gebhart/patrepeval huggingface dataset:
Functional Features of Trans-Differentiated Hair Cells Mediated by Atoh1 Reveals a Primordial Mechanism (2012)

Evolution has transformed a simple ear with few vestibular maculae into a complex three-dimensional structure consisting of nine distinct endorgans. It is debatable whether the sensory epithelia underwent progressive segregation or emerged from distinct sensory patches. To address these uncertainties we examined the morphological and functional phenotype of trans-differentiated rat hair cells to reveal their primitive or endorgan-specific origins. Additionally, it is uncertain how Atoh1-mediated trans-differentiated hair cells trigger the processes that establish their neural ranking from the vestibulocochlear ganglia. We have demonstrated that the morphology and functional expression of ionic currents in trans-differentiated hair cells resemble those of "ancestral" hair cells, even at the lesser epithelia ridge aspects of the cochlea. The structures of stereociliary bundles of trans-differentiated hair cells were in keeping with cells in the vestibule. Functionally, the transient expression of Na⁺ and I(h) currents initiates and promotes evoked spikes. Additionally, Ca²⁺ current was expressed and underwent developmental changes. These events correlate well with the innervation of ectopic hair cells. New "born" hair cells at the abneural aspects of the cochlea are innervated by spiral ganglion neurons, presumably under the tropic influence of chemoattractants. The disappearance of inward currents coincides well with the attenuation of evoked electrical activity, remarkably recapitulating the development of hair cells. Ectopic hair cells underwent stepwise changes in the magnitude and kinetics of transducer currents. We propose that Atoh1 mediates trans-differentiation of morphological and functional "ancestral" hair cells that are likely to undergo diversification in an endorgan-specific manner.
Dielectric function of amorphous tantalum oxide from the far infrared to the deep ultraviolet spectral region measured by spectroscopic ellipsometry (2000)

Amorphous tantalum oxide thin films were deposited by reactive rf magnetron sputtering onto [001] silicon substrates. Growth temperature, oxygen partial pressure, and total gas pressure have been varied to obtain thin films with different densities. The thin films were analyzed by glancing angle-of-incidence x-ray diffraction, atomic force microscopy, and variable angle-of-incidence spectroscopic ellipsometry in the near infrared to vacuum ultraviolet spectral region for photon energies from E=1 to 8.5 eV, and in the infrared region from E=0.03 to 1 eV. We present the dielectric function of amorphous tantalum oxide obtained by line shape analysis of the experimental ellipsometric data over the range from E=0.03 to 8.5 eV (40 μm–145 nm). In the infrared spectral region the ellipsometric data were analyzed using Lorentzian line shapes for each absorption mode observed in the spectra. Amorphous tantalum oxide optical properties in the near infrared to vacuum ultraviolet spectral region were extracted by using a Kim and Garland parameter algorithm [C. C. Kim et al., Phys. Rev. B 45, 11 749 (1992)] in order to model the absorption due to the fundamental band gap of the material. We consider thin film porosity, and therefore analyzed the experimental ellipsometric data by an effective medium approach. We obtain information on the tantalum oxide optical properties, a percentage of void fraction, and film thickness. The “optical” percentage of void fractions corresponds to surface roughness measured by atomic force microscopy and depends on deposition parameters.
Enrichment of Mutations in Multiple DNA Sequences Using COLD-PCR in Emulsion (2012)

TT-fast-eCOLD-PCR expands the versatility of COLD-PCR and enables high-throughput enrichment of low-level mutant alleles over multiple sequences in a single tube.
Synthesis of sibutramine, a novel cyclobutylalkylamine useful in the treatment of obesity, and its major human metabolites (1996)

Synthetic routes to N-{1-[1-(4-chlorophenyl)cyclobutyl]-3-methylbutyl}-N,N-dimethylamine (sibutramine) 1 and its demethylated and hydroxylated human metabolites N-{1-[1-(4-chlorophenyl)cyclobutyl]-3-methylbutyl}-N-methylamine 2, 1-[1-(4-chlorophenyl)cyclobutyl]-3-methylbutylamine 3, 4-amino-4-[1-(4-chlorophenyl)cyclobutyl]-2-methylbutan-1-ol 4 and c-3-(1-amino-3-methylbutyl)-3-(4-chlorophenyl)cyclobutan-r-1-ol 5a are described. Key steps are tandem Grignard–reduction reactions on 1-(4-chlorophenyl)cyclobutanecarbonitrile 7 and its 3-(tetrahydropyran-2-yloxy)-substituted analogue 14 and a convenient one-pot conversion of 4-chlorophenylacetonitrile 6 into the 3-hydroxycyclobutanecarbonitrile 13.
Analysis of proteins with the 'hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins (2009)

