gebhart/patrepeval huggingface dataset:
Data from Apoptotic Activity and Mechanism of 2-Cyano-3,12-Dioxoolean-1,9-Dien-28-Oic-Acid and Related Synthetic Triterpenoids in Prostate Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Synthetic triterpenoids 2-cyano-3, 12-dioxooleana-1, 9-(11)-dien-28-oic acid (CDDO) and CDDO-Me (CDDO-methyl ester) have entered clinical trials for cancer. We determined that CDDO analogues at submicromolar concentrations induce apoptosis of cultured prostate cancer cell lines, LNCaP, ALVA31, Du145, PC3, and PPC1, with lethal dose 50% ∼1 μmol/L for CDDO-Me and an imidazole analogue (CDDO-Im). These compounds induced apoptosis of prostate cancer cells as characterized by cleavage of caspase-3, caspase-7, caspase-8, caspase-9, caspase-10, BID, and poly(ADP)ribose polymerase and by dependence on caspase activity. Moreover, triterpenoid-induced cell death was abolished by caspase-8–targeting small interfering (si) RNA. To explore the mechanism(s) involved in caspase-8 activation, we examined cell surface expression of death receptor (DR)4 and DR5 after triterpenoid treatment. Cell surface DR4 and DR5 expression was significantly up-regulated by CDDO or CDDO-Im but not by CDDO-Me. DR4 and DR5 knockdown with siRNA significantly inhibited apoptosis induced by CDDO and CDDO-Im but had no effect on CDDO-Me–induced killing, suggesting that CDDO and CDDO-Im induce apoptosis by a different mechanism than CDDO-Me. In addition to activating the caspase-8–dependent extrinsic apoptosis pathway, we observed that Bcl-X&lt;sub&gt;L&lt;/sub&gt; overexpression inhibited triterpenoid-mediated killing of prostate cancer cell line Du145, suggesting that the intrinsic pathway (via mitochondria) also participates in triterpenoid-mediated killing. &lt;i&gt;In vivo&lt;/i&gt; antitumor activity of CDDO-Me was shown using a Du145 tumor xenograft model in nude rats. Altogether, these findings suggest CDDO and related synthetic triterpenoids should be further evaluated as potential novel therapeutics for hormone refractory prostate cancers. [Cancer Res 2008;68(8):2927–33]&lt;/p&gt;&lt;/div&gt;
Some Observations on e-caudata in Old English Texts (2016)

It is not a revelation to observe that modern editorial practices obscure many features of the manuscripts that preserve Old English texts. Word division, word spacing, punctuation, capitalization, emendation (even when well justified), and the like construct an alternate text, different in many striking ways from the texts found in manuscripts. But the orthographical variation found in manuscripts is almost always preserved in the standard scholarly editions of Old English texts – conservative editorial principles hold that unusual spellings are not construed as errors (and therefore subject to intervention) in the absence of, as Fulk, Bjork, and Niles (2008: cxc) suggest, “a high degree of linguistic improbability”; spelling normalization may be a feature of classroom grammars and other beginner's texts, but only the most obvious of scribal errors usually compels a modern editor to offer an emended spelling. But one form of spelling variation that is often normalized even in modern critical editions of Old English texts is scribes’ use of ę (sometimes called “cedillated-e” or “e-caudata”), and the relative invisibility of the graph in our edited texts has no doubt disabled some potentially instructive commentary on a small aspect of scribal behavior.
Entity Ranking on Graphs: Studies on Expert Finding (2007)

Todays web search engines try to offer services for finding various information in addition to simple web pages, like showing locations or answering simple fact queries. Understanding the association of named entities and documents is one of the key steps towards such semantic search tasks. This paper addresses the ranking of entities and models it in a graph-based relevance propagation framework. In particular we study the problem of expert finding as an example of an entity ranking task. Entity containment graphs are introduced that represent the relationship between text fragments on the one hand and their contained entities on the other hand. The paper shows how these graphs can be used to propagate relevance information from the pre-ranked text fragments to their entities. We use this propagation framework to model existing approaches to expert finding based on the entity's indegree and extend them by recursive relevance propagation based on a probabilistic random walk over the entity containment graphs. Experiments on the TREC expert search task compare the retrieval performance of the different graph and propagation models.
The Effect of a Fast-Releasing Hydrogen Sulfide Donor on Vascularization of Subcutaneous Scaffolds in Immunocompetent and Immunocompromised Mice (2020)

