gebhart/patrepeval huggingface dataset:
LCox: a tool for selecting genes related to survival outcomes using longitudinal gene expression data (2019)

Longitudinal genomics data and survival outcome are common in biomedical studies, where the genomics data are often of high dimension. It is of great interest to select informative longitudinal biomarkers (e.g. genes) related to the survival outcome. In this paper, we develop a computationally efficient tool, LCox, for selecting informative biomarkers related to the survival outcome using the longitudinal genomics data. LCox is powerful to detect different forms of dependence between the longitudinal biomarkers and the survival outcome. We show that LCox has improved performance compared to existing methods through extensive simulation studies. In addition, by applying LCox to a dataset of patients with idiopathic pulmonary fibrosis, we are able to identify biologically meaningful genes while all other methods fail to make any discovery. An R package to perform LCox is freely available at https://CRAN.R-project.org/package=LCox.
Research data supporting "Oxygen degradation in mesoporous Al2O3 / CH3NH3PbI3-xClx perovskite solar cells - kinetics and mechanisms" (2016)

Initial performance and ageing data for solar cells (IV, TPC, TPV). XRD data for aged solar cells.
Interplay of Structure, Charge‐Carrier Localization and Dynamics in Copper‐Silver‐Bismuth‐Halide Semiconductors (2021)

Abstract Silver‐bismuth based semiconductors represent a promising new class of materials for optoelectronic applications because of their high stability, all‐inorganic composition, and advantageous optoelectronic properties. In this study, charge‐carrier dynamics and transport properties are investigated across five compositions along the AgBiI 4 –CuI solid solution line (stoichiometry Cu 4 x (AgBi) 1− x I 4 ). The presence of a close‐packed iodide sublattice is found to provide a good backbone for general semiconducting properties across all of these materials, whose optoelectronic properties are found to improve markedly with increasing copper content, which enhances photoluminescence intensity and charge‐carrier transport. Photoluminescence and photoexcitation‐energy‐dependent terahertz photoconductivity measurements reveal that this enhanced charge‐carrier transport derives from reduced cation disorder and improved electronic connectivity owing to the presence of Cu + . Further, increased Cu + content enhances the band curvature around the valence band maximum, resulting in lower charge‐carrier effective masses, reduced exciton binding energies, and higher mobilities. Finally, ultrafast charge‐carrier localization is observed upon pulsed photoexcitation across all compositions investigated, lowering the charge‐carrier mobility and leading to Langevin‐like bimolecular recombination. This process is concluded to be intrinsically linked to the presence of silver and bismuth, and strategies to tailor or mitigate the effect are proposed and discussed.
Data management perspectives on business process management (2013)

Traditional approaches to Business Process Management (BPM) focus primarily on the process aspects, and treat the persistent data accessed and manipulated by the business processes as second class citizens. A recent approach to BPM, based on "business artifacts", is centered on a modeling framework that places data and process on an equal footing. The approach has been shown useful in various application domains, and one variant of business artifacts forms the basis of the emerging OMG Case Management Model and Notation (CMMN) standard. Research results have been developed around conceptual models, enterprise interoperation, business intelligence, and verification. This data-centric approach has the potential to provide the basis for a new generation of BPM technology in support of diverse application, and fueled by the insights into abstraction and data management that have been the hallmark of database research since the 70's.
Prognostic Model to Predict Survival Outcome for Curatively Resected Liposarcoma: A Multi-Institutional Experience (2016)

Histologic subtype and primary site were independent prognostic factors for curatively resected liposarcoma. A prognostic model for patients with liposarcoma clarified distinct groups of patients with good prognostic discrimination.
Sweetgum: An ancient source of beneficial compounds with modern benefits (2015)