The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.
Fermentation production of keratinase from Bacillus licheniformis PWD-1 and a recombinant B. subtilis FDB-29 (1999)

PWD-1, the parent strain, and B. subtilis FDB-29, a recombinant strain. In both strains, keratinase was induced by proteinaceous media, and repressed by carbohydrates. A seed culture of B. licheniformis PWD-1 at early age, 6–10 h, is crucial to keratinase production during fermentation, but B. subtilis FDB-29 is insensitive to the seed culture age. During the batch fermentation by both strains, the pH changed from 7.0 to 8.5 while the keratinase activity and productivity stayed at high levels. Control of pH, therefore, is not necessary. The temperature for maximum keratinase production is 37°C for both strains, though B. licheniformis is thermophilic and grows best at 50°C. Optimal levels of dissolved oxygen are 10% and 20% for B. licheniformis and B. subtilis respectively. A scale-up procedure using constant temperature at 37°C was adopted for B. subtilis. On the other hand, a temperature-shift procedure by which an 8-h fermentation at 50°C for growth followed by a shift to 37°C for enzyme production was used for B. licheniformis to shorten the fermentation time and increase enzyme productivity. Production of keratinase by B. licheniformis increased by ten-fold following this new procedure. After respective optimization of fermentation conditions, keratinase production by B. licheniformis PWD-1 is approximately 40% higher than that by B. subtilis FDB-29.
Thiol–ene reaction: a versatile tool in site-specific labelling of proteins with chemically inert tags for paramagnetic NMR (2012)

Site-specific tagging of proteins with paramagnetic lanthanides generates valuable long-range structure restraints for structural biology by NMR spectroscopy. We show that the thiol-ene addition reaction offers a powerful tool for tagging proteins in a chemically stable manner with very small lanthanide tags.
Nucleotide sequence of the cDNA coding for human complement C1r (1986)

C1r is a zymogen of a serine protease that is involved in the activation of the first component of the classical pathway of the complement system. cDNAs coding for human C1r have been isolated from libraries prepared from poly(A) RNA from human liver and Hep G2 cells. From DNA sequence analysis, the overlapping cDNA inserts were shown to span 2493 nucleotides of the C1r mRNA, not including the poly(A) tail. The cDNA sequence coding for C1r contained a 5' noncoding region, 2115 nucleotides coding for a polypeptide precursor of 705 amino acids, and a 3' noncoding region. Some variability in the length of the 3' noncoding sequence was observed with the cDNA inserts, although most contained a polyadenylation signal followed by a poly(A) tail. The A or noncatalytic chain of C-1r, which originates from the amino-terminal end of the precursor molecule, contains a potential growth factor domain and two different pairs of internal repeats. One pair of these internal repeats is closely related to the amino-terminal sequence of C1s, while the other pair of repeats is homologous to the tandem repeats present in beta 2-glycoprotein I, complement factor B, the b subunit of factor XIII, and a single region present in the alpha 1 chain of haptoglobin. The B chain of C-1r contains the catalytic portion of the enzyme and is homologous to the trypsin family of serine proteases.
The problem of optimal robust sensor scheduling (2002)

This paper considers the sensor scheduling problem which consists of estimating the state of an uncertain process based on measurements obtained by switching a given set of noisy sensors. The noise and uncertainty models considered in this paper are assumed to be unknown deterministic functions which satisfy an energy type constraint known as an integral quadratic constraint. The problem of optimal robust sensor scheduling is formulated and solution to this problem is given in terms of the existence of suitable solutions to a Riccati differential equation of the game type and a dynamic programming equation. Furthermore, a real time implementable method for sensor scheduling is also presented.
Treatment of presumed allergic skin disease in cats (2017)