Islet transplantation into subcutaneous polymer scaffolds has shown to successfully induce normoglycemia in type 1 diabetes models. Vascularization of these scaffolds is imperative for optimal control of glucose levels. We studied the effect of the vascular stimulator hydrogen sulfide (H<sub>2</sub>S) on the degree of vascularization of a scaffold and the role of the immune system in this process. Scaffolds were subcutaneously implanted in immunocompetent C57BL/6 and immunocompromised nude mice. Mice received twice-daily intraperitoneal injections of the fast-releasing H<sub>2</sub>S donor sodium hydrosulfide (NaHS, 25 or 50 μmol/kg) or saline for 28 days. After 63 days the vascular network was analyzed by histology and gene expression. Here we showed that the vascularization of a subcutaneous scaffold in nude mice was significantly impaired by H<sub>2</sub>S treatment. Both the CD31 gene and protein expression were reduced in these scaffolds compared to the saline-treated controls. In C57BL/6 mice, the opposite was found, the vascularization of the scaffold was significantly increased by H<sub>2</sub>S. The mRNA expression of the angiogenesis marker CD105 was significantly increased compared to the controls as well as the number of CD31 positive blood vessels. In conclusion, the immune system plays an important role in the H<sub>2</sub>S mediated effect on vascularization of subcutaneous scaffolds.
Probabilistic Active Filtering for Object Search in Clutter (2019)

This paper proposes a probabilistic approach for object search in clutter. Due to heavy occlusions, it is vital for an agent to be able to gradually reduce uncertainty in observations of the objects in its workspace by systematically rearranging them. Probabilistic methodologies present a promising sample-efficient alternative to handle the massively complex state-action space that inherently comes with this problem, avoiding the need for both exhaustive training samples and the accompanying heuristics for traversing a large-scale model during runtime. We approach the object search problem by extending a Gaussian Process active filtering strategy with an additional model for capturing state dynamics as the objects are moved over the course of the activity. This allows viable models to be built upon relatively scarce training data, while the complexity of the action space is also reduced by shifting objects over relatively short distances. Validation in both simulation and with a real Baxter robot with a limited number of training samples demonstrates the efficacy of the proposed approach.
Potential strategies to increase rooftop solar PV penetration in LV networks in Australia (2011)

Residential Solar PV is being deployed in Australia at increasing rates. The distribution grid wasn't designed to accommodate local generation so impacts are expected to happen and challenge the way the LV network is being run today. From the various identified effects, this paper explores Voltage control aspects in particular. A set of 5 different options to deploy and use customer-owned inverters for reactive power compensation are presented, ranging from pure stand-alone inverter control and management to DNSP centralized control scheme. All options come with challenges which are also highlighted in this paper. There are also additional opportunities that could be brought by some of the propositions discussed and contribute to a more efficient and resilient grid. The paper concludes with a brief layout of what regulatory, tariff and standard implications would be implicit by the options forwarded.
Eltrombopag in the treatment of pediatric chronic immune thrombocytopenia — a single-center experience (2021)

Primary immune thrombocytopenia (ITP) is the most common bleeding disorder in pediatric population, defined as an isolated low platelet count below 100 G/l. ITP is an autoimmune disease, mostly associated with the presence of auto-antibodies against platelet membrane antigens. This mechanism leads to shorten platelets half-life and may also inhibit the platelets production in the bone marrow. Approximately 25% of patients develop chronic ITP (cITP), diagnosed if the thrombocytopenia lasts a minimum 12 months. Management of childhood cITP remains controversial and decision about treatment should be individualized, based on general condition, risk of bleeding and the impact on the quality of life. Therapeutic approach includes intravenous immunoglobulins, corticosteroids, oral immunosuppressants, rituximab and splenectomy. New thrombopoietin agonists seem to be an efficacious and safe therapeutic option in the strategy of management of pediatric cITP, both in monotherapy and in combination with other drugs.
Magnetic and optical properties of airborne dust and settling rates of dust at the Phoenix landing site (2010)