Sweetgum trees are large, deciduous trees found in Asia and North America. Sweetgum trees are important resources for medicinal and other beneficial compounds. Many of the medicinal properties of sweetgum are derived from the resinous sap that exudes when the outer bark of the tree has been damaged. The sap, known as storax, has been used for centuries to treat common ailments such as skin problems, coughs, and ulcers. More recently, storax has proven to be a strong antimicrobial agent even against multidrug resistant bacteria such as methicillin-resistant Staphylococcus aureus. In addition to the sap, the leaves, bark, and seeds of sweetgum also possess beneficial compounds such as shikimic acid, a precursor to the production of oseltamivir phosphate, the active ingredient in Tamiflu®-an antiviral drug effective against several influenza viruses. Other extracts derived from sweetgum trees have shown potential as antioxidants, anti-inflammatory agents, and chemopreventive agents. The compounds found in the extracts derived from sweetgum sap suppress hypertension in mice. Extracts from sweetgum seeds have anticonvulsant effects, which may make them suitable in the treatment of epilepsy. In addition to the potential medicinal uses of sweetgum extracts, the extracts of the sap possess antifungal activity against various phytopathogenic fungi and have been effective treatments for reducing nematodes and the yellow mosquito, Aedes aegypti, populations thus highlighting the potential of these extracts as environment-friendly pesticides and antifungal agents. The list of value-added products derived from sweetgum trees can be increased by continued research of this abundantly occurring tree.
MtDNA haplogroups define two phenotypes of osteoarthritis (2010)

peer reviewed
mTOR Inhibition Improves Antitumor Effects of Vaccination with Antigen-Encoding RNA (2013)

Vaccination with in vitro transcribed RNA encoding tumor antigens is an emerging approach in cancer immunotherapy. Attempting to further improve RNA vaccine efficacy, we have explored combining RNA with immunomodulators such as rapamycin. Rapamycin, the inhibitor of mTOR, was used originally for immunosuppression. Recent reports in mouse systems, however, suggest that mTOR inhibition may enhance the formation and differentiation of the memory CD8(+) T-cell pool. Because memory T-cell formation is critical to the outcome of vaccination approaches, we studied the impact of rapamycin on the in vivo primed RNA vaccine-induced immune response using the chicken ovalbumin-expressing B16 melanoma model in C57BL/6 mice. Our data show that treatment with rapamycin at the effector-to-memory transition phase skews the vaccine-induced immune response toward the formation of a quantitatively and qualitatively superior memory pool and results in a better recall response. Tumor-infiltrating immune cells from these mice display a favorable ratio of effector versus suppressor cell populations. Survival of mice treated with the combined regimen of RNA vaccination with rapamycin is significantly longer (91.5 days) than that in the control groups receiving only one of these compounds (32 and 46 days, respectively). Our findings indicate that rapamycin enhances therapeutic efficacy of antigen-specific CD8(+) T cells induced by RNA vaccination, and we propose further clinical exploration of rapamycin as a component of immunotherapeutic regimens.
Amino Acid Catalyzed Neogenesis of Carbohydrates: A Plausible Ancient Transformation (2005)

Hexose sugars play a fundamental role in vital biochemical processes and their biosynthesis is achieved through enzyme-catalyzed pathways. Herein we disclose the ability of amino acids to catalyze the asymmetric neogenesis of carbohydrates by sequential cross-aldol reactions. The amino acids mediate the asymmetric de novo synthesis of natural L- and D-hexoses and their analogues with excellent stereoselectivity in organic solvents. In some cases, the four new stereocenters are assembled with almost absolute stereocontrol. The unique feature of these results is that, when an amino acid is employed as the catalyst, a single reaction sequence can convert a protected glycol aldehyde into a hexose in one step. For example, proline and its derivatives catalyze the asymmetric neogenesis of allose with >99 % ee in one chemical manipulation. Furthermore, all amino acids tested catalyzed the asymmetric formation of natural sugars under prebiotic conditions, with alanine being the smallest catalyst. The inherent simplicity of this catalytic process suggests that a catalytic prebiotic "gluconeogenesis" may occur, in which amino acids transfer their stereochemical information to sugars. In addition, the amino acid catalyzed stereoselective sequential cross-aldol reactions were performed as a two-step procedure with different aldehydes as acceptors and nucleophiles. The employment of two different amino acids as catalysts for the iterative direct aldol reactions enabled the asymmetric synthesis of deoxysugars with >99 % ee. In addition, the direct amino acid catalyzed C(2)+C(2)+C(2) methodology is a new entry for the short, highly enantioselective de novo synthesis of carbohydrate derivatives, isotope-labeled sugars, and polyketide natural products. The one-pot asymmetric de novo syntheses of deoxy and polyketide carbohydrates involved a novel dynamic kinetic asymmetric transformation (DYKAT) mediated by an amino acid.
Wordline & Bitline Pulsing Schemes for Improving SRAM Cell Stability in Low-Vcc 65nm CMOS Designs (2006)

