gebhart/patrepeval huggingface dataset:
A rugged free energy landscape separates multiple functional RNA folds throughout denaturation (2008)

The dynamic mechanisms by which RNAs acquire biologically functional structures are of increasing importance to the rapidly expanding fields of RNA therapeutics and biotechnology. Large energy barriers separating misfolded and functional states arising from alternate base pairing are a well-appreciated characteristic of RNA. In contrast, it is typically assumed that functionally folded RNA occupies a single native basin of attraction that is free of deeply dividing energy barriers (ergodic hypothesis). This assumption is widely used as an implicit basis to interpret experimental ensemble-averaged data. Here, we develop an experimental approach to isolate persistent sub-populations of a small RNA enzyme and show by single molecule fluorescence resonance energy transfer (smFRET), biochemical probing and high-resolution mass spectrometry that commitment to one of several catalytically active folds occurs unexpectedly high on the RNA folding energy landscape, resulting in partially irreversible folding. Our experiments reveal the retention of molecular heterogeneity following the complete loss of all native secondary and tertiary structure. Our results demonstrate a surprising longevity of molecular heterogeneity and advance our current understanding beyond that of non-functional misfolds of RNA kinetically trapped on a rugged folding-free energy landscape.
High retention of genomic variation and fitness-related traits in the effective population of reintroduced wolves in Yellowstone National Park (2022)

Abstract Cooperatively breeding species exhibit numerous strategies to avoid mating with close relatives, inherently reducing effective population size. For species of management concern, accurate estimates of inbreeding and trait depression are crucial for the species’ future. We utilized genomic and pedigree data for Yellowstone National Park gray wolves to investigate the contributions of foundation stock lineages, genetic architecture of the effective population, and putative fitness consequences of inbreeding. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found over 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time, although we found high retention of genetic variation. Strikingly, the effective population carried a significantly lower level of genome-wide inbreeding coefficients and autozygosity with shorter decays for linkage disequilibrium relative to the non-breeding population. Lifespan and heterozygosity were higher in the effective population, although individuals who had their first litter at an older age also had higher inbreeding coefficients. Our findings highlight genetic contributions to fitness, and the importance of effective population size and gene flow to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges.
Synthesis of N-Substituted Indole Derivatives via PIFA-Mediated Intramolecular Cyclization (2006)

[Structure: see text] A variety of N-arylated and N-alkylated indole derivatives were synthesized by way of a phenyliodine bis(trifluoroacetate) (PIFA)-mediated intramolecular cyclization. This novel method allows for the construction of an indole skeleton by joining the N-atom on the side chain to the benzene ring at the last synthetic step. Other novel pyrrole-fused aromatic compounds can also be achieved by this method.
Baseline of visceral fat area and decreased body weight correlate with improved pulmonary function after Roux-en-Y Gastric Bypass in Chinese obese patients with BMI 28–35 kg/m2 and Type 2 diabetes: a 6-month follow-up (2015)

The baseline of VFA and weight loss induced by RYGB independently correlated with improved pulmonary function in Chinese patients.
Electrochemical decontamination of titanium dental implants. An in vitro biofilm model study (2023)

Electrochemical treatments had a bactericidal effect on this multispecies subgingival in vitro biofilm model, being the reduction more effective than the oxidative treatment.
Lattice Boltzmann method for multi-component, non-continuum mass diffusion (2007)

Recently, there has been a great deal of interest in extending the lattice Boltzmann method (LBM) to model transport phenomena in the non-continuum regime. Most of these studies have focused on single-component flows through simple geometries. This work examines an ad hoc extension of a recently developed LBM model for multi-component mass diffusion (Joshi et al 2007 J. Phys. D: Appl. Phys. 40 2961) to model mass diffusion in the non-continuum regime. In order to validate the method, LBM results for ternary diffusion in a two-dimensional channel are compared with predictions of the dusty gas model (DGM) over a range of Knudsen numbers. A calibration factor based on the DGM is used in the LBM to correlate Knudsen diffusivity to pore size. Results indicate that the LBM can be a useful tool for predicting non-continuum mass diffusion (Kn > 0.001), but additional research is needed to extend the range of applicability of the algorithm for a larger parameter space. Guidelines are given on using the methodology described in this work to model non-continuum mass transport in more complex geometries where the DGM is not easily applicable. In addition, the non-continuum LBM methodology can be extended to three-dimensions. An envisioned application of this technique is to model non-continuum mass transport in porous solid oxide fuel cell electrodes.
Center for Frontiers of Subsurface Energy Security: A DOE Energy Frontier Research Center. (2011)

