gebhart/patrepeval huggingface dataset:
Targeted Overexpression of the Transcription Factor XBP-1 in B Cells Promotes Plasma Cell and Lymphoplasmacytic Neoplasms in Transgenic Mice. (2005)

Abstract The transcription factor X-box binding protein-1 (XBP-1) plays critical roles in the unfolded protein response (UPR), the differentiation of plasma cells, and the regulation of growth factor signaling pathways. XBP-1 is subject to regulation by alternative RNA processing producing XBP-1-spliced (S) and -unspliced (U) mRNAs encoding proteins with identical DNA-binding and bZIP domains yet distinct C-terminal transactivation domains. The weaker transactivation potential of XBP-1(U) has prompted speculation that it may influence XBP-1(S) activity as a transdominant mutant. While elevated XBP-1 expression has been reported in transformed cells, the relative ratios of these XBP-1 isoforms and associated physiological relevance in cancer are uncertain. Here, we assessed the differential impact of enforced XBP-1(S) versus XBP-1(U) transgene expression in the B cell lineage. Both transgenes elicited early onset antibody-dependent autoimmune disease characterized by elevated levels of serum immunoglobulin (Ig) and IL-6 production, increased numbers of marginal zone and mature follicular B cells in the spleen, and expanded mature B cell populations in the bone marrow. Notably, aged XBP-1(S) mice developed clonal plasma cell expansions, culminating in the human-equivalent of Monoclonal Gammopathy of Undetermined Significance (MGUS) or Multiple Myeloma (MM). Conversely, XBP-1(U) mice develop multi-organ lymphoplasmacytic infiltrates and, with advancing age, succumb to neoplasms resembling human Lymphoplasmacytic Lymphoma/Waldenstrom’s Macroglobulinemia (LPL/WM). These unanticipated genetic observations in the mouse were translated to human disease with documentation of elevated levels of XBP-1(S) in MM and XBP-1(U) in LPL/WM. Together, these results indicate that imbalances in XBP-1(S) and XBP-1(U) alters B cell lineage homeostasis and can drive two distinct types of lymphoplasmacytic neoplasms in vivo. The findings of this study, together with the known capacity of XBP-1 to regulate various cancer-relevant growth factor signaling pathways, predicts that epigenetic dysregulation of alternate XBP-1 RNA processing can promote age-associated B cell malignancies in humans.
Control of downward migration of dense nonaqueous phase liquid during surfactant flooding by design simulations (2007)

Sand tank experiments have been used to study a surfactant‐enhanced aquifer remediation (SEAR) process during which downward migration of dense nonaqueous phase liquid (DNAPL) has been observed in some of these experiments. Through numerical simulation of one particular sand tank experiment conducted at Sandia National Laboratories we show in this paper that this downward migration of DNAPL can be anticipated and controlled even in a very difficult geosystem environment. The results indicate that design simulations play a significant role in the design of either laboratory column experiments or field SEAR application and that surfactant flooding can be accomplished without loss of hydraulic control of DNAPL under typical alluvial aquifer/aquitard conditions and with only minor vertical mobilization within the aquifer (i.e., &lt;1% of the DNAPL present). The design simulations are considered as a sensitivity analysis exercise in which the heterogeneity in the permeability field and DNAPL saturation and other critical variables are varied to produce a robust design. The simulation results indicate that the significant downward mobilization of DNAPL as observed in the Sandia sand tank experiment is a result of the use of high‐permeability materials, weak viscous (horizontal) forces, and low surfactant solubilization potential. The downward mobilization of DNAPL is a design issue to be evaluated and controlled rather than an inevitable consequence of the use of surfactants to remove DNAPL.
High-Speed, Whole-Column Fluorescence Imaging Detection for Isoelectric Focusing on a Microchip Using an Organic Light Emitting Diode as Light Source (2006)

