gebhart/patrepeval huggingface dataset:
Hybrid Living Materials: Digital Design and Fabrication of 3D Multimaterial Structures with Programmable Biohybrid Surfaces (2019)

Abstract Significant efforts exist to develop living/non‐living composite materials—known as biohybrids—that can support and control the functionality of biological agents. To enable the production of broadly applicable biohybrid materials, new tools are required to improve replicability, scalability, and control. Here, the Hybrid Living Material (HLM) fabrication platform is presented, which integrates computational design, additive manufacturing, and synthetic biology to achieve replicable fabrication and control of biohybrids. The approach involves modification of multimaterial 3D‐printer descriptions to control the distribution of chemical signals within printed objects, and subsequent addition of hydrogel to object surfaces to immobilize engineered Escherichia coli and facilitate material‐driven chemical signaling. As a result, the platform demonstrates predictable, repeatable spatial control of protein expression across the surfaces of 3D‐printed objects. Custom‐developed orthogonal signaling resins and gene circuits enable multiplexed expression patterns. The platform also demonstrates a computational model of interaction between digitally controlled material distribution and genetic regulatory responses across 3D surfaces, providing a digital tool for HLM design and validation. Thus, the HLM approach produces biohybrid materials of wearable‐scale, self‐supporting 3D structure, and programmable biological surfaces that are replicable and customizable, thereby unlocking paths to apply industrial modeling and fabrication methods toward the design of living materials.
High-performance electrode profile generation method (1985)

High-performance electrodes for gas discharge devices such as lasers often require surfaces of compound curvature which are both difficult to describe and difficult to manufacture. This paper describes a simple microcomputer method for generating sophisticated electrode shapes on a numerically controlled milling machine. As an example, a Rogowski cross-section electrode with end profiling was fabricated using an Apple IIe computer with an RS-232 serial interface to the milling machine.
WLCp1-13: How to Gain 1.5 dB in Vector Precoding (2006)

A vector-precoding technique known as "vector-perturbation" achieves near-capacity on a multi- antenna multi-user wireless channel. However, the technique currently requires choices for certain regularization and perturbation parameters and these parameters are currently chosen in a rather ad-hoc manner. We analyze the statistical properties of the vector- perturbation scheme and provide guidelines for choosing these parameters in a more systematic manner. These properties suggest that a large perturbation-parameter can give better performance at low SNR. We also propose a receiver that incorporates the statistical properties of the perturbation, thereby improving receiver performance over known methods. Finally, we incorporate an iteration loop between the demodulator and inner decoder. The net result of these improvements puts us approximately 1.5 dB closer to capacity.
Estimation of trapping position in three-dimensional off-axis trapping with optical vortices (2014)

Dynamics of micrometer-sized dielectric objects can be controlled by optical tweezers with scanning light, however, the trapped objects fail to track the scan when drag exceeds the trapping by too quick movement. On the other hand, optical vortices (OVs), which have a property of carrying angular momenta, can directly control torque on objects rather than their position. Laguerre-Gaussian (LG) beams are the most familiar examples of OV and have been studied extensively so far. Revolution of the objects trapped by the LG beams provides typical models of nonequilibrium statistical system, but stable mid-water trapping by the LG beams becomes essential to evaluate physical properties of the system without extrinsic hydrodynamic effects,. Nevertheless, off-axis revolutions of small objects trapped in mid-water by the LG beams have not yet been established with secure evidences. Here we report stable off-axis trapping of dielectric spheres in mid-water using high-quality LG beams generated by a holographic complex-amplitude modulation method. Direct evidence of the three-dimensional off-axis LG trapping was established via estimating the trapping position by measuring the change of revolution radii upon pressing the spheres onto glass walls. Resultantly, the axial trapping position was determined as about half the wavelength behind the beam waist position. This result provides a direct scientific evidence for possibility of off-axis three-dimensional trapping with a single LG beam, moreover, suggests applications as powerful tools for studying energy-conversion mechanisms and nonequilibrium nature in biological molecules under torque.
ChemInform Abstract: A Method for the Parallel Synthesis of Multiply Substituted Oxazolidinones. (2002)

