between CORS stations GARF and WOOS, when SVN 26 was at about 12.0° elevation. Gradients between 200-300 mm/km were also discovered at other station pairs between 2100 and 2130 UT. Spatial&#13;\ngradients to another low elevation satellite with a similar azimuth angle, SVN 29, were observed to be about 100−150 mm/km. While comparison of the L1-L2 ionosphere estimates with L1 code-minus-carrier measurements is hindered by higher noise and loss-oflock&#13;\non L2, sufficient similarity between the two sets of ionosphere gradient estimates exists to allow us to state that at least some of these observations, including the two&#13;\nlargest-gradient cases, can be declared &amp;amp;quot;validated&amp;amp;quot; based on the preponderance of the evidence. This paper details our recent study of low-elevation&#13;\nsatellite observations from the 20 November 2003 ionosphere storm and shows how we arrived at the ionosphere gradient estimates cited above. These newfound observations imply that the means by which the Local Area Augmentation System (LAAS) mitigates&#13;\nanomalous ionosphere spatial gradients may need to be revised.