gebhart/patrepeval huggingface dataset:
SP-333, a Guanylate Cyclase-C Agonist, Inhibits NF-κB Signaling and Modulates Related Genes and miRNAs Implicated in GI Inflammation and Carcinogenesis (2013)

Purpose: Micro RNAs (miRs), small non-coding RNAs, are known to regulate expression of genes involved in the processes leading to inflammation and carcinogenesis. SP-333, a proteolytically resistant analog of uroguanylin, activates guanylate cyclase-C (GC-C) expressed on the epithelial cells lining the gastrointestinal (GI) mucosa to stimulate production of cyclic GMP (cGMP), a second messenger known to mediate anti-inflammatory effects on NF-κB and downstream signaling. Previously, we reported that SP-333 ameliorated colitis through inhibition of NF-κB signaling in mice. The objective of this study was to examine the effect of SP-333 treatment on expression of genes and miRs that are implicated in processes underlying GI inflammation and cancer. Methods: T84 cell line was used to evaluate the ability of SP-333 to stimulate cGMP production. Total RNA and miRs were isolated from SP-333-treated T84 cells, and levels of gene transcripts were determined using the TaqMan Open Array platform. Extracted total miRs were analyzed by miR array. Statistical analyses were performed using Student's t-test. Results: SP-333 stimulated cGMP synthesis in T84 cells with an EC50 of 2.83 × 10-7M. As compared to vehicle, SP-333 treatment down-regulated NF-κB subunits, IKK-β, c-Src, and c-Myc, as judged by reduction in their transcript and protein levels. In addition, treatment with SP-333 also upregulated miRs such as miR-15a (p<0.05), miR-16 (p<0.01), let-7i (p<0.01), miR-125b (p<0.001), and the family of miR-29 (p<0.05), all of which are negative regulators of NF-κB signaling, which is known to augment production of pro-inflammatory cytokines during GI inflammation. SP-333 also significantly increased levels of miR-141-3p (p<0.01), which is a negative regulator of c-Src. Activation of c-Src is known to activate proto-oncogene c-Myc, and suppress GC-C signaling. Activation of c-Myc transcriptionally suppresses miR-29b, resulting in enhanced proliferation and resistance to apoptosis in malignant cells. In addition, SP-333 treatment reduced transcripts of several putative c-Myc target genes, such as cell division cycle 25a, cyclin D1, and p53. Consistent with these findings, SP-333 treatment increased levels of anti-carcinogenic miR-126 (p<0.01), miR-133a (p<0.01), miR-30c (p<0.05), and reduced levels of pro-carcinogenic miR-21 (p<0.005), miR-155 (p<0.005), miR-92a (p<0.05), miR-200c (p<0.01), and miR-494 (p<0.005). Conclusion: This is the first report demonstrating that SP-333-mediated activation of GC-C signaling may contribute to its anti-inflammatory effects through suppression of c-Src, c-Myc, IKK-β, and NF-κB signaling, possibly through modulation of related miRs implicated in GI inflammation and cancer. Disclosure - Dr. Palejwala and Dr. Shailubhai - Employees: Synergy Pharmaceuticals Inc. Dr. Arjunan, Dr. Saykhedkar, and Dr. Zhang - no relationship.
Olivine Coated Spinel: 5-Volt System for High Energy Lithium Batteries (2012)

LiMn1.5Ni0.5O4 (LMN) has attracted considerable attention as 5-volt cathode materials for Li-ion batteries. Here, the coating of nano LiFePO4 (LFP) onto the surface of the spinel particles is reported for the first time. Two processes were used to prepare LFP-coated LMN: a traditional sol-gel method in Ar and a mechano-fusion dry process, which provides a simple way to obtain surface coating for battery materials. Surface elemental analyses indicate that nano-LFP is intimately covered on the LMN surface. LiMn1.5Ni0.5O4 showed better rate property especially at high rate (&gt;10C) after LiFePO4 coating. Good performance such as 82 mAh g-1 of capacity was still obtained for the LiFePO4-coated LiMn1.5Ni0.5O4 with 75% of capacity retention after 140 cycles under 1C.
Auto-configuration through cloud: Initial case studies for universal and personalised access for all (2013)

