gebhart/patrepeval huggingface dataset:
Bacillus subtilis Spore Display of Laccase for Evolution under Extreme Conditions of High Concentrations of Organic Solvent (2014)

Protein libraries were displayed on the spore coat of Bacillus subtilis, and this method was demonstrated as a tool for directed evolution under extreme conditions. Escherichia coli, yeast, and phage display suffer from protein folding, and viability issues. On the other hand, spores avoid folding concerns by the natural sporulation process, and they remain viable under harsh chemical and physical environments. The naturally occurring B. subtilis spore coat protein, CotA, was evolved for improved activity under conditions of high organic solvent concentrations. CotA is a laccase, which is a copper-containing oxidase enzyme. A CotA library was expressed on the spore coat, and ∼ 3000 clones were screened at 60% dimethyl sulfoxide (DMSO). A Thr480Ala variant (Thr480Ala-CotA) was identified that was 2.38-fold more active than the wild-type CotA. In addition, Thr480Ala-CotA was more active with different concentrations of DMSO ranging from 0 to 70%. The mutant was also found to be more active compared with the wild-type CotA in different concentrations of methanol, ethanol, and acetonitrile.
Glimpse: Fall 2001 (2001)

- A. B. Johnson, Treatise on Language, or the Relation Which Words Bear to Things, 1836 Science - a Human Activity Can science improve on our ability to perceive the truth? San Francisco Chronicle's Jon Carroll discusses the difficulties of using a human (and therefore flawed) scientific tool to detect lies: Science is not some monolithic body of knowledge; it's a mishmash of old beliefs, new beliefs, superstitions, guesses, counter-arguments and disputes. It's not useless - far from it - but it has to be understood as a cultural artifact, a production of the flawed human mind.... polygraph, the writings machine, measures small changes in heart rate, respiration, perspiration and other bodily functions. theory behind the polygraph is that people who lie get nervous when they lie, and the nervousness is reflected in the polygraph results.... reasons that people get nervous are many and various; only some of them have to do with guilty knowledge of a crime. There are sociopaths who have guilty knowledge, but it does not make them nervous. And there are tricks - you can bite your tongue at odd times, for instance, to confuse the control responses. Indeed, one of the interesting things about polygraphs is that they are only as good as their operators. An experienced polygraph operator can tease info out of data that others cannot. It seems like science, but it's actually intuition.... A thermometer, for instance, does not require intuitive interpretation to be useful. thermometer, we may say, is good science - provided it is placed in the right location and calibrated correctly. raw data of a polygraph may be as good as the raw data of a good thermometer, but the interpretation is just an art form, like Afro-Cuban dancing. And yet, because we want to believe - even though the legal system itself doesn't believe - we keep using polygraphs. We keep attaching significance to their results, even though that's wrong. In My Opinion If the WORD is not the thing, how about the thought? Does a thought constitute an act? Does thinking about doing something have the same effect as doing that thing? I came across this proverb on a quotes page (http://www.geocities.com/~spanoudi/topic-v1.html) The willing contemplation of vice is vice. I believe this proverb confuses two levels of abstraction in such a way as to result in confusion and needless difficulty in those who would try to act in accordance with it. consequences of a thought that does not lead to action, in my mind, differs in meaningful ways from the consequences of taking the action, regardless of any evaluation of the morality of the action itself. Does this medium become the message? Advertising delivered in a very unusual place. …
Mobile projectors versus mobile displays (2012)

Mobile projectors are gaining momentum, with many pocket sized products reaching the market and projector phones being close to production. Although the usefulness of such devices for entertainment, collaboration as well as many other tasks is obvious, it is not yet clear how their limitations in terms of image quality, brightness and jitter due to hand motion might affect performance. To answer these questions, we conduct two experiments based on traditional psychophysical methods. Using a visual search and a text reading study we compare task performance on a mobile phone display and a mobile projector. In addition, we examine whether performance is affected when devices are handheld rather than placed on a stable surface. We find that the perceived task difficulty is worse on the mobile projector cases for both tasks, while only in the visual search task leads to quantitatively worse performance. In contrast, we find that the stability of the projection plays no role in task performance but tasks performed on a handheld device may be perceived as harder to complete.
Configurable Low‐Cost Plotter Device for Fabrication of Multi‐Color Sub‐Cellular Scale Microarrays (2014)