An integrated and simplified microfluidic device using a 250 microm x 1-4 cm of organic light emitting diode (OLED) array as a two-dimensional light source for single-channel and multichannel whole-column imaging detection was developed. This fluorescence detection system was used for isoelectric focusing (IEF) of R-phycoerythrin in a microchip. The IEF conditions were optimized, and the total analysis time was extremely reduced to 30 s for 2-cm-long microchannels at 700 V/cm of electric field strength without the presence of electroosmotic flow. The compression of pH gradient caused by electrolytes drawing into the microchannels was efficiently restrained when 1% hydroxylpropylmethyl cellulose in 2% ampholyte was used as the carrier for IEF. Under optimized IEF conditions, the detection limit of this system was approximately 0.6 microg/mL or 45 pg at 75 nL/column injection of R-phycoerythrin. This OLED-induced fluorescence detection system for WCID provides a high-speed IEF technique with quantitative ability and the potential for high integration and throughput microchip systems.
ChemInform Abstract: A Phosphine‐Mediated Construction of 1,4‐Oxazepines and 1,3‐Oxazines. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Update on the DIII-D ECH system: experiments, gyrotrons, advanced diagnostics, and controls (2017)

The ECH system on DIII-D is continuing to be upgraded, while simultaneously being operated nearly daily for plasma experiments. The latest major hardware addition is a new 117.5 GHz gyrotron, which generated 1.7 MW for short pulses during factory testing. A new gyrotron control system based on Field Programmable Gate Array (FPGA) technology with very high speed system data acquisition has significantly increased the flexibility and reliability of individual gyrotron operation. We have improved the performance of the fast mirror scanning, both by increasing the scan speeds and by adding new algorithms for controlling the aiming using commands generated by the Plasma Control System (PCS). The system is used for transport studies, ELM control, current profile control, non-inductive current generation, suppression of MHD modes, startup assist, plasma density control, and other applications. A program of protective measures, which has been in place for more than two years, has eliminated damage to hardware and diagnostics caused by overdense operation. Other activities not directly related to fusion research have used the ECH system to test components, study methods for improving production of semiconductor junctions and materials, and test the feasibility of using ground based microwave systems to power satellites into orbit.
Small differences in tibial contact locations following kinematically aligned TKA from the native contralateral knee (2019)

Therapeutic, Level III.
Departmental-level approaches to gender equity in biology (2018)

Gender equity remains a large issue in academia, with women comprising only about one fifth of professors in the US. There are many changes that can be made to increase equity, including institutional policies, cultural change and bottom-up strategies, but these can be difficult or slow to implement at a departmental level. Hiring is one area that can be easily tackled at a departmental level and is strongly influenced by implicit and systematic bias. Here we focus on two methods of tackling bias in recruitment – redefining merit and identified positions.
Crystal structure of human CK2α at 1.06 Å resolution (2013)

The Ser/Thr kinase CK2 consists of two catalytic subunits (CK2α) and a dimer of the regulatory subunits (CK2β), and is a ubiquitous enzyme that regulates growth, proliferation and the survival of cells. CK2 is a remarkable drug target for potentially treating a wide variety of tumours and glomerulonephritis. The purified CK2α protein was crystallized using ethylene glycol as a precipitant. The crystal structure of CK2α with 21 loci of alternative conformations, including a niacin, 19 ethylene glycols and 346 waters, was determined at 1.06 Å resolution to an Rwork of 14.0% (Rfree = 16.5%). The alternative ensemble in the internal hydrophobic core underpins the plasticity of the αD-helix responsible for the regulation of ATP/GTP binding. The clear density map indicates that a niacin molecule, contained in the Escherichia coli culture medium, binds to the ATP binding site. An ethylene glycol molecule binds in the hydrophobic pocket lateral to the αD-helix forming the rim of the active site. The other ethylene glycol molecules occupy physiologically significant sites, including the CK2β binding interface and substrate binding site, as well as the gap in the crystal packing. Together with water molecules in the active site, these structural insights should facilitate drug discovery.
O2‐01‐01: A TRANSCRIPTOMIC LANDSCAPE OF MICROGLIAL ACTIVATION IN ALZHEIMER'S DISEASE (2018)