Feline dermatology presents a number of challenges when it comes to diagnosing individual diseases, due to the more subtle and varied nature of skin lesions in cats compared to those commonly seen in dogs. In feline allergic skin disease (FASD), the diagnostic challenge is increased further as cats present with one or more of four patterns of disease, rather than the more typical character and distribution of lesions seen in canine hypersensitivity dermatitis cases. Cats are also generally more solitary animals and secretive in their behaviour, which can lead to the absence of important clues in the clinical history. There can also be challenges in both the administration of treatment and the comparatively poor treatment responses seen in some patients. This article reviews the important steps that should be taken to diagnose and successfully manage FASD, with particular reference to head and neck excoriations or pruritus, which can be among the more challenging presentations to treat.
Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): analysis of molecular predictors, signatures, cell cycle state and patient survival (2007)

Aiming to find key genes and events, we analyze a large data set on diffuse large B-cell lymphoma (DLBCL) gene-expression (248 patients, 12196 spots). Applying the loess normalization method on these raw data yields improved survival predictions, in particular for the clinical important group of patients with medium survival time. Furthermore, we identify a simplified prognosis predictor, which stratifies different risk groups similarly well as complex signatures. We identify specific, activated B cell-like (ABC) and germinal center B cell-like (GCB) distinguishing genes. These include early (e.g. CDKN3) and late (e.g. CDKN2C) cell cycle genes. Independently from previous classification by marker genes we confirm a clear binary class distinction between the ABC and GCB subgroups. An earlier suggested third entity is not supported. A key regulatory network, distinguishing marked over-expression in ABC from that in GCB, is built by: ASB13, BCL2, BCL6, BCL7A, CCND2, COL3A1, CTGF, FN1, FOXP1, IGHM, IRF4, LMO2, LRMP, MAPK10, MME, MYBL1, NEIL1 and SH3BP5. It predicts and supports the aggressive behaviour of the ABC subgroup. These results help to understand target interactions, improve subgroup diagnosis, risk prognosis as well as therapy in the ABC and GCB DLBCL subgroups.
The cytotoxicity of methyl protoneogracillin (NSC‐698793) and gracillin (NSC‐698787), two steroidal saponins from the rhizomes of Dioscorea collettii var. hypoglauca, against human cancer cells in vitro (2003)

In our continuous studies of anticancer activity of steroidal saponins from the rhizomes of Dioscorea collettii var. hypoglauca (Dioscoreaceae), methyl protoneogracillin (NSC-698793) and gracillin (NSC-698787) were tested for cytotoxicity against human cancer cell lines from leukemia and eight solid tumor diseases. As a result, methyl protoneogracillin was cytotoxic against all the test cell lines with GI(50) < 100 micro M, especially selectively against two leukemia lines (CCRF-CEM and RPMT-8226), one colon cancer line (KM12), two central nervous system (CNS) cancer lines (SF-539 and U251), one melanoma line (M14), one renal cancer line (786-0), one prostate cancer line (DU-145), and one breast cancer line (MDA-MB-435), with GI(50) < or = 2.0 micro M. Leukemia, CNS cancer, and prostate cancer were the most sensitive subpanels, while ovarian cancer was the least sensitive subpanels. The preliminary toxicity studies showed that the maximum tolerant dose was 600 mg/kg for methyl protoneogracillin to mice. Gracillin was cytotoxic against most cell lines with GI(50), TGI and LC(50) at micromolar levels, but no activity against EKVX (non-small cell lung cancer), HT29 (colon cancer), OVCAR-5 (ovarian cancer), and SN12C (renal cancer). Based on structure-activity relationship, C-25 R/S con fi guration was critical for leukemia selectivity between methyl protoneogracillin and methyl protogracillin. F-ring was critical to selectivity between furostanol (methyl protoneogracillin and methyl protogracillin) and spirostanol (gracillin) saponins in this study. By an analysis of COMPARE software, no compounds in the NCI's database had similar mean graphs to those of methyl protoneogracillin and gracillin, respectively, indicating potential novel mechanism(s) of action involved. Put all in together, methyl protoneogracillin has been selected as a potential anticancer candidate for hollow fi ber assay to nude mice, but gracillin will not be pursued due to lack of selectivity against human cancer diseases.
Designing Nanosensors Based on Charged Derivatives of Gramicidin A (2007)