This paper aims to present the case studies that have been developed in the context of Cloud4all project (Cloud platforms Lead to Open and Universal access for people with Disabilities and for All; CN: FP7-289016). Cloud4all is an international collaborative effort to build and test key elements of the Global Public Inclusive Infrastructure (GPII) (http://gpii.net/). Cloud4all/GPII aims to develop a complete new paradigm in accessibility, by replacing adaptation of individual products and services for a person with automatic-personalisation of any mainstream product or service, using cloud technologies to activate and augment any natural (built-in) accessibility the product or service has, based on a profile of the user's needs (http://www.cloud4all.info). A first step in the implementation path that has already started to be followed in the project has been the identification of those case studies that would be of primary concern for Cloud4all and the overall GPII.
A Plan for Increasing Latino Student’s Attendance Rates at Sky View Middle School (2009)

In terms of subgroups, our Latino students have the lowest attendance rate of all subgroups. On average, their attendance rate is 1.9% lower that the all student average. During the 2006/07 school year, the Latino student attendance rate was an all-time low of 88.2%. Although this subgroup does not make up a large percentage of our overall student enrollment (approximately 5%), it still is a concern. We would like for all subgroups to be at or above the 93% mark. The School Improvement Goal (SIP) that will be addressed in this project is as follows: ATTENDANCE FOR LATINO STUDENTS WILL RISE FROM 91.8%TO 93% BY THE END OF THE 2009/10 SCHOOL YEAR AS MEASURED ON THE 2009/10 SCHOOL REPORT CARD BY DATE GATHERED FROM eSIS.
Low dimensionalization of magnetic ordering inSr2VO4by hydride ion substitution (2015)

Substitution of an oxygen anion with a hydrogen anion induced the low dimensionalization of magnetic ordering in a transition metal oxide $\mathrm{S}{\mathrm{r}}_{2}\mathrm{V}{\mathrm{O}}_{4}$. Upon increasing $x$ up to $\ensuremath{\sim}1$ in $\mathrm{S}{\mathrm{r}}_{2}\mathrm{V}{\mathrm{O}}_{4\ensuremath{-}x}{\mathrm{H}}_{x}$, the hydride ions were ordered linearly, and the magnetic susceptibility was simultaneously suppressed. It was found that this suppression was attributed to the formation of a quasi-one-dimensional antiferromagnetic spin chain, maintaining that each of the vanadium cations is two-dimensionally bridged by hydride and oxide ions. Density functional theory calculations demonstrate that the quasi-one-dimensional property is caused by much enhanced anisotropic exchange couplings $({J}_{1}/{J}_{2}\ensuremath{\sim}6)$ originating from the absence of $\ensuremath{\pi}$ bonding between $\mathrm{H}\phantom{\rule{0.28em}{0ex}}1s$ and $\mathrm{V}\phantom{\rule{0.28em}{0ex}}3d$ orbitals. Utilizing a hydride ion that has an ionic radius similar to an oxygen anion and only one energetically available orbital of $1s$ is a different approach to realization of magnetic low dimensionalization in $3d$ early transition metal oxides.
Cancer Therapy Meets p53 (1994)

Although gene therapy and immunotherapy hold great promise for the future, cancer treatment now centers around surgical resection, radiation therapy, and chemotherapy. The therapeutic basis of surgical resection is obvious, but the same cannot be said for the other approaches. What accounts for the selective killing of malignant cells while normal cells are spared? It is clearly not simple differences in rates of replication. Why do cancers even of the same histologic type vary in their sensitivity to chemotherapy and radiotherapy? What accounts for the frustrating development of drug resistance? Recent findings provide a possible link between these questions and . . .
The mutated human gene encoding hepatocyte nuclear factor 1β inhibits kidney formation in developing Xenopus embryos (2000)