Pulsed wordline (PWL) & pulsed bitline (PBL) techniques to improve SRAM cell stabilities in single-Vcc microprocessor designs are evaluated in 65nm CMOS. At 0.7V Vcc, PWL improves cell failure rate by 15times while incurring <1% area overhead. Both PBL & PWL with read-modify-write (PWL-RMW) provide the best improvements (26times) in cell stability, with significant area overheads (4-8%)
Patient care quality and teamwork (2009)

Abstract Chapter 26 discusses patient care quality and teamwork, including structure, process, and outcome.
The role of allergen‐specific IgE, IgG and IgA in allergic disease (2021)

Immunoglobulin E (IgE)-mediated allergy is the most common hypersensitivity disease affecting more than 30% of the population. Exposure to even minute quantities of allergens can lead to the production of IgE antibodies in atopic individuals. This is termed allergic sensitization, which occurs mainly in early childhood. Allergen-specific IgE then binds to the high (FcεRI) and low-affinity receptors (FcεRII, also called CD23) for IgE on effector cells and antigen-presenting cells. Subsequent and repeated allergen exposure increases allergen-specific IgE levels and, by receptor cross-linking, triggers immediate release of inflammatory mediators from mast cells and basophils whereas IgE-facilitated allergen presentation perpetuates T cell-mediated allergic inflammation. Due to engagement of receptors which are highly selective for IgE, even tiny amounts of allergens can induce massive inflammation. Naturally occurring allergen-specific IgG and IgA antibodies usually recognize different epitopes on allergens compared with IgE and do not efficiently interfere with allergen-induced inflammation. However, IgG and IgA antibodies to these important IgE epitopes can be induced by allergen-specific immunotherapy or by passive immunization. These will lead to competition with IgE for binding with the allergen and prevent allergic responses. Similarly, anti-IgE treatment does the same by preventing IgE from binding to its receptor on mast cells and basophils. Here, we review the complex interplay of allergen-specific IgE, IgG and IgA and the corresponding cell receptors in allergic diseases and its relevance for diagnosis, treatment and prevention of allergy.
Inhibition of Cytomegalovirus in vitro and in vivo by the Experimental Immunosuppressive Agent Leflunomide (1999)

Despite progress in antiviral chemotherapy, cytomegalovirus (CMV) remains a major cause of morbidity and mortality among pharmacologically immunosuppressed transplant recipients, frequently engaging the clinician in a struggle to balance graft preservation with control of CMV disease. Leflunomide, an inhibitor of protein kinase activity and pyrimidine synthesis, is an experimental immunosuppressive agent effective against acute and chronic rejection in animal models. Herein we summarize our recent studies demonstrating that leflunomide inhibits the production of multiple clinical CMV isolates (including multi-drug-resistant virus) in both human fibroblasts and endothelial cells. In contrast to all other anti-CMV drugs currently in use, leflunomide does not inhibit viral DNA synthesis, but rather appears to interfere with virion assembly. Finally, preliminary studies in a rat model suggest that this agent reduces viral load in vivo. These findings imply that leflunomide, an effective immunosuppressive agent, shows potential to concurrently attenuate a major complication of immunosuppression, CMV disease, by a novel mechanism of antiviral activity.
Applying gene expression microarrays to pulmonary disease (2011)