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.
Design and Synthesis of Enantiomerically Pure Decahydroquinoxalines as Potent and Selective κ-Opioid Receptor Agonists with Anti-Inflammatory Activityin Vivo (2017)

In order to develop novel κ agonists restricted to the periphery, a diastereo- and enantioselective synthesis of (4aR,5S,8aS)-configured decahydroquinoxalines 5-8 was developed. Physicochemical and pharmacological properties were fine-tuned by structural modifications in the arylacetamide and amine part of the pharmacophore as well as in the amine part outside the pharmacophore. The decahydroquinoxalines 5-8 show single-digit nanomolar to subnanomolar κ-opioid receptor affinity, full κ agonistic activity in the [<sup>35</sup>S]GTPγS assay, and high selectivity over μ, δ, σ<sub>1</sub>, and σ<sub>2</sub> receptors as well as the PCP binding site of the NMDA receptor. Several analogues were selective for the periphery. The anti-inflammatory activity of 5-8 after topical application was investigated in two mouse models of dermatitis. The methanesulfonamide 8a containing the (S)-configured hydroxypyrrolidine ring was identified as a potent (K<sub>i</sub> = 0.63 nM) and highly selective κ agonist (EC<sub>50</sub> = 1.8 nM) selective for the periphery with dose-dependent anti-inflammatory activity in acute and chronic skin inflammation.
Characterization of OpdH, a Pseudomonas aeruginosa Porin Involved in the Uptake of Tricarboxylates (2006)

The Pseudomonas aeruginosa outer membrane is intrinsically impermeable to many classes of antibiotics, due in part to its relative lack of general uptake pathways. Instead, this organism relies on a large number of substrate-specific uptake porins. Included in this group are the 19 members of the OprD family, which are involved in the uptake of a diverse array of metabolites. One of these porins, OpdH, has been implicated in the uptake of cis-aconitate. Here we demonstrate that this porin may also enable P. aeruginosa to take up other tricarboxylates. Isocitrate and citrate strongly and specifically induced the opdH gene via a mechanism involving derepression by the putative two-component regulatory system PA0756-PA0757. Planar bilayer analysis of purified OpdH demonstrated that it was a channel-forming protein with a large single-channel conductance (230 pS in 1 M KCl; 10-fold higher than that of OprD); however, we were unable to demonstrate the presence of a tricarboxylate binding site within the channel. Thus, these data suggest that the requirement for OpdH for efficient growth on tricarboxylates was likely due to the specific expression of this large-channel porin under particular growth conditions.
‘E‐Boxes’ as Promoter Elements in B Cell Lines and Untransformed B Lymphocytes (1991)

The penta-deca (pd) promoter element from the SP6 kappa promoter and the muE2 box from the Ig heavy chain intron enhancer were analysed in an electrophoretic mobility shift assay (EMSA), utilising cell extracts from total mouse splenic B cells before and after stimulation with lipopolysaccharide. With both probes a changed EMSA pattern was observed after stimulation of the cells, where higher molecular weight DNA/protein complexes became dominant. When the pd and muE2 sequence elements were cloned in front of a TATA box and analysed for their transcriptional promoting activity in lipopolysaccharide stimulated B cells, they were inactive. On the contrary, the same constructs were transcriptionally active in some but not all B cell lines. Thus, E-boxes display functional heterogeneity as transcriptional activators depending on host cell.
Prostate cancer regulatory networks (2009)

Although the timing with which common epithelial malignancies arise and become established remains a matter of debate, it is clear that by the time they are detected these tumors harbor hundreds of deregulated, aberrantly expressed or mutated genes. This enormous complexity poses formidable challenges to identify gene pathways that are drivers of tumorigenesis, potentially suitable for therapeutic intervention. An alternative approach is to consider cancer pathways as interconnected networks, and search for potential nodal proteins capable of connecting multiple signaling networks of tumor maintenance. We have modeled this approach in advanced prostate cancer, a condition with current limited therapeutic options. We propose that the integration of three signaling networks, including chaperone-mediated mitochondrial homeostasis, integrin-dependent cell signaling, and Runx2-regulated gene expression in the metastatic bone microenvironment plays a critical role in prostate cancer maintenance, and offers novel options for molecular therapy.
Recovery Time of an Optimally Secreting Meibomian Gland (2009)