The transcription factor hepatocyte nuclear factor 1beta (HNF1beta) is a tissue-specific regulator that also plays an essential role in early development of vertebrates. In humans, four heterozygous mutations in the HNF1beta gene have been identified that lead to early onset of diabetes and severe primary renal defects. The degree and type of renal defects seem to depend on the specific mutation. We show that the frameshift mutant P328L329fsdelCCTCT associated with nephron agenesis retains its DNA-binding properties and acts as a gain-of-function mutation with increased transactivation potential in transfection experiments. Expression of this mutated factor in the Xenopus embryo leads to defective development and agenesis of the pronephros, the first kidney form of amphibians. Very similar defects are generated by overexpressing in Xenopus the wild-type HNF1beta, which is consistent with the gain-of-function property of the mutant. In contrast, introduction of the human HNF1beta mutant R137-K161del, which is associated with a reduced number of nephrons with hypertrophy of the remaining ones and which has an impaired DNA binding, shows only a minor effect on pronephros development in Xenopus. Thus, the overexpression of both human mutants has a different effect on renal development in Xenopus, reflecting the variation in renal phenotype seen with these mutations. We conclude that mutations in human HNF1beta can be functionally characterized in Xenopus. Our findings imply that HNF1beta not only is an early marker of kidney development but also is functionally involved in morphogenetic events, and these processes can be investigated in lower vertebrates.
Critical dynamics, Lifshitz tricriticality, and supersymmetry: The Ising model on the hcp lattice (1985)

Critical dynamics in d dimensions can be mapped onto a supersymmetric equilibrium problem in d+1 with a Lifshitz tricritical point. The existence of such a point is demonstrated for the Ising model on the hcp lattice by Monte Carlo simulation.
A Teaching Language for Building Object Detection Models (2020)

Object detection is a key application of machine learning. Currently, these detector models rely on deep networks that offer model builders limited agency over model construction, refinement and maintenance. Human-centered approaches to address these issues explore the exchange of knowledge between a human-in-the-loop and a learning system. This exchange, mediated through a teaching language, is often restricted to the specification of labels and constrains user expressiveness communicating other forms of knowledge to the system. We propose and assess an expressive teaching language for specifying object detectors which includes constructs such as concepts and relationships. From a formative study, we identified language building blocks and articulated design goals for creating interactive experiences in teaching object detection. We applied these goals through a design probe that highlighted further research questions and a set of design takeaways.
Comparative study of water‐processable polymeric binders in LiMn2O4 cathode for aqueous electrolyte batteries (2021)

Abstract Energy storage systems utilizing neutral pH aqueous electrolytes are increasing in importance, as they are inherently cheaper and safer when compared to their traditional lithium‐ion battery counterparts. However, no thorough study on binder characteristics in the aqueous environment has been reported. This work reports the performance and characterization of multiple binders: a polyacrylonitrile‐based binder (LA133), LA133+carboxymethyl cellulose (CMC), styrene‐butadiene rubber (SBR), SBR+CMC, polytetrafluoroethylene (PTFE), and PTFE+CMC as implemented with a LiMn 2 O 4 cathode in a neutral pH aqueous electrolyte. Data presented include cyclic voltammetry (CV), resistivity, and scanning electron microscopy (SEM) results. PTFE+CMC is the overall superior binder, particular touting superior rate performance owing to the strength of PTFE coupled with electrolyte swelling ability of CMC. This work hopes to serve as a resource for rational design of sustainable battery chemistries.
Mobile Apps Prioritizing Privacy, Efficiency and Equity: A Decentralized Approach to COVID-19 Vaccination Coordination (2021)

In this early draft, we describe a decentralized, app-based approach to COVID-19 vaccine distribution that facilitates zero knowledge verification, dynamic vaccine scheduling, continuous symptoms reporting, access to aggregate analytics based on population trends and more. To ensure equity, our solution is developed to work with limited internet access as well. In addition, we describe the six critical functions that we believe last mile vaccination management platforms must perform, examine existing vaccine management systems, and present a model for privacy-focused, individual-centric solutions.
SAXS from Four‐Arm Polyelectrolyte Stars in Semi‐Dilute Solutions (2003)