Homeostatic microglia adopt distinct disease-associated-microglial (DAM) transcriptomic profiles in Alzheimer's disease (AD) and the key transcriptional regulators of microglial states and factors responsible for microglial state transitions in AD need to be defined. Using weighted correlation network analysis (WGCNA) of microglial transcriptomic data, we recently identified 20 distinct microglial networks including a homeostatic profile and pro-inflammatory and anti-inflammatory sub-profiles within DAM. Each network represents a distinct microglial activation state and the genes at the interface of two adjacent networks may represent transitional checkpoints (or bottlenecks). Application of bioinformatics approaches to this framework of microglial diversity in AD may help elucidate key transcriptional and molecular regulators of these diverse microglial activation states in AD. Log2 transformed normalized expression data for key members of the 20 WGCNA networks (gene-level kME≥0.65) were used to generate viSNE plots using the Rtsne Barnes-Hut-Stochastic Neighbor Embedding R package. The promoter regions of top 25 genes (Kme≥0.9) of homeostatic and DAM modules were searched for transcription factor binding sites using TRANSFAC and then shared module-specific TFs were identified. Transcriptional factors were also predicted for each network's hubs using Metacore. DAVID Gene Ontology, TF prediction and canonical pathway analyses (Metacore) were performed for interface genes between two adjacent networks. Chemical and genetic perturbagens likely to yield specific transcriptional profiles were determined using Connectivity map analysis (CMAP, Broad Institute). ViSNE (Fig 1a) revealed a framework of microglial activation whereby homeostatic microglia (Blue network) transition towards DAM via distinct pro-inflammatory and anti-inflammatory pathways containing intermediary transition states and potential bridges between pathways. Distinct TFs for microglial states were identified (Fig 1B; Homeostatic: Crem Tau 1&2, CEBPα/β; Pro-inflammatory DAM: En1, Unc-86, Pou1F1, NFkB, RelA; Anti-inflammatory DAM: p300, LXRα/β, Atf1). Upstream TFs and predicted regulators of interface genes were also identified (Fig 1C; Homeostatic: TGFβ1, IGF1; Pro-inflammatory pathway: Il1b, ephrin A/B, estradiol, thyroxine; Anti-inflammatory pathway: PDGFα, IGF-1/2, FSHβ, Noradrenaline, CSF1). CMAP analysis suggested that several chemotherapeutic agents can promote pro-inflammatory DAM activation.
Effects of home confinement on mental health and lifestyle behaviours during the COVID-19 outbreak: Insight from the ECLB-COVID19 multicenter study (2020)

Although recognised as effective measures to curb the spread of the COVID-19 outbreak, social distancing and self-isolation have been suggested to generate a burden throughout the population. To provide scientific data to help identify risk factors for the psychosocial strain during the COVID-19 outbreak, an international cross-disciplinary online survey was circulated in April 2020. This report outlines the mental, emotional and behavioural consequences of COVID-19 home confinement. The ECLB-COVID19 electronic survey was designed by a steering group of multidisciplinary scientists, following a structured review of the literature. The survey was uploaded and shared on the Google online survey platform and was promoted by thirty-five research organizations from Europe, North Africa, Western Asia and the Americas. Questions were presented in a differential format with questions related to responses "before" and "during" the confinement period. 1047 replies (54% women) from Western Asia (36%), North Africa (40%), Europe (21%) and other continents (3%) were analysed. The COVID-19 home confinement evoked a negative effect on mental wellbeing and emotional status (P < 0.001; 0.43 ≤ d ≤ 0.65) with a greater proportion of individuals experiencing psychosocial and emotional disorders (+10% to +16.5%). These psychosocial tolls were associated with unhealthy lifestyle behaviours with a greater proportion of individuals experiencing (i) physical (+15.2%) and social (+71.2%) inactivity, (ii) poor sleep quality (+12.8%), (iii) unhealthy diet behaviours (+10%), and (iv) unemployment (6%). Conversely, participants demonstrated a greater use (+15%) of technology during the confinement period. These findings elucidate the risk of psychosocial strain during the COVID-19 home confinement period and provide a clear remit for the urgent implementation of technology-based intervention to foster an Active and Healthy Confinement Lifestyle AHCL).
Understanding and predicting the orientation of heteroleptic phosphors in organic light-emitting materials(Conference Presentation) (2016)