This report shows that (1) a single OSMG can be drained of its liquid secretion in 8-20 seconds upon application of a constant force of 1 g/mm, and (2) a partial recovery occurs after approximately 2 hours, evidenced by detectable liquid secretion which then expressed for only half of the original time.
Early events in the folding of four-helix-bundle heme proteins (2005)

Topologically homologous four-helix-bundle heme proteins exhibit striking diversity in their refolding kinetics. Cytochrome b562 has been reported to fold on a sub-millisecond time scale, whereas cytochrome c' refolding requires 10 s or more to complete. Heme dissociation in cytochrome b562 interferes with studies of folding kinetics, so a variant of cytochrome b562 (cytochrome c-b562) with a covalent c-type linkage to the heme has been expressed in Escherichia coli. Early events in the electron transfer-triggered folding of Fe(II)-cytochrome c-b562, along with those of Fe(II)-cytochrome c556, have been examined by using time-resolved absorption spectroscopy. Coordination of S(Met) to Fe(II) occurs within 10 mus after reduction of the denatured Fe(III)-cytochromes, and shortly thereafter (100 micros) the heme spectra are indistinguishable from those of the folded proteins. Under denaturing conditions, carbon monoxide binds to the Fe(II)-hemes in approximately 15 ms. By contrast, CO binding cannot compete with refolding in the Fe(II)-cytochromes, thereby confirming that the polypeptide encapsulates the heme in <10 ms. We suggest that Fe-S(Met) ligation facilitates refolding in these four-helix-bundle heme proteins by reducing the conformational freedom of the polypeptide chain.
Structure and properties of generalized adaptive neural filters for signal enhancement (1996)

This article addresses the structure and properties of a new class of nonlinear adaptive filters called generalized adaptive neural filters (GANFs). Various properties, such as an upper bound of the mean absolute error of the filters, are analytically derived. Experimental results are presented to demonstrate the performance of the filters for signal and image enhancement. It is shown that GANFs not only extend the class of stack filters, but also have better performance in noise suppression.
Sonochemically Prepared BSA Microspheres as Adsorbents for the Removal of Organic Pollutants from Water (2021)

This work investigates, for the first time, the application of sonochemically prepared bovine serum albumin (BSA) microspheres (BSAMS) as adsorbents of industrial organic pollutant dyes, such as rhodamine B (RhB), rhodamine 6G (Rh6G), and methylene blue (MB). These dyes also serve as model compounds for other organic pollutants such as bisphenol A and 2-nitrophenol. Adsorption kinetics of the dyes by the BSAMS was studied using pseudo-first-order (PFO) and pseudo-second-order (PSO) kinetic models. It was found that RhB follows PFO, with an adsorption capacity, <i>q</i><sub>e,cal</sub>, of 7.9 mg/g, which was closer to the experimental adsorption capacity of <i>q</i><sub>e,exp<i>.</i></sub> of 7.6 mg/g. However, MB and Rh6G were controlled by PSO kinetics, with a <i>q</i><sub>e,cal</sub> of 5.6 mg/g for MB and 6.6 mg/g for Rh6G, closer to the experimental adsorption capacity of 5.7 and 6.4 mg/g, respectively. The intraparticle diffusion (ID) model applied to the three dyes indicated multi-linearity with ID as the rate-limiting step in the adsorption process. Furthermore, the adsorption equilibria for each of the organic pollutants were studied through various isotherm models such as Langmuir, Freundlich, Temkin, and Halsey, which indicated physical interaction between the BSAMS and the dye pollutants, thus suggesting the applicability of the BSAMS as pollutant adsorbent materials. It was found that the BSAMS can effectively remove RhB, MB, and Rh6G from wastewater with efficiencies of 95.5, 83.3, and 97.9%, respectively.
Blue Lasers for Optical Wireless Communications (2023)

Distributed feedback (DFB) lasers based on gallium nitride (GaN) have been fabricated and characterised for use in optical wireless communications. These devices find applications in free space visible light communication (VLC), but also play a fundamental role in underwater and space environments due to the low loss transmission at blue wavelengths. Devices have shown Gbit/s performance making them ideal candidates for low-cost, high speed data transmission.
An electret-based electrostatic ?-generator (2004)