Abstract We have performed small‐angle X‐ray scattering experiments on semi‐dilute solutions of highly charged star polyelectrolytes. Poly(sodium acrylate) (PANa) and poly(cesium acrylate) (PACs) stars with four arms were successfully synthesized by a combination of atom transfer radical polymerization and chemical modifications. Over a wide range of polyelectrolyte concentration C p , these two systems as well as their equivalent linear polyelectrolytes were investigated at different ionic strengths. Scattering experiments show the existence of a scattering peak denoted as q max , which disappears with the addition of a simple electrolyte, evidencing the electrostatic character of the interactions. We have also studied the effect of the charge parameter and the nature of the counterion (Na and Cs) on the scattering properties of these star polyelectrolytes. In the case of PACs, q max scales with the polyelectrolyte concentration as C p 1/2 over the whole range of studied concentrations, whereas it scales as C p 1/2 (for C p &lt; 45 mg · ml −1 ) and C p 1/4 (for C p &gt; 45 mg · ml −1 ) in the case of PANa. Variation of q max as a function of polyelectrolyte concentration C p for PA1Cs (○) and PA2Cs (•) stars (error bars are indicated). magnified image Variation of q max as a function of polyelectrolyte concentration C p for PA1Cs (○) and PA2Cs (•) stars (error bars are indicated).
Einstein@Home search for periodic gravitational waves in early S5 LIGO data (2009)

This paper reports on an all-sky search for periodic gravitational waves from sources such as deformed isolated rapidly spinning neutron stars. The analysis uses 840 hours of data from 66 days of the fifth LIGO science run (S5). The data were searched for quasimonochromatic waves with frequencies f in the range from 50 to 1500 Hz, with a linear frequency drift f˙ (measured at the solar system barycenter) in the range -f/τ<f˙<0.1f/τ, for a minimum spin-down age τ of 1000 years for signals below 400 Hz and 8000 years above 400 Hz. The main computational work of the search was distributed over approximately 100 000 computers volunteered by the general public. This large computing power allowed the use of a relatively long coherent integration time of 30 hours while searching a large parameter space. This search extends Einstein@Home’s previous search in LIGO S4 data to about 3 times better sensitivity. No statistically significant signals were found. In the 125–225 Hz band, more than 90% of sources with dimensionless gravitational-wave strain tensor amplitude greater than 3×10[superscript -24] would have been detected.
The Immune System and Its Contribution to Variability in Regenerative Medicine (2020)

The immune system plays a critical role in directing tissue repair and regeneration outcomes. Tissue engineering technologies that are designed to promote new tissue growth will therefore be impacted by immune factors that are present in patients both locally at the site of intervention and systemically. The immune state of patients can be influenced by many factors, including infection, nutrition, and other disease comorbidities. As a result, the immune state is highly variable and may be a source of variability in tissue-engineered products in the clinic, which is not found in preclinical models. In this review, we will summarize key immune cells and evidence of their activity in tissue repair and potential in tissue engineering systems. We also discuss how clinical translation of tissue engineering strategies, in particular stem cells, helped elucidate the importance of the immune system. With increased understanding of the immune system's role in repair and tissue engineering systems, it will likely become a therapeutic target and component of future therapies.
Microbial Upcycling of Polyethylene into Recombinant Proteins (2023)

Abstract Herein, we report the development of a new strain of Pseudomonas bacteria capable of upcycling deconstructed polyethylene into high value bespoke recombinant protein products. Using hexadecane, a proxy for depolymerized polyethylene, as a sole carbon nutrient source, we optimized media compositions that facilitate robust biomass growth, with results suggesting the benefits of lower hydrocarbon concentrations and the use of NH 4 Cl as a nitrogen source. We genomically integrated recombinant genes for green fluorescent protein and spider dragline-inspired silk protein, and we showed their expression in Pseudomonas aeruginosa , reaching titers of approximately 10 mg/L when hexadecane was used as the sole carbon source. Lastly, we demonstrated that chemically depolymerized polyethylene, comprised of a mixture of branched and unbranched alkanes, could be upcycled into silk protein by Pseudomonas aeruginosa at titers of 11.3 ± 1.1 mg/L. Thus, this work establishes a versatile microbial platform for valorizing recalcitrant plastic waste.
Cell alignment by smectic liquid crystal elastomer coatings with nanogrooves (2020)

Control of cells behavior through topography of substrates is an important theme in biomedical applications. Among many materials used as substrates, polymers show advantages since they can be tailored by chemical functionalization. Fabrication of polymer substrates with nano- and microscale topography requires processing by lithography, microprinting, etching, and so forth. In this work, we introduce a different approach based on anisotropic elastic properties of polymerized smectic A (SmA) liquid crystal elastomer (LCE). When the SmA liquid crystal coating is deposited onto a substrate with planar alignment of the molecules, it develops nanogrooves at its free surface. After photopolymerization, these nanogrooves show an excellent ability to align human dermal fibroblasts over large areas. The alignment quality is good for both bare SmA LCE substrates and for substrates coated with fibronectin. The SmA LCE nano-topographies show a high potential for tissue engineering.
Lineage switching of the cellular distribution of BRAF V600E in multisystem Langerhans cell histiocytosis (2022)