Abstract not provided.
Simulation of Hydraulic Roll Bending System for Shape Control (2007)

For hydraulic roll bending system of profile control,the model about electro-hydraulic servo pressure control system was designed.In this model,flux-equation of servo valve was specially applied and some non-linear characteristics were considered.Furthermore,SIMULINK toolbox of MATLAB language software was used to solve mathematic model and simulation curves of some variables were obtained.At last,through changing simulation parameters,some characteristics of parameters affecting system characteristic were summarized.The calculation results are in good agreement with the experimental results.
Endoplasmic Reticulum Dynamics, Inheritance, and Cytoskeletal Interactions in Budding Yeast (2002)

The endoplasmic reticulum (ER) in Saccharomyces cerevisiae consists of a reticulum underlying the plasma membrane (cortical ER) and ER associated with the nuclear envelope (nuclear ER). We used a Sec63p-green fluorescent protein fusion protein to study motility events associated with inheritance of cortical ER and nuclear ER in living yeast cells. During M phase before nuclear migration, we observed thick, apparently rigid tubular extensions emanating from the nuclear ER that elongate, undergo sweeping motions along the cell cortex, and shorten. Two findings support a role for microtubules in this process. First, extension of tubular structures from the nuclear ER is inhibited by destabilization of microtubules. Second, astral microtubules, structures that undergo similar patterns of extension, cortical surveillance and retraction, colocalize with nuclear ER extensions. During S and G(2) phases of the cell cycle, we observed anchorage of the cortical ER at the site of bud emergence and apical bud growth. Thin tubules of the ER that extend from the anchored cortical ER display undulating, apparently random movement and move into the bud as it grows. Finally, we found that cortical ER morphology is sensitive to a filamentous actin-destabilizing drug, latrunculin-A, and to mutations in the actin-encoding ACT1 gene. Our observations support 1) different mechanisms and cytoskeletal mediators for the inheritance of nuclear and cortical ER elements and 2) a mechanism for cortical ER inheritance that is cytoskeleton dependent but relies on anchorage, not directed movement.
Anticoagulation Drug Therapy: A Review (2015)

Historically, most patients who required parenteral anticoagulation received heparin, whereas those patients requiring oral anticoagulation received warfarin. Due to the narrow therapeutic index and need for frequent laboratory monitoring associated with warfarin, there has been a desire to develop newer, more effective anticoagulants. Consequently, in recent years many novel anticoagulants have been developed. The emergency physician may institute anticoagulation therapy in the short term (e.g. heparin) for a patient being admitted, or may start a novel anticoagulation for a patient being discharged. Similarly, a patient on a novel anticoagulant may present to the emergency department due to a hemorrhagic complication. Consequently, the emergency physician should be familiar with the newer and older anticoagulants. This review emphasizes the indication, mechanism of action, adverse effects, and potential reversal strategies for various anticoagulants that the emergency physician will likely encounter.
Identification of a Developmental Gene Expression Signature, Including HOX Genes, for the Normal Human Colonic Crypt Stem Cell Niche: Overexpression of the Signature Parallels Stem Cell Overpopulation During Colon Tumorigenesis (2013)