This paper proposes a new approach towards mechanical waste energy scavenging, using a micromachined electrostatic converter. The device consists of a vibration sensitive variable capacitor polarized by an electret. The variation of the capacitance results in a current through a load circuit. A physical model of the device is described; in order to obtain a closed form expression for the converted power a linear model is presented. This model shows that 50 /spl mu/W can be generated with a 5 /spl mu/m vibration. A first prototype design based on SOI MPW-service is proposed.
The combination of sorafenib and everolimus in patients with solid tumors: Results of a phase I study. (2011)

e13613 Background: The combination of the multi-kinase inhibitor sorafenib (S) and the mTOR inhibitor everolimus (E) may increase anti-tumor efficacy by dual inhibition of key nodules of signaling pathways regulating angiogenesis and cellular proliferation. FDG-PET might be a suitable method for the assessment of pharmacodynamic activity of E. Methods: Patients with advanced solid tumors after failure of standard therapy were treated with E in a dose escalating schedule of 1x 2.5-10mg daily in combination with a fixed dose of 2x 400mg S daily. The primary objective was to determine the maximum tolerated dose (MTD) of the combination. Dose-limiting toxicity (DLT) was defined as any of the following toxicities occurring during the first 29 treatment days(DLT interval): hematological or non-hematological toxicity of CTC grade IV, any toxicity requiring hospitalization or any toxicity leading to delay of treatment for more than 2 weeks. In addition to pharmacokinetics, pharmacodynamic analyses using dynamic FDG-PET were performed on days 0, 5 and 14. Response after 8 weeks of treatment was assessed by CT. Results: Sixteen patients have been enrolled. The DLT was not reached according to protocol definition. However, at a dose level of 1x 10mg E daily and 2x 400mg S daily the following toxicities occurred in the non DLT interval: upper respiratory tract infection III°, treatment delay caused by leukopenia III° and thrombopenia III° and sudden cardiac death probably due to arrhythmia. Based on these observations the dose level of 1x 7.5mg E daily and 2x 400mg S daily was defined as MTD. Data analysis of patients treated on MTD is currently ongoing. Response after 8 weeks could be evaluated in 9 patients, showing progressive disease in one patient (pancreatic cancer) and stable disease in 8 patients (NSCLC, melanoma, CUP, ovarian, colorectal, vaginal and breast cancer). Conclusions: Combination of S and E is feasible for the treatment of patients with advanced solid tumors. The full analysis including pharmacodynamics and pharmakokinetics will be presented.
[The history of the pituitary gland: evolution of mental representation and concepts over time]. (2014)

The hypothalamo pituitary axis, as the true conductor of the endocrine orchestra, is frequently involved in a large variety of pathological conditions such as acromegaly, behavioral disorders, obesity or dwarfism. It is paradoxical to note that, in spite of its importance, this system has been almost ignored by the physiologists of the late centuries. From the physiological conceptions of the physicians and philosophers of antiquity to the theories of the medieval and of the Renaissance physiologists, we will try to understand why the role of pituitary remained so long unrecognized.
Common SNPs in HMGCR in Micronesians and Whites Associated With LDL-Cholesterol Levels Affect Alternative Splicing of Exon13 (2008)

We identified variants in HMGCR that are associated with LDL-C across populations and affect alternative splicing of HMGCR exon13.
Carney’s complex (2011)