Most children with high-risk Langerhans cell histiocytosis (LCH) have BRAFV600E mutation. BRAFV600E alleles are detectable in myeloid mononuclear cells at diagnosis but it is not known if the cellular distribution of mutation evolves over time. Here, the profiles of 16 patients with high-risk disease were analyzed. Two received conventional salvage chemotherapy, 4 patients on inhibitors were tracked at intervals of 3 to 6 years, and 10 patients, also given inhibitors, were analyzed more than 2 years after diagnosis. In contrast to the patients responding to salvage chemotherapy who completely cleared BRAFV600E within 6 months, children who received inhibitors maintained high BRAFV600E alleles in their blood. At diagnosis, mutation was detected predominantly in monocytes and myeloid dendritic cells. With time, mutation switched to the T-cell compartment, which accounted for most of the mutational burden in peripheral blood mononuclear cells, more than 2 years from diagnosis (median, 85.4%; range, 44.5%-100%). The highest level of mutation occurred in naïve CD4+ T cells (median, 51.2%; range, 3.8%-93.5%). This study reveals an unexpected lineage switch of BRAFV600E mutation in high-risk LCH, which may influence monitoring strategies for the potential withdrawal of inhibitor treatment and has new implications for the pathogenesis of neurodegeneration, which occurred in 4 patients.
Coordination environment and fluoride binding of type 2 copper in the blue copper protein ascorbate oxidase (1980)

The coordination environment of the type 2 (nonblue) copper in native ascorbate oxidase (L-ascorbate:oxygen oxidoreductase, EC 1.10.3.3) and of a derivative of the enzyme having the type 1 (blue) copper reversibly bleached has been examined by electron paramagnetic resonance (EPR) spectroscopy. In the g[unk] region of the spectrum of bleached ascorbate oxidase, a seven-line superhyperfine pattern is seen that is attributed to the presence of three nitrogen-donor ligands to a type 2 copper having tetragonal geometry. The superhyperfine splitting patterns in the g parallel region of the EPR spectra of native and bleached ascorbate oxidase show that as many as two fluorides may bind to type 2 copper. Because fluoride inhibits the enzyme competitively with respect to ascorbic acid, it is proposed that the type 2 copper is part of the ascorbate binding site.
Appearance of Discontinuities in Spectra Transformed by the Piecewise Direct Instrument Standardization Procedure (1996)

Several years ago, we noted that spectra transformed by the piecewise direct standardization (PDS) method may contain discontinuities. Having noticed that the problem was a recurring one, we studied it and recently diagnosed its source. Our investigations suggest that this problem also occurs in applications of window factor analysis, evolving factor analysis, and any other procedure that uses piecewise principal component models. In this work, we report the source of the problem and illustrate it with one example. A procedure is presented for eliminating the problem that is effective in PDS pattern recognition applications. Further work is needed to develop modified algorithms suitable for calibration applications.
Characterization and correction of the effects of hepatic iron on T1ρ relaxation in the liver at 3.0T (2022)

LIC can affect T<sub>1ρ</sub> in the liver. We developed an iron-correction method for the quantification of T<sub>1ρ</sub> in the liver at 3.0T.
X-ray magnetic circular dichroism studies of multilayered thin films of 3d transition metals (invited) (abstract) (1994)

X-ray magnetic circular dichroism (XMCD) is used to probe both the spin and orbital d moments of Co in Co/Pd, Co/Pt, and Co/Ni multilayers, and in a Au/Co-wedge/Pd structure. While the spin moment per Co atom is found to be constant within the experimental error, the orbital moment shows a strong dependence both on the chemical environment and on the thickness of the Co layer. In particular, we find an orbital moment enhancement of up to a factor of three for a Co layer thickness of four atomic layers in the present Au/Co/Pd sandwich structure. This enhancement decays to the bulk Co value, roughly following a 1/dCo dependence, thus confirming its interfacial origin. The relevance of these observations with respect to the perpendicular magnetic anisotropy in these samples will be discussed.