Our goal was to identify a unique gene expression signature for human colonic stem cells (SCs). Accordingly, we determined the gene expression pattern for a known SC-enriched region--the crypt bottom. Colonic crypts and isolated crypt subsections (top, middle, and bottom) were purified from fresh, normal, human, surgical specimens. We then used an innovative strategy that used two-color microarrays (∼18,500 genes) to compare gene expression in the crypt bottom with expression in the other crypt subsections (middle or top). Array results were validated by PCR and immunostaining. About 25% of genes analyzed were expressed in crypts: 88 preferentially in the bottom, 68 in the middle, and 131 in the top. Among genes upregulated in the bottom, ∼30% were classified as growth and/or developmental genes including several in the PI3 kinase pathway, a six-transmembrane protein STAMP1, and two homeobox (HOXA4, HOXD10) genes. qPCR and immunostaining validated that HOXA4 and HOXD10 are selectively expressed in the normal crypt bottom and are overexpressed in colon carcinomas (CRCs). Immunostaining showed that HOXA4 and HOXD10 are co-expressed with the SC markers CD166 and ALDH1 in cells at the normal crypt bottom, and the number of these co-expressing cells is increased in CRCs. Thus, our findings show that these two HOX genes are selectively expressed in colonic SCs and that HOX overexpression in CRCs parallels the SC overpopulation that occurs during CRC development. Our study suggests that developmental genes play key roles in the maintenance of normal SCs and crypt renewal, and contribute to the SC overpopulation that drives colon tumorigenesis.
Effects of Plus and Minus Loads and Alloxan induced Diabetes on the Wax Ester of Carp Lipids (1979)

Carps of about 10 g weight were grouped and treated as follows, 1) removing swimbladder, 2) loading with lead belt, 3) stressed with laparotomy and vinyl belt, 4) loading with float, and 5) un loaded control. They were fed the diets supplemented with 1-hexadecanol, palmitic acid, and hexadecyl palmitate for 10, 20, and 30 d. The concentration ratio of wax esters (WE) to triglycerides (TG) were increased significantly in the plus loaded group and decreased in the minus loaded group in comparison to the stress and control groups. In either case the tendencies of ratios were 1>2>3=5>4 with a few exceptions in the case of palmitic acid supplement.The diabetic carps induced with alloxan donation were characterized by the liberation of free fatty acids and by the significant increase of WE against the reciprocal decrease of TG comparing to the controls. The higher incorporation of [1-14C] acetic acid into WE in the swimbladderectomized carp and that of [1-14C] 1-hexadecanol in the hepatopancreas homogenate of diabetic carp were obserbed, respectively. The relationship of the two lipid classes, namely WE and TG, seems to be regulated by the hydrostatic conditions concerning the buoyancy and through the metabolism of the ester counterparts of fatty acids.
Tools and Products (2008)

Department editor Dave Kasik highlights some of the new computer graphics tools and products on the market.
Innovative Treatment Alternatives for Oily Wastes Generated During the Exploration and Production of Oil and Gas (1992)

Abstract The Exploration and Production (E &amp; P) of oil and gas generates significant quantities of oily wastes, including oily drill cuttings, spent oil-based drilling muds, crude oil contaminated soils, crude oil tank bottoms, and reserve pit oily sludges. As E &amp; P companies have become increasingly aware of environmental liabilities (past, present, and future) associated with E &amp; P operations, they have sought alternatives to their present oily waste management practices. This paper discusses two innovative treatment alternatives for E&amp;P oily wastes, thermal desorption and biological liquid/solids treatment. These two technologies are fully developed and have just recently been demonstrated at full-scale on refinery oily wastes and at pilot-scale on E &amp; P oily wastes. Results of pilot-scale testing indicate that biological liquid/solids treatment of E &amp; P oily waste can significantly decrease the oil and grease (O &amp; G) fraction of the waste in a reasonable time period and for a reasonable cost (&amp;lt;$75/yd3). O &amp; G half-lives were measured at &amp;lt;15 days. Thermal desorption can reduce O &amp; G to &amp;lt; 1% in oily drill cuttings at a cost of &amp;lt;$100/yd3. Both technologies are currently being applied to the treatment of refinery oily wastes. An overview of both treatment technologies is presented in this paper, including process fundamentals, operational considerations, and results of recent pilot-scale testing on E &amp; P oily wastes.
Aprendre a empendre en el sector audiovisual. El MOOC com a eina per millorar l’empleabilitat (2015)