The Magnetic Properties Experiment (referred to as iSweep or Caltarget) onboard the Phoenix lander was executed in the arctic region of Mars during the mission's 152 sols lifetime. The iSweep experiment involved periodic multispectral imaging of a series of permanent ring magnets. It was designed to attract airborne magnetic dust particles to certain areas on the iSweeps thereby sorting all settling airborne particles at least to some degree according to their magnetic properties. The dust on the area directly above the strong magnets of the iSweep was found to be brighter than that collected on the precursor Sweep Magnet Experiment onboard the Mars Exploration Rovers near Mars' equator, and also this dust is found to be brighter than both surface soil near the lander and soil in the region surrounding the lander. As most other dust and soils on Mars, the Phoenix dust lacks strong spectral signatures of highly crystalline phases. For the first time, based on the complete calibrated data set of images of the iSweeps, spectra were extracted of the putative dust falling on the magnetically protected areas of the iSweeps. These areas are accessible only for particles with a magnetic susceptibility below 10 −3 . Spectra of this nonmagnetic dust are interpreted as signals from nonmagnetic minerals such as tectosilicates or glasses pigmented by poorly crystalline ferric oxides. Rates of dust settling were determined to be 1.08 μ m/sol on the magnets and 0.06 μ m/sol for the magnetically protected areas.
Using deeply trapped intermediates to map the cytochrome c folding landscape (2002)

Replacement of iron with cobalt(III) selectively introduces a deep trap in the folding-energy landscape of the heme protein cytochrome c. Remarkably, neither the protein structure nor the folding thermodynamics is perturbed by this metal-ion substitution, as shown by data from spectroscopic and x-ray diffraction experiments. Through kinetics measurements, we have found parallel folding pathways involving several different misligated Co(III) species, and, as these folding intermediates persist for several hours under certain conditions, we have been able to elucidate fully their spectroscopic properties. The results, along with an analysis of the fluorescence energy-transfer kinetics during refolding, show that rapidly equilibrating populations of compact and extended polypeptide conformations are present until all molecules have reached the native structure. These measurements provide direct evidence that collapsed denatured structures are not substantially more stable than extended conformations of cytochrome c.
Tachyarrhythmias and electrical instabilities in cardiac tissue (2002)

Unstable cardiac rhythm is known to precede dangerous cardiac arrhythmias. Despite a considerable body of experimental data the underlying mechanism of electrical instabilities still remains unclear. This study presents a numerical analysis of the dynamic instabilities in the circulation of a pulse in a ring of excitable tissue that helps to determine physical mechanisms of these instabilities and to understand their potential correlation with complex cardiac rhythms. The authors demonstrate that a pulse width begins to oscillate after an initial perturbation for any length of the ring and the corresponding propagation velocity. The oscillations were found to be either damped or incremental. The incremental oscillations occurred when the ratio of the steady-state circulation period to the period of the pulse width oscillations was of the order of /spl sim/0.5. Under the same conditions the external pacing of the ring gives rise to complex rhythms incorporating alternans-like patterns.
Catalytic Asymmetric C−H Functionalization under Photoredox Conditions by Radical Translocation and Stereocontrolled Alkene Addition (2016)

Abstract This work demonstrates how photoredox‐mediated C(sp 3 )−H activation through radical translocation can be combined with asymmetric catalysis. Upon irradiation with visible light, α,β‐unsaturated N‐acylpyrazoles react with N‐alkoxyphthalimides in the presence of a rhodium‐based chiral Lewis acid catalyst and the photosensitizer fac ‐[Ir(ppy) 3 ] to provide a C−C bond‐formation product with high enantioselectivity (up to 97 % ee ) and, where applicable, with some diastereoselectivity (3.0:1 d.r.). Mechanistically, the synthetic strategy exploits a radical translocation (1,5‐hydrogen transfer) from an oxygen‐centered to a carbon‐centered radical with a subsequent stereocontrolled radical alkene addition.
Plant NLR immune receptor Tm-22 activation requires NB-ARC domain-mediated self-association of CC domain (2020)