Organic light-emitting diodes (OLEDs) have made tremendous progress in recent years. The internal quantum efficiency was continuously improved and is nowadays close to the ideal value of unity in state-of-the-art OLEDs. However, still only a small fraction of the internally generated power can be used for lighting aspects as most of the light is captured inside the device due to low outcoupling factors of typically 25%. One promising approach to increase this limiting factor is using an anisotropic orientation of the dye molecules. In particular, horizontal orientation of transition dipole vectors (TDV) of the emitting species is a powerful tool to improve the efficiency of OLEDs. In order to understand the underlying mechanisms for emitter orientation of heteroleptic phosphors, we compared the anisotropy factor of emissive guest/host systems prepared by thermal evaporation using different Ir-complexes incorporating coumarin and phenylpyridin based ligands. These molecules exhibit similar high permanent dipole moments and electrostatic surface potentials but differ in their molecular structure. Interestingly, only molecules with both aromatic and aliphatic ligands show non-isotropic distributions of their TDVs when co-deposited with a matrix material. From these findings we conclude that molecular orientation of heteroleptic Ir-complexes occurs instantaneously at the surface of the growing film and is driven by chemical interactions with the surrounding media, i.e. the vacuum and the aromatic matrix side. Furthermore, it is possible to predict the anisotropy factor for arbitrary molecular orientation with a mathematical model taking into account the geometrical distribution of the TDV on the molecules.
A New Integrated All-Optical Switch Based on a Micro-Cavity (1996)

The proposed all optical switching device consists of a micro-cavity surrounded by a NLO material and sandwiched between two waveguides NLO switching can be expected if the cavity is close to resonance Then by increasing the intensity of the incident light. the high Q-resonance frequency will shift towards the incident frequency due to the refractive index change in the NLO material In this way most of the power IS coupled into the micro-cavity Because of the symmetric shape of the device. most of the power of the micro-cavity then will be coupled back into the upper waveguide It can be seen that coupling between the mode of the wave guide and the mode of the micro-cavity is possible This device shows a certain analogy with a NLO Fabry-Perot where high and low power output are the transmitted and reflected wave, respectively Because of the high4 values very low switching powers are sufficient when using presently available polymers like AKZO NOBEL-DANS Due to the small dimensions, the device can be integrated in a complex optical circuit
Outcomes After Transcatheter Aortic Valve Replacement: First Report from the National Registry (2013)

Transcatheter aortic valve replacement (TAVR) was approved for use in the U.S. in November 2011. Today, about 250 clinical sites report post-TAVR
Assessing cellulose dissolution efficiency in solvent systems based on a robust experimental quantification protocol and enthalpy data (2019)

Abstract Dissolution of microcrystalline cellulose (MCC) in pure ionic liquids (ILs) and IL/dimethyl sulfoxide (DMSO) mixtures (mole fraction χ DMSO = 0.2–0.9) was quantified using a specially constructed mechanical stirring system that allows reproducible agitation speed; temperature control, and minimum solution-air contact. The electrolytes employed were: 1-( n -butyl)-3-methylimidazolium acetate (C 4 MeIm AcO), 1-(methoxyethyl)-3-methylimidazolium acetate (C 3 OMeIm AcO), 1,8-diazabicyclo[5.4.0]undec-7-enium acetate (DBU AcO), tetramethylguanidinium acetate (TMG AcO), and tetra( n- butyl)ammonium fluoride hydrate (TBAF·xH 2 O). The effects on MCC dissolution of IL/DMSO composition, and temperature (50, 70°C) were studied. C 4 MeIm AcO and C 4 MeIm AcO/DMSO were more efficient solvents than their C 3 OMeIm AcO counterparts, due to “deactivation” of the ether oxygen of C 3 OMeIm AcO. MCC dissolution by C 4 MeIm AcO/DMSO was compared with DBU AcO/DMSO, TMG AcO/DMSO at χ DMSO = 0.6, and TBAF·xH 2 O/DMSO at χ DMSO = 0.95. The relative efficiency was (solutions in DMSO): C 4 MeIm AcO &gt; C 3 OMeIm AcO &gt; DBU AcO &gt; TMG AcO &gt; TBAF·xH 2 O. The efficiency of C 4 MeIm AcO relative to C 3 OMeIm AcO is due to higher solution basicity. Isothermal titration calorimetry was used to study cellobiose-solvent interactions. Except for TBAF·xH 2 O/DMSO, these interactions are exothermic; the relative solvent efficiency increases with increasing dissolution |enthalpy|. Using the mole fraction concentration scale to report cellulose dissolution avoids possible ambiguities.
Skin Thickness of the Anterior, Anteromedial, and Anterolateral Thigh: A Cadaveric Study for Split-Skin Graft Donor Sites (2014)

