gebhart/patrepeval huggingface dataset:
Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome (2018)

Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor widely used to treat MDS and AML, yet the impact of AZA on the cell-surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome, the transcriptome, and the cell-surface proteome. Untreated AML cell lines showed substantial overlap at all three omics levels; however, while AZA treatment globally reduced DNA methylation in all cell lines, changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteome analysis found no commonly regulated proteins. Gene set enrichment analysis of differentially regulated RNA and surface proteins showed a decrease in metabolic pathways and an increase in immune defense response pathways. As such, AZA treatment led to diverse effects at the individual gene and protein levels but converged to common responses at the pathway level. Given the heterogeneous responses in the four cell lines, we discuss potential therapeutic strategies for AML in combination with AZA.
Immediate targeting of host ribosomes by jumbo phage encoded proteins (2023)

Abstract Bacteriophages must seize control of the host gene expression machinery to promote their own protein synthesis. Since the bacterial hosts are armed with numerous anti-phage defence systems, it is essential that mechanisms of host take-over act immediately upon infection. Although individual proteins that modulate components of the bacterial gene expression apparatus have been described in several different phages, systematic approaches which capture the phage’s arsenal for immediate targeting of host transcription and translation processes have been lacking. In particular, there are no known phage factors that associate directly with host ribosomes to modulate protein synthesis. Here, we take an integrative high-throughput approach to uncover numerous new proteins encoded by the jumbo phage ΦKZ that target the gene expression machinery of the Gram-negative human pathogen Pseudomonas aeruginosa immediately upon infection. By integrating biochemical and structural analyses, we identify a conserved phage factor that associates with the large ribosomal subunit by binding the 5S ribosomal RNA. This highly abundant factor is amongst the earliest ΦKZ proteins expressed after infection and stays bound to ribosomes during the entire translation cycle. Our study provides a general strategy to decipher molecular components of phage-mediated host take-over and argues that phage genomes represent a large discovery space for proteins that modulate the host gene expression machinery.
A Multi-LED Dome Bulb Prototype for Dense Visible Light Communication Networks (2022)

In this paper, we employ imaging-basedbeam-steering to enable multi-datastream visible light communication networks serving dense Internet-of-Things (IoT) deployments. We demonstrate a “dome bulb” transmitter that consists of a multi-LED array with a dome-shaped lens to separate each LED’s beam for better spatial reuse. Each LED has a Lambertian irradiance distribution that is collected efficiently and directed along a particular line-of-sight using a wide field-of-view lens system. At focus, the image of the LED array is projected to a distant conjugate plane, and LED beam divergence is minimized to the geometric limit. This improves spatial reuse by minimizing interference between adjacent beams but results in spotty illumination due to gaps between LEDs in the array. Moderate defocusing blurs the beams to increase illumination uniformity at the expense of increased cross-channel interference. We present a model for the bulb that correlates to the experimental results and quantify the performance of the prototype for dense IoT networks.
Hypoxic Regulation of Metastasis via Hypoxia-Inducible Factors (2008)

Metastases formation is a major factor in disease progression and accounts for the majority of cancer deaths. The molecular mechanisms controlling invasion, dissemination to blood or lymphatic systems and spread of tumor cells to distant organs are still poorly understood. Recent observations indicate that the meta-static phenotype may already be present during the angiogenic switch of tumors. Intratumoral hypoxia correlates with poor prognosis and enhanced metastases formation. The Hypoxia Inducible Factors (HIFs) are key molecules in the hypoxic response and play critical roles during tumor cell expansion by regulating energy metabolism and the induction of angiogenesis. Increasing evidence implicates HIF function in metastatic cell characteristics, like epithelial to mesenchymal transition, cell detachment, invasion and tumor cell seeding. Here, we review the link between tumor cell hypoxia and the acquisition of metastatic behavior. We hypothesize that polyclonal tumor selection by hypoxia enhances metastatic capacity by transcriptional control of key regulators of metastasis. This polyclonal hypoxic gene profile potentially develops into a metastatic profile, driving metastasis formation. The hypoxic gene profile in primary tumors may therefore provide a prognostic indicator in clinical decision-making.
Assessment of Cutaneous Photosensitivity of TOOKAD (WST09) in Preclinical Animal Models and in Patients¶ (2005)