Detection of chemical processes on a single molecule scale is the ultimate goal of sensitive analytical assays. We recently reported the possibility to detect chemical modifications on individual molecules by monitoring a change in the single ion channel conductance of derivatives of gramicidin A (gA) upon reaction with analytes in solution. These peptide-based nanosensors detect reaction-induced changes in the charge of gA derivatives that were engineered to carry specific functional groups near their C-terminus.1 Here, we discuss five key design parameters to optimize the performance of such chemomodulated ion channel sensors. In order to realize an effective sensor that measures changes in charge of groups attached to the C-terminus of a gA pore, the following conditions should be fulfilled: (1) the change in charge should occur as close to the entrance of the pore as possible; (2) the charge before and after reaction should be well-defined within the operational pH range; (3) the ionic strength of the recording buffer should be as low as possible while maintaining a detectable flow of ions through the pore; (4) the applied transmembrane voltage should be as high as possible while maintaining a stable membrane; (5) the lipids in the supporting membrane should either be zwitterionic or charged differently than the derivative of gA. We show that under the condition of high applied transmembrane potential (>100 mV) and low ionic strength of the recording buffer (< or =0.10 M), a change in charge at the entrance of the pore is the dominant requirement to distinguish between two differently charged derivatives of gA; the conductance of the heterodimeric gA pore reported here does not depend on a difference in charge at the exit of the pore. We provide a simple explanation for this asymmetric characteristic based on charge-induced local changes in the concentration of cations near the lipid bilayer membrane. Charge-based ion channel sensors offer tremendous potential for ultrasensitive functional detection since a single chemical modification of each individual sensing element can lead to readily detectable changes in channel conductance.
Use of Ozone + Hydrogen Peroxide To Degrade Macroscopic Quantities of Chelating Agents in an Aqueous Solution (1996)

Ozone in the presence of hydrogen peroxide has been employed succesfully for the oxidative degradation of polycarboxylic and diphosphonic acid chelating agents present at the 0.1 M level in a neutral or weakly alkaline aqueous solution. The geminal diphosphonic acid complexants methanediphosphonic acid and (1-hydroxyethylidene)bisphosphonic acid have been successfully mineralized, as have the polycarboxylic acids ethylenediaminetetraacetic acid and tetrahydrofurantetracarboxylic acid.
Forest conservation genetics: principles and practice (2000)

<title>Abstract</title> The aim of this multiauthor book is to introduce readers with a wide variety of backgrounds to the principles and practice of forest conservation genetics through 22 chapters which deal with: genetic principles and basic genetic processes; genetic threats to forest species and in situ conservation; the effects of domestication and ex situ restoration on forest gene pools; and the interations between genetics and socio-economics as they relate to formation of forest policy. Where possible, case studies have been emphasized to provide practical illustrations of concepts being discussed. To this end, the population genetics package, POPGENE, is included with the book as a CD-ROM to provide a hands-on tool for the analysis and interpretation of a wide range of genetic data. The references are all given at the end of the book. There is a subject index. The individual chapters are noticed separately on CAB Abstracts.
Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria (2010)

The Calvin-Benson-Bassham cycle (Calvin cycle) catalyzes virtually all primary productivity on Earth and is the major sink for atmospheric CO(2). A less appreciated function of CO(2) fixation is as an electron-accepting process. It is known that anoxygenic phototrophic bacteria require the Calvin cycle to accept electrons when growing with light as their sole energy source and organic substrates as their sole carbon source. However, it was unclear why and to what extent CO(2) fixation is required when the organic substrates are more oxidized than biomass. To address these questions we measured metabolic fluxes in the photosynthetic bacterium Rhodopseudomonas palustris grown with (13)C-labeled acetate. R. palustris metabolized 22% of acetate provided to CO(2) and then fixed 68% of this CO(2) into cell material using the Calvin cycle. This Calvin cycle flux enabled R. palustris to reoxidize nearly half of the reduced cofactors generated during conversion of acetate to biomass, revealing that CO(2) fixation plays a major role in cofactor recycling. When H(2) production via nitrogenase was used as an alternative cofactor recycling mechanism, a similar amount of CO(2) was released from acetate, but only 12% of it was reassimilated by the Calvin cycle. These results underscore that N(2) fixation and CO(2) fixation have electron-accepting roles separate from their better-known roles in ammonia production and biomass generation. Some nonphotosynthetic heterotrophic bacteria have Calvin cycle genes, and their potential to use CO(2) fixation to recycle reduced cofactors deserves closer scrutiny.
Perovskite‐Based Hybrid Solar Cells Exceeding 10% Efficiency with High Reproducibility Using a Thin Film Sandwich Approach (2013)