Based on skin thickness measurements, the anterolateral thigh had the thickest epidermal and dermal layers. We suggest that the anterolateral thigh region is the optimal donor site for split-skin graft harvests from the thigh.
Electrochemical elaboration of electrodes and electrolytes for 3D structured batteries (2013)

The challenges associated with the fabrication of three-dimensional (3D) electrode and electrolyte materials for Li-ion batteries are discussed. The basic issues for achieving a solid 3D cell foundation, which can simultaneously offer sufficient electronic conductivity to enable stable cycling, as well as enough compatibility with the incorporation of complementary components, have been addressed. Various electrochemical strategies for elaborating such systems are discussed and critically examined. Several current collector systems are presented including electrochemically prepared Cu and Al nanorods and commercial aperiodic carbon structures. Further electrochemical coating approaches then provide a direct method for the deposition of thin layers of active materials successfully demonstrated here as coatings on both 3D metal structures and commercially available 3D-structured carbon substrates. Enhanced capacities per foot print area are demonstrated for a number of 3D electrode materials, namely polyaniline on reticulated vitreous carbon, Cu2O on copper nanorods and TiO2 on Al nanorods. The crucial points for achieving a thin conformal coating of the corresponding 3D electrode structures with solid polymer electrolytes are also carefully analysed and discussed. In this context electro-polymerisation is proposed as a viable route to form thin electrolyte layers with promising characteristics. The high versatility of electro-polymerisation in combination with the various structures and methodologies adopted here represents a further step towards the development of cost-effective 3D microbattery devices.
Development and Practical Use of fcc-AlTiN Films with High Al Content for Cutting Tools (2021)

Aluminum Titanium Nitride films deposited by thermal CVD method (CVD-AlTiN) has attracted cutting tools suppliers because of their high potential for milling of alloy steel and cast iron. One of the most interesting characteristics of CVD-AlTiN films is the amount of Al. It is higher than that of AlTiN films deposited by PVD method. It is well-known that conventional AlTiN films deposited by PVD method has cubic structure in the range of Al content lower than about 0.7, while they obtain hexagonal structure in the range of Al content higher than 0.7. However, CVD-AlTiN films can keep cubic structure in Al content higher than 0.7, which prevents their cutting properties from getting worse.
Natural indoles, indole-3-carbinol (I3C) and 3,3’-diindolylmethane (DIM), attenuate staphylococcal enterotoxin B-mediated liver injury by downregulating miR-31 expression and promoting caspase-2-mediated apoptosis (IRC4P.605) (2015)

Abstract Staphylococcal enterotoxin B (SEB) is a potent superantigen capable of inducing inflammation characterized by robust immune cell activation and proinflammatory cytokine release. In the current study, we investigated the effect of natural indoles, I3C and DIM on SEB-mediated liver injury. Injection of SEB into D-galactosamine-sensitized female C57BL/6 mice resulted in liver injury as indicated by an increase in enzyme AST levels, induction of inflammatory cytokines, and massive infiltration of immune cells into the liver. Administration of I3C and DIM (40mg/kg), by intraperitonal injection, attenuated SEB-induced acute liver injury, as evidenced by decrease in AST levels, inflammatory cytokines and cellular infiltration in the liver. I3C and DIM triggered apoptosis in SEB-activated cells primarily through activation of the intrinsic mitochondrial pathway. In addition, inhibitor studies involving caspases revealed that I3C and DIM-mediated apoptosis in these activated cells was dependent on caspase-2 but independent of caspase-8, 9 and 3. I3C and DIM also caused a decrease in Bcl-2 expression. Both compounds also down-regulated miR-31, which directly targets caspase-2 and influences apoptosis in SEB-activated cells. Our data demonstrate for the first time that indoles can effectively suppress acute hepatic inflammation caused by SEB and that this may be mediated by decreased expression of miR-31 and consequent caspase-2-dependent apoptosis in T cells.
Reporting of quality measures in gynecologic oncology programs at Prospective Payment System (PPS)-Exempt Cancer Hospitals: An early glimpse into a challenging initiative (2013)

There is wide variability in ranking of quality measures, and may relate to provider or institutional factors. Despite the mandatory reporting in PPS-exempt cancer hospitals, work remains to define gynecologic cancer quality measures.