Abstract Carney’s complex (CNC) is an autosomal dominant disorder, which was described in 1985 as ‘the complex of myxomas, spotty pigmentation, and endocrine overactivity’ in 40 patients (1). Since then, more than 500 index cases have been reported, resulting in better definition of the disease and the establishment of diagnostic criteria (2, 3). As implied from the initial description, CNC is not only a multiple neoplasia syndrome, but also causes a variety of pigmented lesions of the skin and mucosae. (4) Several patients described in earlier years under the acronyms NAME (nevi, atrial myxomas, and ephelides) and LAMB (lentigines, atrial myxomas, and blue nevi) probably had CNC (5, 6). Thus, lentigines, blue nevi, café-au-lait spots, and cutaneous tumours, such as myxomas, fibromas, and others, are major features of the disease (4, 7–10). The clinical characteristics of CNC have been reviewed and are presented in Box 6.15.1 (2, 9). A definite diagnosis of CNC is given if two or more major manifestations are present (4, 9, 11, 12). A number of related manifestations may accompany or suggest the presence of CNC but are not considered diagnostic of the disease (Box 6.15.1). Cutaneous manifestations constitute three of the major disease manifestations: (1) spotty skin pigmentation with a typical distribution (lips, conjunctiva, and inner or outer canthi, genital mucosa); (2) cutaneous or mucosal myxoma; and (3) blue nevi (multiple) or epithelioid blue nevus. Suggestive or associated with CNC findings but not diagnostic are: (1) intense freckling (without darkly pigmented spots or typical distribution); (2) multiple blue nevi of common type; (3) café-au-lait spots or other ‘birthmarks’; and (4) multiple skin tags or other skin lesions, including lipomas and angiofibromas. The relationship between the cutaneous and noncutaneous manifestations of CNC appears to be an essential clue to the molecular aetiology of the disease. According to the latest reports, more than half of CNC patients present with both characteristic dermatological and endocrine signs; however, a significant number of patients present with skin lesions that are only ‘suggestive’ and not characteristic of CNC (9). A recent classification based on both dermatological and endocrine markers has subgrouped CNC patients as: multisymptomatic (with extensive endocrine and skin signs); intermediate (with few dermatological and endocrine manifestations); and, paucisymptomatic (with isolated primary pigmented nodular adrenocortical disease (PPNAD) alone and no cutaneous signs) (9).
Electrochemical and X-ray Absorption Spectroscopy Investigations of Novel Self-supported Cobalt Porphyrin-based Electrocatalysts (2007)

Abstract not Available.
0013 THE ASTROCYTIC FABP7 GENE REGULATES SLEEP ACROSS PHYLOGENY (2017)

Sleep is found widely in the animal kingdom. Despite this, few conserved molecular pathways that govern sleep across phyla have been described. The mammalian brain-type fatty acid binding protein (Fabp7) is expressed in astrocytes, and its mRNA oscillates in tandem with the sleep-wake cycle. In this study, we examined whether Fabp7 is necessary for normal sleep/wake behavior in phylogenetically diverse species, including humans, mice, and the fruit fly, Drosophila melanogaster. Adult 2–4 month old male C57BL/6J wild-type (WT, N=7) mice were compared to age-matched isogenic Fabp7 knock-out (KO, N=8) mice using standard EEG/EMG techniques to examine sleep. Actigraphy measures of sleep in human adult male Fabp7 T61M mutant carriers (N=29) were compared to age-matched male non-carriers (N=265). The 7 day sleep profiles were assessed from the actigraphy records in conjunction with sleep diaries, and genotypes were blinded for the analysis. In order to test whether an astrocyte-specific functional Fabp7 is required for normal sleep in Drosophila, we generated transgenic flies that express either the human FABP7 WT (FABP7.WT, N=32) or FABP7 T61M (FABP7.T61M, N=27) under UAS-control, and used the Astrocyte-specific Alrm-GAL4 driver to control transgene expression. We measured sleep using the Drosophila Activity Monitoring System, and standard sleep scoring analytics. Fabp7 KO mice showed decreased average dark-phase NREM sleep bout duration (p<0.05) and an increase in the frequency of dark-phase NREM sleep bouts (p<0.05) compared to control mice. Increased frequency of dark-phase REM sleep bouts (p<0.05) was also observed. Humans which carry a Fabp7 Thr61Met missense mutation showed a decrease in average 7 d sleep bout duration (p<0.01) and an increase in the frequency of sleep bouts (p<0.05) compared to non-carriers. Similar to human FABP7 T61M carriers, the effects of FABP7.T61M in flies show increased sleep fragmentation compared to FABP7.WT flies. The FABP7.T61M flies had shorter bout durations (p<0.05), a reduction in the maximum sleep bout duration (p<0.05) and an increase in the frequency of sleep bouts (p<0.05). These results provide novel evidence for the astrocyte-specific gene, Fabp7, in regulating sleep across phylogenetically diverse species. MEXT KAKENHI 221S0002, NIH-HL007713, NIH-HL111725, NIH-MH099544, and ONR-N00014-13-1-0302.