The construction and operation of a low-cost plotter for fabrication of microarrays for multiplexed single-cell analyses is reported. The printing head consists of polymeric pyramidal pens mounted on a rotation stage installed on an aluminium frame. This construction enables printing of microarrays onto glass substrates mounted on a tilt stage, controlled by a Lab-View operated user interface. The plotter can be assembled by typical academic workshops from components of less than 15,000 Euro. The functionality of the instrument is demonstrated by printing DNA microarrays on the area of 0.5 cm2 using up to three different oligonucleotides. Typical feature sizes are 5 μm diameter with a pitch of 15 μm, leading to densities of up to 10(4)-10(5) spots/mm2. The fabricated DNA microarrays are used to produce sub-cellular scale arrays of bioactive epidermal growth factor peptides by means of DNA-directed immobilization. The suitability of these biochips for cell biological studies is demonstrated by specific recruitment, concentration, and activation of EGF receptors within the plasma membrane of adherent living cells. This work illustrates that the presented plotter gives access to bio-functionalized arrays usable for fundamental research in cell biology, such as the manipulation of signal pathways in living cells at subcellular resolution.
Downscaling of monthly precipitation using CMIP5 climate models operated under RCPs (2016)

ABSTRACT Downscaling of general circulation model ( GCM ) outputs extracted from CMIP5 datasets to monthly precipitation for the Gediz Basin, Turkey, under Representative Concentration Pathways ( RCPs ) was performed by statistical downscaling models, multi‐ GCM ensemble and bias correction. The output databases from 12 GCMs were used for the projections. To determine explanatory predictor variables, the correlation analysis was applied between precipitation observed at 39 meteorological stations located over the Basin and potential predictors of ERA‐I nterim reanalysis data. After setting both artificial neural networks and least‐squares support vector machine‐based statistical downscaling models calibrated with determined predictor variables, downscaling models producing the most suitable results were chosen for each meteorological station. The selected downscaling model structure for each station was then operated with historical and future scenarios RCP 4.5, RCP 6.0 and RCP 8.5. Afterwards, the monthly precipitation forecasts were obtained from a multi‐ GCM ensemble based on Bayesian model averaging and bias correction applications. The statistical significance of the foreseen changes for the future period 2015–2050 was investigated using Student's t test. The projected decrease trend in precipitation is significant for the RCP8 .5 scenario, whereas it is less significant for the RCP4 .5 and RCP6 .0 scenarios.
Modeling and design of LTI controllers for multirate systems (2009)

In this paper we provide a frequency domain approach to model multirate SISO systems which facilitates design of linear time-invariant (LTI) controllers. To illustrate the approach we consider a dual-rate system with slow output measurements and fast control actions. We obtain necessary and sufficient conditions for the existence of stabilizing LTI controllers for which model matching is also achieved with a desired single-rate system. Moreover, a solution is given to the problem of parametrizing the set of such LTI controllers.
FcγR receptors activate MAP kinase and up-regulate the cyclooxygenase pathway without increasing arachidonic acid release in monocytic cells (2002)

THP-1 monocytic cells were stimulated with IgG-ovalbumin equivalence immune complexes (IC) and mAb reacting with both FcgammaRI and FcgammaRIIA. All of these stimuli were capable of activating the cells; however, different patterns of response were observed as regards activation of the p42-MAP/ERK kinase, triggering of the NF-kappaB/Rel system, production of chemotactic cytokines, and induction of the expression of cyclooxygenase-2 (COX-2). Activation of p42-MAP/ERK kinase was a constant finding, which occurred regardless of the type of stimulus applied, for instance, homotypic stimulation of a single type of receptor by cross-linking with specific mAb or heterotypic stimulation with both types of antibodies and IC. However, the activation of the MAP/ERK kinase cascade was not connected to the triggering of cytosolic phospholipase A(2) (cPLA(2)) and arachidonic acid (AA) release. The heterotypic stimulation of FcgammaR induced the expression of COX-2 in a time and dose-dependent manner and activated the NF-kappaB system as judged from the degradation of IkappaB-alpha protein. In summary, the present data indicate that activation of the p42-MAP/ERK pathway occurs after cross-linking FcgammaRI and FcgammaRIIA receptors in monocytic cells; however, this is not coupled to the cPLA(2) route, which leads to the release of AA. Noteworthy,heterotypic activation involving combined cross-linking of both FcgammaRI and FcgammaRIIA has a robust effect on the oxidative metabolism of AA by a mechanism involving kappaB-dependent trans-activation of COX-2.
Using Outcrop Exposures on the Road to Yellowknife Bay to Build a Stratigraphic Column, Gale Crater, Mars (2013)