Gene expression microarrays are high throughput technologies that can simultaneously measure the expression levels of most known genes in the human genome within a biological sample. The study of gene expression has revealed new understanding into the biological complexities of the cell and can impact the field of medicine by providing new insights into disease. Examining gene expression in samples from patients with pulmonary disease can elucidate molecular mechanisms responsible for disease pathogenesis or uncover novel molecular subtypes within a disease. Gene expression signatures of disease pathogenesis can further be used to suggest novel therapeutic compounds. Biomarkers can be developed from gene expression data that can aid clinicians in diagnosing disease or can guide clinicians in tailoring therapeutic strategies to individual patients. To demonstrate the applications of gene expression microarray technology, we will review several studies in pulmonary disease that utilize gene expression profiling techniques to gain biological insights into disease or to develop clinically relevant biomarkers for disease management.
Bordetella Avium Phase-Shift Markers: Characterization of Whole Cell, Cell Envelope, and Outer Membrane Proteins (1995)

Antigenic variation has been studied extensively in Bordetella pertussis , 8 , 1 2 and more recently in B. bronchiseptica , 2 , 1 3 and is characterized by the loss of virulence factors. This ability to switch between virulent and avirulent forms is controlled by the bvg locus and can be either phenotypic (antigenic modulation) or genotypic (phase variation). Antigenic modulation occurs in response to temperature, ions, or nutrients in the growth medium and is readily reversible. Phase variation is due to a frame shift mutation or deletion in the bvg locus and is considerably less reversible, with a frequency of 1 x 10 to 1 x 10 Regardless of the mechanism, the outcome is the same: a loss of antigenic properties and virulence-associated factors that correlate with a loss of pathogenicity in those bacteria. Phase variation has been recently reported in B. avium. When a nalidixic acid-resistant mutant of B. avium was plated on medium containing nicotinamide and nalidixic acid, 2 spontaneously induced variants were observed that lacked dermonecrotic toxin and 4 other outer membrane proteins (OMP). Those variants reverted to a pathogenic state following inoculation into 3-day-old turkeys. Recently a reversible colonial phenotypic variation occurring in B. avium was reported/ Two naturally occurring colony types (smooth and rough) were observed at a frequency of approximately 1 x 10 on artificial medium without antibiotics or other selection method. Characterization of those colony types revealed that isolates of B. avium with the smooth colonial morphology were pathogenic for turkey poults, whereas isolates with the rough colony type were nonpathogenic. Alterations in the protein profiles of B. bronchiseptica and B. pertussis are associated with a phase change. Unique proteins called phase-shift markers were identified in those bacteria and could be used to distinguish between pathogenic and nonpathogenic organisms. As a first step in determining whether the rough colony type represents a phase change in B. avium and to identify phase-shift markers that could be exploited in a diagnostic test, soluble proteins from whole cells (WC), cell envelopes (CE), and Sarkosyl-insoluble OMPenriched fractions of pathogenic smooth and nonpathogenic rough colony types were examined. Three smooth colony wild type B. avium isolates (002/S, 170/S, 198/S) and 3 isolates of the rough colony type originating from wild type isolates (002/R, 170/R, 198/R) were previously characterized and used in this study. The bacteria
Supplementary Table 1 from A Novel Class of Ribosome Modulating Agents Exploits Cancer Ribosome Heterogeneity to Selectively Target the CMS2 Subtype of Colorectal Cancer (2023)

&lt;p&gt;Table showing the top 20 MYC gene targets with the highest positive charge density&lt;/p&gt;
61.4: LEDs for Microdisplay Illumination (2006)

Abstract Recent advances in LEDs are bringing about commercialization for LED Illumination in rear‐projection TV systems using microdisplays. We discuss practical concerns for various imagers. We track performance and Lumens‐per‐Etendue results for new designs. The brightest systems use liquid‐crystal‐on‐silicon (LCoS) panels.
Impact of Ambient Pressure on Titania Nanoparticle Formation During Spray-Flame Synthesis (2015)

Nanocrystalline titania was synthesized via liquid-fed spray-flame synthesis in a hermetically closed system at various pressures. Titanium tetraisopropoxide dissolved in isopropanol was used as precursor. The size, crystal structure, degree of agglomeration, morphology and the band gap of the as-prepared particles were investigated ex situ by nitrogen adsorption, transmission electron microscopy, X-ray diffraction, and UV-VIS absorption spectroscopy. In comparison to synthesis at atmospheric pressure it was found that decreasing pressure has a significant influence on the particle size distribution leading to smaller particles with reduced geometric standard deviation while particle morphology and crystal structure are not affected. Computational fluid dynamics simulations support the experimental findings also indicating a significant decrease in particle size at reduced pressure. Although it is well known that decreasing pressure leads to smaller particle sizes, it is (to our knowledge) the first time that this relation was investigated for spray-flame synthesis.
015 Combined Data of Intravaginal Prasterone against Vulvovaginal Atrophy of Menopause (2017)