TOOKAD (WST09) is a new, long-wavelength palladium bacteriopheophorbide photosensitizer that targets tissue vasculature. The cutaneous phototoxicity of TOOKAD was assessed in normal rat and pig animal models and in patients in a Phase-I trial of TOOKAD-mediated photodynamic therapy (PDT) for recurrent prostate cancer. Controlled skin exposures were administered using solar-simulated light at various times after drug administration. Two different spectral ranges were used. In the first, the UV portion of the spectrum was removed (UV(-)) because UV irradiation in nondrugged control animals produced an erythema response at incident energy densities (J/cm(2)) lower than those required to induce a PDT response. In the second, the full solar spectrum (UV(+)) was used, and the potentiation by the photosensitizer of the UV-mediated minimum erythema dose was assessed. Results showed that the PDT skin response was negligible at clinical drug doses of 2 mg/kg for any period after administration at light doses of 128 J/cm(2) in the animal models. In patients, there was no observed UV(-) skin response at doses of up to 2 mg/kg, drug-light intervals of 1-3 h or greater and light exposures up to 128 J/cm(2). At higher drug doses in the rat and pig models, the duration of skin phototoxicity was found to be approximately 3 h and less than 1 h, respectively. Using the full spectrum of solar-simulated light, the presence of TOOKAD did not measurably enhance the UV(+)-induced erythema in the rats, pigs or patients.
Encapsulation in the food industry: a review (1999)

Encapsulation involves the incorporation of food ingredients, enzymes, cells or other materials in small capsules. Applications for this technique have increased in the food industry since the encapsulated materials can be protected from moisture, heat or other extreme conditions, thus enhancing their stability and maintaining viability. Encapsulation in foods is also utilized to mask odours or tastes. Various techniques are employed to form the capsules, including spray drying, spray chilling or spray cooling, extrusion coating, fluidized bed coating, liposome entrapment, coacervation, inclusion complexation, centrifugal extrusion and rotational suspension separation. Each of these techniques is discussed in this review. A wide variety of foods is encapsulated--flavouring agents, acids bases, artificial sweeteners, colourants, preservatives, leavening agents, antioxidants, agents with undesirable flavours, odours and nutrients, among others. The use of encapsulation for sweeteners such as aspartame and flavours in chewing gum is well known. Fats, starches, dextrins, alginates, protein and lipid materials can be employed as encapsulating materials. Various methods exist to release the ingredients from the capsules. Release can be site-specific, stage-specific or signalled by changes in pH, temperature, irradiation or osmotic shock. In the food industry, the most common method is by solvent-activated release. The addition of water to dry beverages or cake mixes is an example. Liposomes have been applied in cheese-making, and its use in the preparation of food emulsions such as spreads, margarine and mayonnaise is a developing area. Most recent developments include the encapsulation of foods in the areas of controlled release, carrier materials, preparation methods and sweetener immobilization. New markets are being developed and current research is underway to reduce the high production costs and lack of food-grade materials.
Miller–Fisher syndrome complicated by Bickerstaff brainstem encephalitis (2018)

These results suggest that BBE and MFS might be a pedigree disease and timely hormone therapy is expected to improve patients'outcomes.
El sistema de coordinación sectorial en el norte de Uganda (2008)

El Consejo Noruego para los Refugiados (NRC, por sus&#13;\nsiglas en inglés) tiene el firme convencimiento de que el&#13;\nsistema de coordinación sectorial supondrá una mejora&#13;\nde la respuesta internacional al desplazamiento interno.&#13;\nConstituye un decidido intento por parte de Naciones Unidas,&#13;\nONG, organizaciones internacionales y gobiernos de cubrir&#13;\nlas lagunas que presenta el sistema de asistencia&#13;\nhumanitaria. Queremos que este esfuerzo por llevar a cabo&#13;\nla reforma tenga éxito y desempeñe un papel activo en el&#13;\nnorte de Uganda para apoyar el trabajo de los clusters y&#13;\naumentar su eficacia.
Materials for step and flash imprint lithography (S-FIL®) (2007)

Step and flash imprint lithography, or S-FIL®, was introduced in 1999 by The University of Texas at Austin (Proc. SPIE-Int. Soc. Opt. Eng., 1999, 3676, 379), and has progressed from an academic curiosity to commercialization in less than five years (J. Microlithogr., Microfabr., Microsyst., 2005, 4, 1). It has proven to be a cost effective, high resolution alternative to traditional optical lithography and has been placed on The International Technology Roadmap for Semiconductors (ITRS) as a potential candidate for 32 nm device fabrication (http://www.itrs.net/Links/2006Update/FinalToPost/08_Lithography2006Update.pdf.). This article summarizes the efforts made towards the development of imprint materials for S-FIL and the obstacles that have yet to be overcome.
1983 Design of Angle-Controlled Current Source Inverter-Fed Induction Motor Drive (1984)