Es presenta la posada en marxa d’una accio d’innovacio docent, promoguda des de l'ensenyament de Comunicacio Audiovisual de la Facultat de Biblioteconomia i Documentacio de la UB, i portada a terme pel Grup Consolidat d’Innovacio Docent GIDC-CAV. Aquesta te com a objectius generals crear continguts i recursos digitals sobre l’emprenedoria en l'ambit de la comunicacio audiovisual en format MOOC i el desenvolupament i l’aplicacio d’eines de seguiment del proces d’avaluacio i d’aprenentatge.
Epilogue (2019)

On 21 June 1998 Germans celebrated the fiftieth anniversary of the introduction of the D-Mark, the German Mark. According to a January 1998 poll published in Der Spiegel, 56 percent of Germans were against the Euro. Many East German voters associated the Christian Democratic Party-east with the Christian Democrats in West Germany, especially when they saw Helmut Kohl endorsing it at mass rallies in Leipzig and elsewhere. The East German Socialist Democratic Party (SPD) is more like an American party in its structure than like the old SPD. In July 1997 Chancellor Kohl’s government produced a report on the “State of German Unity.” German security authorities estimated the number of rightwing group members at 6,400 in 1996 as compared with 6,200 in 1995. Many East Germans are skeptical about the European Union (EU) and the Euro, they overlook the fact that their part of Germany has received massive help from the European Investment Bank and from other EU funds.
Learning Risk-Aware Costmaps via Inverse Reinforcement Learning for Off-Road Navigation (2023)

The process of designing costmaps for off-road driving tasks is often a challenging and engineering-intensive task. Recent work in costmap design for off-road driving focuses on training deep neural networks to predict costmaps from sensory observations using corpora of expert driving data. However, such approaches are generally subject to over-confident mispredictions and are rarely evaluated in-the-loop on physical hardware. We present an inverse reinforcement learning-based method of efficiently training deep cost functions that are uncertainty-aware. We do so by leveraging recent advances in highly parallel model-predictive control and robotic risk estimation. In addition to demonstrating improvement at reproducing expert trajectories, we also evaluate the efficacy of these methods in challenging off-road navigation scenarios. We observe that our method significantly outperforms a geometric baseline, resulting in 44% improvement in expert path reconstruction and 57% fewer interventions in practice. We also observe that varying the risk tolerance of the vehicle results in qualitatively different navigation behaviors, especially with respect to higher-risk scenarios such as slopes and tall grass.
Formation and Evaluation of a Two-Phase Polymer System in Human Plasma as a Method for Extracellular Nanovesicle Isolation (2021)

The aim of the study was to explore the polyethylene glycol-dextran two-phase polymer system formed in human plasma to isolate the exosome-enriched fraction of plasma extracellular nanovesicles (ENVs). Systematic analysis was performed to determine the optimal combination of the polymer mixture parameters (molecular mass and concentration) that resulted in phase separation. The separated phases were analyzed by nanoparticle tracking analysis and Raman spectroscopy. The isolated vesicles were characterized by atomic force microscopy and dot blotting. In conclusion, the protein and microRNA contents of the isolated ENVs were assayed by flow cytometry and by reverse transcription followed by quantitative polymerase chain reaction (RT-qPCR), respectively. The presented results revealed the applicability of a new method for plasma ENV isolation and further analysis with a diagnostic purpose.
Glycine receptors in a population of adult mammalian cones (2006)