Organometal halide perovskites have tremendous potential as light absorbers for photovoltaic applications. In this work we demonstrate hybrid solar cells based on the mixed perovskite CH3 NH3 PbI2 Cl in a thin film sandwich structure, with unprecedented reproducibility and generating efficiencies up to 10.8%. The successfulness of our approach is corroborated by the experimental electronic structure determination of this perovskite.
Active Knit Actuation Architectures. (2014)

Actuators move our world. While conventional and smart material actuators have enabled myriad applications, many advanced applications (e.g., morphing aircraft, deployable space structures, and medical devices) require complex, distributed, three-dimensional motions that are limited by current actuation capabilities. This dissertation explores a new cellular architectural actuator, active knits, and provides the fundamental scientific understanding of the active knit actuation architecture to enable the design, analysis, and synthesis of simultaneous large force and strain actuators that produce complex three-dimensionally distributed motions. The active knit architecture leverages a smart material fiber through a continuous network of hierarchically organized loops that generate complex motions (contraction, scrolling, coiling, accordion, arching, etc.), while simultaneously delivering high strain (10-600%) and force (1-100 N). This dissertation defines a four level active knit hierarchy (knitted loops, knit patterns, grid patterns, restructured grids), establishing a language to design, synthesize, and analyze new actuators and a framework to explore the breadth of actuator motions. To provide high fidelity predictive capabilities of planar active knit actuators, a two-dimensional analytical model is derived using Euler-Bernoulli beam bending and Elastica theory assuming dual-stiffness material behavior. To provide predictive capabilities of three-dimensional knit patterns early in the design process, a segment superposition modeling approach is developed that segments the unit cell and creates simple mechanical models that are superimposed to yield coarse prediction of the textile’s global performance. All models were experimentally validated against shape memory alloy (SMA) active knit prototypes with strong correlation of the force-deflection and actuation performance, confirming predictive capabilities for this simultaneous large strain and force actuation architecture. To further demonstrate the actuation potential, an active flow control case study was conducted using rib pattern actuators. The study verified that active knits can generate the simultaneous large displacements (23 mm/75%) and forces (4.4 kPa/44.4 N) that are necessary for extreme applications. While further research will be necessary to bring active knits into practice, this research established the necessary language, models, and experimental techniques to provide the scientific understanding essential for design, analysis, and synthesis of this novel cellular actuator architecture – opening the door to applications not yet imagined.
Stokes emission in GdF3:Nd3+nanoparticles for bioimaging probes (2013)

There is increasing interest in rare earth (RE) doped nanoparticles (NPs) due to their sharp absorption and photoluminescence (PL) in the near infrared (NIR) spectral region. These NIR based nanoparticles (NPs) could allow biological imaging at substantial depths with enhanced contrast and high spatial resolution due to the absence of auto fluorescence in biological samples under infrared excitation. Here, we present the highly efficient infrared photoluminescence in GdF₃:Nd(3+) nanoparticles under 800 nm excitation within the hydrodynamic size limitations for bio-applications. The downconversion (Stokes emission) absolute quantum yields (QY) in powder, polymaleic anhydride-alt-1-octadicene (PMAO) coated powder and colloidal solutions have been investigated. QY measurements have revealed that downconversion (Stokes emission) QYs of approximately 5 ± 2 nm sized GdF₃:1% Nd(3+) colloidal NPs are 2000 times higher than those of efficient upconversion (UC) particles NaYF₄:20% Er/2% Yb of the same size. Furthermore, the utility of these NIR emitting nanoparticles for bioimaging probes has been demonstrated by confocal imaging and spectroscopic study.