The current source inverter-fed induction motor drive (hereafter referred to as CSIM drive) is one of the widely used drives in the industry. Of the many strategies employed for the control of CSIM drive, angle control is the simplest scheme to incorporate the aspect of "frequency compensation," thus paving the way for a fast response CSIM drive. A step-by-step design of the angle-controlled CSIM drive is described. A systematic design of inner current loop, slip speed loop, outer speed loop, and frequency compensation loop is given. The design incorporates a linear relationship between the reference input and output of electromagnetic torque and a strategy to obtain maximum torque per ampere. The commutation delay in the current source inverter is taken care of in the design of the frequency compensator. Experimental results are given in support of the design procedure.
Mechanism of Cadherin Switching in Breast Carcinoma (2005)

Abstract : During the progression of cancer, cells often undergo an epithelial-mesenchymal transition (EMT). This is associated with trading intercellular adhesion for a motile phenotype, as cells lose E-cadherin and gain the pro- migratory N-cadherin. While this process of cadherin switching has been described previously, the underlying molecular mechanism has yet to be elucidated. Here, we examine the role of p12O catenin (pl2Octn) and the Kaiso transcription factor as mediators of cadherin switching in breast cancer. It is proposed that EMT-induced loss of E-cadherin results in the interaction of pl2Octn with kaiso transcription factor to induce expression of N- Cadherin. This is supported by the presence of putative Kaiso binding sites in the N-cadherin promoter. Moreover, pl2Octn co-localizes with kaiso in cells that have lost E-cadherin but not in those that maintain its expression. To confirm this role for pl2Octn, co-immunoprecipitation of this protein with Kaiso will be utilized in an EMT model of breast cancer. Further, siRNA will be employed to demonstrate the necessity of these two proteins in EMT-induced cadherin switching. These experiments will describe a reasonable and novel mechanism for cadherin in breast cancer, while lending itself directly to the design of new therapies targeted at inhibiting breast cancer metastasis.
Membrane Dynamics and Regulation of Subcellular Changes during Senescence (2017)

Abstract The sections in this article are Introduction Loss of Membrane Structural Integrity during Senescence Role of Proteolysis in Membrane Senescence Dismantling of Membranes in Senescing Tissue Role of Autophagy Metabolism of Membrane Fatty Acids in Senescing Tissues Translational Regulation of Senescence
Photodegradation and photostabilization of europium compounds in polyvinyl chloride (2008)

The photolysis kinetics was studied, and methods were suggested for photostabilization of complexes of europium with β-diketones and europium cinnamates and quinaldates in polyvinyl chloride.
ChemInform Abstract: N‐Halogen Reagents. Synthesis of N‐Halogenoamines and Their Application in Organic Synthesis (1998)

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.
Stereocontrolled Elaboration of Quaternary Carbon Centers through the Asymmetric Michael-Type Alkylation of Chiral Imines/Secondary Enamines:  Enantioselective Synthesis of (+)-Vincamine (1997)

An enantioselective synthesis of (+)-vincamine (1) has been developed. The key strategic element was the stereocontrolled elaboration of a quaternary carbon center (future C-20 center of 1) by using the asymmetric Michael reaction involving chiral imines/secondary enamines under neutral conditions. Thus, addition of enaminolactam (S)-12, derived from ketolactam 7 (itself prepared in four steps from commercially available tryptamine) and (S)-1-phenylethylamine, to methyl acrylate led, after hydrolytic workup, to adduct (R)-6 with a 90% stereoselectivity. The critical removal of the additional keto group of 6 was then examined. After extensive experimentation, we finally established that the most efficient deoxygenation procedure was the Wolff−Kishner reduction of the corresponding keto acid, which proceeded with a 55% yield. The cornerstone [ABD]-tricyclic lactam ester 38 thus obtained was next cyclized under Bischler−Napieralski reaction conditions to afford, after catalytic hydrogenation of the intermediary iminium perchlorate salt, a mixture of the desired, known indoloquinolizidine 5 and its epimer 39, in a ratio of 6:1, respectively. Basic treatment of 5 led to (+)-homoeburnamonine 4, which was finally converted, according to a known procedure, into our goal (+)-vincamine (1). Thus, synthesis of (+)-vincamine (1) has been achieved by a linear sequence of 15 chemical operations, starting from tryptamine, with an overall yield of 1.2%.
Reprint of: Microstructural design of aerated food systems by soft-solid materials (2017)