Since landing in Gale Crater on August 5, 2012, the Curiosity rover has driven 450 m east, descending approximately 15 m in elevation from the Bradbury landing site to Yellowknife Bay. Outcrop exposure along this drive has been discontinuous, but isolated outcrops may represent windows into underlying inplace stratigraphy. This study presents an inventory of outcrops targeted by Curiosity (Figs. 1-2), grouped by lithological properties observed in Mastcam and Navcam imagery. Outcrop locations are placed in a stratigraphic context using orbital imagery and first principles of stratigraphy. The stratigraphic models presented here represent an essential first step in understanding the relative age relationships of lithological units encountered at the Curiosity landing site. Such observations will provide crucial context for assessing habitability potential of ancient Gale crater environments and organic matter preservation.
Phosphosilicate Glass Passivation for ULSI Cu Metallization (1992)

Phosphosilicate glass (PSG) passivation for Cu metallization is proposed, and the Cu diffusion rate into Si substrates through various oxide structures is measured quantitatively.Cu diffusion is suppressed effectively by the PSG passivation resulting in reduction of the diffused Cu atoms to about an order of magnitude less than when passivated by nondoped SiO., films.The passivation is effective when the annealing temperature is less than 600~ The apparent activation energy of Cu diffusion for the nondoped SiO2/Si substrate and PSG/nondoped SiO~/Si is 1.2 and 1.6 eV, respectively.However, most of the diffused Cu precipitates near the oxide/Si substrate interface and the amount of the diffused Cu is comparable to the limit for ordinary device contamination.Thus, further improvement or optimization of the passivation layer structure is desired.
Comparison of Arthroscopic Microfracture for Osteochondral Lesions of the Talus With and Without Subchondral Cyst (2015)

OLT with and without subchondral cysts treated with arthroscopic microfracture showed similarly good clinical results. The study results suggest that microfracture could be a primary treatment strategy for treating small to midsized OLT regardless of the existence of subchondral cysts.
EFFECTS OF INCREASING UV‐B RADIATION DUE TO OZONE DEPLETION ON PHOTOSYNTHESIS OF ANTARCTIC CYANOBACTERIA (2000)

Ground level ultraviolet‐B (UV‐B; 290–320 nm) fluxes in Antarctica have been increasing due to stratospheric ozone depletion. Although mat‐forming cyanobacteria are major component of freshwater algal biomass in Antarctica, little is known about their response to increasing ultraviolet radiation (UVR). The present study evaluated the sensitivity to UVR of two strains of mat‐forming cyanobacteria with different cell size, Phormidium murrayi (6.0 x 3.2 μm) and Schizothrix calcicola (2.2 x 2.3 μm). Cyanobacterial photosynthesis was measured under different UV spectral quality and quantity achieved by polychromatic filters with different cutoff wavelengths and neutral density screens. The productivity and irradiance data were used to generate biological weighting functions (BWF) for the assessment of UV inhibition on photosynthesis. The kinetics of UV inhibition, as determined by PAM fluorometry, differed between the two species so that inhibition of P. murrayi and S. calcicola were modeled based on UV‐irradiance and cumulative exposure, respectively. After a one hour exposure, BWF's did not differ between the two isolates of cyanobacteria despite their differences in cell size. To evaluate the negative impact of increased UV‐B exposure due to ozone depletion on cyanobacteria, the BWF's were applied to two solar spectra obtained from McMurdo Station, one on a day when the ozone hole was prominent (O 3 = 170 Dobson units; DU = 10‐3 cm O 3 ), and the other on a day with high ozone concentration (O 3 = 328 DU). The decrease in ozone level would reduce productivity by 3–8%. Seasonal variation of UVR has a bigger impact on cyanobacterial productivity than ozone depletion.
A physics-based compact model for FETs from diffusive to ballistic carrier transport regimes (2014)

This paper discusses a new emission-diffusion-based compact model for FETs to describe carrier transport in both short and long channel devices. The new model provides a description of the current at any drain bias without empirical fitting and predicts the injection velocity (device on-current). The new model is fully consistent with the widely used virtual-source model for describing transport in quasi-ballistic transistors. The accuracy of the new model is demonstrated by comparison with measured I-V data of III-V HEMTs and ETSOI silicon MOSFETs.
Photosystem I: Structural and functional studies. (1994)

In this article we describe the current knowledge of the structure of photosystem I, in particular the cyanobacterial form of this photosynthetic complex. We also describe recent experiments on the stability of the complex in detergents and denaturants and discuss the results in relation to the functional properties of the complex in electron transport across the thylakoid membrane.
Pediatric Oncology Providers’ Attitudes and Practice Patterns Regarding Fertility Preservation in Adolescent Male Cancer Patients (2015)

This study illustrates an unmet need in the education of pediatric oncology providers, as knowledge gaps and discomfort are common themes reported by health care professionals within the context of adolescent male FP care. In addition, this study reveals a high level of receptiveness to FP training by these same providers.
Biometrie – Beschleuniger oder Bremser von Identitätsdiebstahl (2009)