The nucleotide-binding, leucine-rich repeat-containing (NLR) class of immune receptors of plants and animals recognize pathogen-encoded proteins and trigger host defenses. Although animal NLRs form oligomers upon pathogen recognition to activate downstream signaling, the mechanisms of plant NLR activation remain largely elusive. Tm-22 is a plasma membrane (PM)-localized coiled coil (CC)-type NLR and confers resistance to Tobacco mosaic virus (TMV) by recognizing its viral movement protein (MP). In this study, we found that Tm-22 self-associates upon recognition of MP. The CC domain of Tm-22 is the signaling domain and its function requires PM localization and self-association. The nucleotide-binding (NB-ARC) domain is important for Tm-22 self-interaction and regulates activation of the CC domain through its nucleotide-binding and self-association. (d)ATP binding may alter the NB-ARC conformation to release its suppression of Tm-22 CC domain-mediated cell death. Our findings provide the first example of signaling domain for PM-localized NLR and insight into PM-localized NLR activation.
Effect of HOXB13 and FOXA1 on the AR cistrome during prostate tumorigenesis in primary human tissue. (2014)

5018 Background: The androgen receptor (AR) is central to prostate carcinogenesis and cancer progression. Current understanding of the prostate AR cistrome - the genome-wide set of AR binding sites (ARBS) - is driven largely by tumor model systems. The role of the AR cistrome in prostate tumorigenesis in human tissue is unknown. We map the AR cistrome in 20 normal and tumor human prostate samples using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Methods: Chromatin was extracted from 13 tumor and 7 matched histologically normal foci (>70% enrichment) from fresh-frozen radical prostatectomy specimens. Tissue was pulverized, fixed and sonicated then immunoprecipitated with antibody to AR; DNA was isolated; libraries were constructed for the Illumina platform; sequencing reads were aligned to the human genome using MACS (false discovery rate 0.01) Results: Median 19,602 ARBS were called per sample. In unsupervised pairwise analysis of each AR cistrome, specimens clustered distinctly into tumor and normal groups. 9,181 ARBS were consistently enriched in tumor relative to normal (T-ARBS) and 2,690 were enriched in normal relative to tumor (N-ARBS). DNA binding motif analysis showed that AR itself is the most significantly enriched motif in N-ARBS, while FOXA1, and HOXB13 and AR were most significantly enriched in T-ARBS (z-score < -15). HOXB13 ChIP and FOXA1 ChIP in VCaP cell line showed substantial overlap with T-ARBS (68% and 76% of T-ARBS, respectively) and their knockdown via shRNA adversely affects prostate cell line survival. We identified genes within 1 megabase of T-ARBS or N-ARBS that are differentially expressed in tumor and normal. Expression levels of these genes in large clinically annotated patient cohorts are highly associated with multiple clinical parameters, including tumor grade and development of metastasis. Conclusions: We performed the most comprehensive study of the AR cistrome in human tumor and normal prostate tissue. We demonstrate that the AR cistrome is dynamic and implicate HOXB13 and FOXA1 as factors that reprogram the AR during transformation. These findings attest to the power of performing epigenetic analysis in both normal and tumor human tissue.
Metal‐Free, Solid‐State, Paperlike Rechargeable Batteries Consisting of Redox‐Active Polyethers (2019)

Metal-free and totally organic based batteries were fabricated from functional polyethers. Aliphatic polyethers, in which 2,2,6,6-tetramethylpiperidin-1-oxyl and viologen were introduced with high density, were used as the cathode and anode active materials, respectively. By stacking nanosheets of the polymers and an imidazolium-substituted polyether as the electrolyte, a solid-state cell only 2 μm thick was made. The anion-type rocking-chair cell showed reversible charge/discharge even at a high rate of 5 C without adding any solvents or plasticizers. Although the unsealed cell was measured under ambient conditions, no significant side reactions (including self-discharging and capacity decay) occurred, whereas conventional electrodes are sensitive to air and water in the charged state. The intrinsic plasticity of the polyethers is also compatible with making free-form, 3D-printable batteries.
Simple, Scalable Mechanosynthesis of Metal-Organic Frameworks Using Liquid-Assisted Resonant Acoustic Mixing (LA-RAM) (2020)