Glycinergic interplexiform cells provide a feedback signal from the inner retina to the outer retina. To determine if cones receive such a signal, glycine was applied on cultured porcine cone photoreceptors recorded with the patch clamp technique. A minor population of cone photoreceptors was found to generate large currents in response to puff application of glycine. These currents reversed close to the calculated equilibrium potential for chloride ions. These glycine-elicited currents were sensitive to strychnine but not to picrotoxin consistent with the expression of alpha-beta-heteromeric glycine receptors. Glycine receptors were also activated by taurine and beta-alanine. The glycine receptor antibody mAb4a labelled a minority of the cone photoreceptors identified by an antibody specific for cone arrestin. Finally, expression of the beta subunit of the glycine receptor was demonstrated by single cell RT-PCR in a similar proportion (approximately 13%) of cone photoreceptors freshly isolated by lectin-panning. The identity of cone photoreceptors was assessed by their specific expression of the cone arrestin mRNA. The population of cone photoreceptors expressing the glycine receptor was not correlated to a specific colour-sensitive subtype as demonstrated by single cell RT-PCR experiments using primers for S opsin, cone arrestin and glycine receptor beta subunit. This glycine receptor expression in a minority of cones defines a new cone population suggesting an unexpected role for glycine in the visual information processing in the outer retina.
Athermalizing Refractive Optics with Fluid Lenses (2002)

ABSTRACT. Astronomical optics may encounter a wide range of nighttime temperatures (∼10C to20C) at mountaintop observatories. Complex refractive optics used in high-performance spectrographs and focal reducers may perform poorly at temperature extremes unless special care is taken in their design. Refocusing will not always restore image quality, and thermally induced focal length changes may introduce troublesome image motion. We describe the techniques that we have used to predict the thermal behavior of the Binospec Spectrograph, an instrument under development for the converted Multiple Mirror Telescope. This thermal analysis must account for (1) the change in optical power due to thermal expansion of the optical elements, (2) thermal variations in the refractive indices of the optical elements, and (3) element respacings due to the interplay between the thermal expansions of the optical elements and cell materials. Binospec’s multiplets are fluid coupled to reduce the reflection losses that would occur at glass-air surfaces; to athermalize the Binospec optics, we form weak lenses in the optical coupling fluid within multiplets. The large variation of the coupling fluid’s refractive index with temperature allows these weak fluid lenses to correct thermal changes in the optical elements and cell. This athermalization technique is attractive because it introduces no additional mechanical complexity. 1.
Evaluation of antioxidant properties of a new compound, pyrogallol-phloroglucinol-6,6'-bieckol isolated from brown algae,Ecklonia cava (2011)

In this study, antioxidant and free radical scavenging activities of the natural antioxidative compound, pyrogallol-phloroglucinol-6,6'-bieckol (PPB) isolated from brown algae, Ecklonia cava was assessed in vitro by measuring the radical scavenging activities (DPPH, alkyl, hydroxyl, and superoxide) using electron spin resonance (ESR) spectrometry, intracellular reactive oxygen species (ROS) scavenging activity, and DNA damage assay. According to the results of these experiments, the scavenging activity PPB against difference radicals was in the following order: DPPH, alkyl, hydroxyl, and superoxide radicals (IC(50); 0.90, 2.54, 62.93 and 109.05 µM). The antioxidant activities of PPB were higher than that of the commercial antioxidant, ascorbic acid. Furthermore, PPB effectively inhibited DNA damage induced by H(2)O(2). These results suggest that the natural antioxidative compound, PPB, can be used by the natural food industry.
A numerical investigation of the resin flow front tracking applied to the RTM process (2011)

Resin Transfer Molding (RTM) is largely used for the manufacturing of high-quality composite components and the key stage during processing is the resin infiltration. The complete understanding of this phenomenon is of utmost importance for efficient mold construction and the fast production of high quality components. This paper investigates the resin flow phenomenon within the mold. A computational application was developed to track the resin flow-front position, which uses a finite volume method to determine the pressure field and a FAN (Flow Analysis Network) technique to track the flow front. The mass conservation problem observed with traditional FE-CV (Finite Element-Control Volume) methods is also investigated and the use of a finite volume method to minimize this inconsistency is proposed. Three proposed case studies are used to validate the methodology by direct comparison with analytical and a commercial software solutions. The results show that the proposed methodology is highly efficient to determine the resin flow front, showing an improvement regarding mass conservation across volumes.