Pseudomonas stutzeri, isolated from crude oil-contaminated soil, was used to degrade diesel oil. Of three surfactants, 120 mg rhamnolipids 1(-1) significantly increased degradation of diesel oil giving 88% loss after 14 days compared to 54% loss without the surfactant. The system with rhamnolipids was characterised by relatively high particle homogeneity. However, the addition of saponins to diesel oil caused the cells to aggregate (the polydispersity index: 0.542) and the biodegradation of diesel oil was only 46%. The cell yield was 0.22 g l(-1).
Derandomizing Directed Random Walks in Almost-Linear Time (2022)

In this article, we present the first deterministic directed Laplacian L systems solver that runs in time almost-linear in the number of non-zero entries of L. Previous reductions imply the first deterministic almost-linear time algorithms for computing various fundamental quantities on directed graphs including stationary distributions, personalized PageRank, hitting times and escape probabilities. We obtain these results by introducing partial symmetrization, a new technique that makes the Laplacian of an Eulerian directed graph ``less directed'' in a useful sense, which may be of independent interest. The usefulness of this technique comes from two key observations: Firstly, the partially symmetrized Laplacian preconditions the original Eulerian Laplacian well in Richardson iteration, enabling us to construct a solver for the original matrix from a solver for the partially symmetrized one. Secondly, the undirected structure in the partially symmetrized Laplacian makes it possible to sparsify the matrix very crudely, i.e. with large spectral error, and still show that Richardson iterations convergence when using the sparsified matrix as a preconditioner. This allows us to develop deterministic sparsification tools for the partially symmetrized Laplacian. Together with previous reductions from directed Laplacians to Eulerian Laplacians, our technique results in the first deterministic almost-linear time algorithm for solving linear equations in directed Laplacians. To emphasize the generality of our new technique, we show that two prominent existing (randomized) frameworks for solving linear equations in Eulerian Laplacians can be derandomized in this way: the squaring-based framework of Cohen, Kelner, Peebles, Peng, Rao, Sidford and Vladu (STOC 2017) and the sparsified Cholesky-based framework of Peng and Song (STOC 2022).
Performance Comparison and Applications of Sparsity Based Techniques for Denoising of ECG Signal (2019)

ECG denoising using different kinds of scientific techniques and methods has been an interesting research area among the signal processing research fraternity. There are various kinds of noises that interfere with ECG signal at different levels. Powerline interference, baseline wander noise and electromyography noise are at highest priority to remove from the desired signal. Several sparsity based adaptive and wavelet digital filtering techniques have been proposed in previous investigations for denoising of ECG signal. But there qualitative and quantitative performance analysis against each other is lacking in the literature. In this paper, we reviewed various sparsity based noise reduction techniques of adaptive and wavelet algorithms. Using the benchmark dataset of MIT/BIH, a detailed and fair comparison of LMS, RLS and DWT were implemented for their performance analysis. The qualitative analysis has been presented in terms of the morphology differences in the denoised signal and the quantitative analysis is presented in terms of various performance measuring parameters of signal-to-noise ratio (SNR), mean square error (MSE), percentage root mean square difference (PRD) and peak-signal-to-noise ratio (PSNR). The obtained results show that adaptive filtering using RLS algorithm performs better in more dense noisy conditions whereas the wavelet filtering is better to perform in less noisy conditions. Further, all three algorithms were tested on different kinds of noises like power-line interference, baseline wander and abrupt shift in the ECG data, where, DWT based filtering approach was found superior on removal of powerline and baseline wander interferences, but it fails to remove the abrupt shift kind of noise. The abrupt shift noise was best removed by both LMS and RLS adaptive algorithms but at the cost of low speed and poor quality. Thus, the presented optimized analysis of advanced three sparsity based filtering techniques would provide great potential benefits in biomedical applications of ECG signal processing, feature extraction, analysis and other related fields.
Surgeon Specialty and Outcomes After Elective Spine Surgery (2014)

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The mucin-degradation strategy ofRuminococcus gnavus: The importance of intramoleculartrans-sialidases (2016)

We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit.
The Human Proteoform Project: Defining the human proteome (2023)

Proteins are the primary effectors of function in biology, and thus, complete knowledge of their structure and properties is fundamental to deciphering function in basic and translational research. The chemical diversity of proteins is expressed in their many proteoforms, which result from combinations of genetic polymorphisms, RNA splice variants, and posttranslational modifications. This knowledge is foundational for the biological complexes and networks that control biology yet remains largely unknown. We propose here an ambitious initiative to define the human proteome, that is, to generate a definitive reference set of the proteoforms produced from the genome. Several examples of the power and importance of proteoform-level knowledge in disease-based research are presented along with a call for improved technologies in a two-pronged strategy to the Human Proteoform Project.