We present a methodology for the rapid and readily scalable mechanosynthesis of diverse metal-organic frameworks (MOFs) in the absence of milling media, typically required for other types of mechanochemical syntheses. We demonstrate the use of liquid-assisted resonant acoustic mixing (LA-RAM) methodology for the synthesis of two- and three-dimensional MOFs based on Zn, Co(II) and Cu(II), including single- and mixed-ligand systems, imidazolate or carboxylate ligands. The LA-RAM approach also allowed the synthesis of the ZIF-L, a framework never previously obtained in a solventless environment, as well as its Co(II) analogue. Straightforward scale-up from milligrams to at least 25 grams is demonstrated using ZIF-L as the model.
The prolyl isomerase Pin1 induces LC-3 expression and mediates tamoxifen resistance in breast cancer. (2011)

VOLUME 285 (2010) PAGES 23829–23841 Dr. Shim's name was misspelled. The correct spelling is shown above.
Eye Movements during Anagram Tasks (1969)

5-letter anagram problems were presented to field-independent and field-dependent Ss and their corneally reflected EMs were examined concomitantly. The data suggest that field-independent Ss are apt to spend less initial time examining specific letters than field-dependent Ss and that males are more deliberate in their visual search than females. The results are discussed in terms of two factors reflecting analytical perception, number of shifts between letters and mean latency to first 5 looks.
The Application of Microfluidic Devices for Viral Diagnosis in Developing Countries (2012)

Whilst diseases such as diabetes and cardiovascular disorders are increasing in the developed world, the main threat to global health remains viral-based infectious disease. Such diseases are notably prevalent in developing countries, where they represent a major cause of mortality; however, their detection and prevention is typically hampered by poor infrastructure and a lack of resources to support the sophisticated diagnostic tools commonly found in modern laboratories. Microfluidic-based diagnostics has the potential to close the gap between developed and developing world medical needs due to the robustness and reduced operating costs such technology offers. The most recent developments in microfluidic diagnostics for viral infections have explored the separation and enumeration of immune cells, the capture and identification of viral particles, and antiviral drug evaluation within microchannels and chambers. Advances in solid-phase separation, isothermal amplification, real-time detection of nucleotide products, and improved efficiency of detection systems in microfluidic platforms have also opened up opportunities for diagnostic innovation. This chapter reviews the potential capability microfluidic technology can offer in addressing the practical challenges of providing diagnostic technology for developing countries, illustrated by research on key viral diseases.
Enhancing the Imaging and Biosafety of Upconversion Nanoparticles through Phosphonate Coating (2015)

Upconversion nanoparticles (UCNPs), which are generated by doping with rare earth (RE) metals, are increasingly used for bioimaging because of the advantages they hold over conventional fluorophores. However, because pristine RE nanoparticles (NPs) are unstable in acidic physiological fluids (e.g., lysosomes), leading to intracellular phosphate complexation with the possibility of lysosomal injury, it is important to ensure that UCNPs are safely designed. In this study, we used commercially available NaYF4:Er/Yb UCNPs to study their stability in lysosomes and simulated lysosomal fluid. We demonstrate that phosphate complexation leads to REPO4 deposition on the particle surfaces and morphological transformation. This leads to a decline in upconversion fluorescence efficiency as well as inducing pro-inflammatory effects at the cellular level and in the intact lung. In order to preserve the imaging properties of the UCNPs as well as improve their safety, we experimented with a series of phosphonate chemical moieties to passivate particle surfaces through the strong coordination of the organophosphates with RE atoms. Particle screening and physicochemical characterization revealed that ethylenediamine tetra(methylenephosphonic acid) (EDTMP) surface coating provides the most stable UCNPs, which maintain their imaging intensity and do not induce pro-inflammatory effects in vitro and in vivo. In summary, phosphonate coating presents a safer design method that preserves and improves the bioimaging properties of UCNPs, thereby enhancing their biological use.
Axonal growth : modes, molecules and mechanisms (1989)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 1989.