The mechanism of adsorbing particles in creating super stable bubbles has been underlined and described but designing particles with these characteristics based of food grade materials is still a challenge. Moreover, food systems are rarely “pure” and the presence of more than one functional ingredients at a given formulation is usually the norm. This highlights the importance of mixed systems where particles and surface active ingredients are present. It has been demonstrated that particles made from food based materials although often not able to stabilised foams on their own, mostly due to limitations in size and hydrophobicity, they can aid significantly in the stability of foams without their ability to adsorb on the interface being a limiting factor. Evidence is presented where particles made from protein (whey) and hydrocolloid (κ-carageenan) sources can significantly extend the life of foams by affecting the rheological properties of these systems in both a macro and micro level. The technology of creating fluid gels poses an advantage in the production of these particles in a scalable manner that can provide solutions for industrial applications that demand liquid and powder formulations. The importance of surfactants (high or low molecular weight) that are either intrinsically present or added in the systems is also being underlined. Finally, a universal mechanism is proposed which allows the design of particulate systems from soft-solid materials that can produce edible liquid foams with enhanced stability.
Novel YAP1‐TFE3 fusion defines a distinct subset of epithelioid hemangioendothelioma (2013)

Conventional epithelioid hemangioendotheliomas (EHE) have a distinctive morphologic appearance and are characterized by a recurrent t(1;3) translocation, resulting in a WWTR1-CAMTA1 fusion gene. We have recently encountered a fusion-negative subset characterized by a somewhat different morphology, including focally well-formed vasoformative features, which was further investigated for recurrent genetic abnormalities. Based on a case showing strong transcription factor E3 (TFE3) immunoreactivity, fluorescence in situ hybridization (FISH) analysis for TFE3 gene rearrangement was applied to the index case as well as to nine additional cases, selected through negative WWTR1-CAMTA1 screening. A control group, including 18 epithelioid hemangiomas, nine pseudomyogenic HE, and three epithelioid angiosarcomas, was also tested. TFE3 gene rearrangement was identified in 10 patients, with equal gender distribution and a mean age of 30 years old. The lesions were located in somatic soft tissue in six cases, lung in three and one in bone. One case with available frozen tissue was tested by RNA sequencing and FusionSeq data analysis to detect novel fusions. A YAP1-TFE3 fusion was thus detected, which was further validated by FISH and reverse transcription polymerase chain reaction (RT-PCR). YAP1 gene rearrangements were then confirmed in seven of the remaining nine TFE3-rearranged EHEs by FISH. No TFE3 structural abnormalities were detected in any of the controls. The TFE3-rearranged EHEs showed similar morphologic features with at least focally, well-formed vascular channels, in addition to a variably solid architecture. All tumors expressed endothelial markers, as well as strong nuclear TFE3. In summary, we are reporting a novel subset of EHE occurring in young adults, showing a distinct phenotype and YAP1-TFE3 fusions.
Binding and Electron Transfer between Putidaredoxin and Cytochrome P450cam. Theory and Experiments (1998)

We present a detailed atomic level view of the interactions between cytochrome P450cam (CYP101) and its natural redox partner, putidaredoxin (Pdx). A combined theoretical (Poisson−Boltzmann electrostatic calculations, electron transfer pathways, and molecular dynamics) and experimental (site-directed mutagenesis and kinetic analysis) study is used to pinpoint surface residues in both proteins that are important for electron transfer, binding, or both. We find a situation where the electrostatically complementary regions at the surface of both proteins overlap strongly with regions that have large electron transfer couplings to the redox centers. This means that a small surface patch in each protein is involved in binding and electron transfer. A dominant electron transfer pathway is identified, corresponding to an electron leaving the reduced Fe2S2 in Pdx, going through Cys39 and Asp38, and transferring across the interprotein interface to Arg112 (CYP101), then to a heme propionate group, and finally to the heme iron center.
Development of a Versatile Methodology for the Synthesis of Poly(2,5-benzophenone) Containing Coil−Rod−Coil Triblock Copolymers (2004)

A short, simple, versatile methodology was developed for the synthesis of poly(2,5-benzophenone) containing coil−rod−coil triblock copolymers. After a model study, poly(2,5-benzophenone) macroinitiators were synthesized via end-capping poly(2,5-dichlorobenzophenone) synthesized by Ni(0)-catalyzed polymerization and functionalization of the chain ends utilizing phase transfer chlorination. Varying molecular weights of polystyrene-b-poly(2,5-benzophenone)-b-polystyrene were synthesized using the macroinitiators in the atom transfer radical polymerization of styrene. The materials were characterized by gel permeation chromatography, nuclear magnetic resonance, differential scanning calorimetry, and transmission electron microscopy. Applications were explored through dynamic mechanical analysis and the construction of a distributed junction photovoltaic device.