Recent evidence shows that the cause of vulvovaginal atrophy (VVA) is decreased DHEA availability, thus showing that the appropriate treatment should be local DHEA replacement. The objective was to analyse the effects of intravaginal prasterone obtained in the three randomized clinical trials performed in postmenopausal women suffering from VVA. In three independent 12-week prospective, randomized, double-blind and placebo-controlled clinical trials, the effect of daily intravaginal 0.50% (6.5 mg) prasterone administered was examined on four co-primary objectives in women having moderate to severe (MS) pain at sexual activity (dyspareunia) identified as their most bothersome symptom (MBS). In 436 women treated with 0.50% prasterone and 250 women who received placebo, an average 35.1% decrease over placebo in the percentage of parabasal cells (P<0.0001), an average 7.7% increase in the percentage of superficial cells (P<0.0001) and a mean 0.72 pH unit decrease in vaginal pH (P<0.0001) was observed. The severity score of MBS dyspareunia was decreased by a 0.46 unit (49%) (P<0.0001 over placebo), while the severity score of MS vaginal dryness decreased by 0.31 unit (P<0.0001 over placebo). A very positive evaluation was obtained on the acceptability of the technique of administration of the insert while the male partners reported a very positive assessment of the changes observed in their sexual partner.
Analysis of Force Mitigation by Boots in Axial Impacts using a Lower Leg Finite Element Model (2020)

Lower extremity injuries caused by floor plate impacts through the axis of the lower leg are a major source of injury and disability for civilian and military vehicle occupants. A collection of PMHS pendulum impacts was revisited to obtain data for paired booted/unbooted test on the same leg. Five sets of paired pendulum impacts (10 experiments in total) were found using four lower legs from two PMHS. The PMHS size and age was representative of an average young adult male. In these tests, a PMHS leg was impacted by a 3.4 or 5.8 kg pendulum with an initial velocity of 5, 7, or 10 m/s (42-288 J). A matching LS-DYNA finite element model was developed to replicate the experiments and provide additional energy, strain, and stress data. Simulation results matched the PMHS data using peak values and CORA curve correlations. Experimental forces ranged between 1.9 and 12.1 kN experimentally and 2.0 and 11.7 kN in simulation. Combat boot usage reduced the peak force by 36% experimentally (32% in simulation) by compressing the sole and insole with similar mitigations for calcaneus strain. The simulated Von Mises stress contours showed the boot both mitigating and shifting stress concentrations from the calcaneus in unbooted impacts to the talus-tibia joint in the booted impacts, which may explain why some previous studies have observed shifts to tibia injuries with boot or padding usage.
Structure‐based Pharmacophore Screening Coupled with QSAR Analysis Identified Potent Natural‐product‐derived IRAK‐4 Inhibitors (2021)

Interleukin-1 Receptor-Associated Kinase 4 (IRAK-4) has crucial functions in inflammation, innate immunity, and malignancy. Structure-based pharmacophore modeling integrated with validated QSAR analysis was implemented to discover structurally novel IRAK-4 inhibitors from natural products database. The QSAR model combined molecular descriptors with structure-based pharmacophore capable of explaining bioactivity variation of structurally diverse IRAK-4 inhibitors. Manually built pharmacophore model, validated with receiver operating characteristic curve, and selected using the statistically optimum QSAR equation, was applied as a 3D-search query to mine AnalytiCon Discovery database of natural products. Experimental in vitro testing of highest-ranked hits identified uvaretin, saucerneol, and salvianolic acid B as active IRAK-4 inhibitors with IC<sub>50</sub> values in low micromolar range.
ChemInform Abstract: Crystallinity of Inorganic Films Grown by Atomic Layer Deposition: Overview and General Trends (2013)

Abstract Review: 2454 refs.