gebhart/patrepeval huggingface dataset:
Lipid Biosynthetic Genes Affect Candida albicans Extracellular Vesicle Morphology, Cargo, and Immunostimulatory Properties (2015)

Microbial secretion is integral for regulating cell homeostasis as well as releasing virulence factors during infection. The genes encoding phosphatidylserine synthase (CHO1) and phosphatidylserine decarboxylase (PSD1 and PSD2) are Candida albicans genes involved in phospholipid biosynthesis, and mutations in these genes affect mitochondrial function, cell wall thickness, and virulence in mice. We tested the roles of these genes in several agar-based secretion assays and observed that the cho1Δ/Δ and psd1Δ/Δ psd2Δ/Δ strains manifested less protease and phospholipase activity. Since extracellular vesicles (EVs) are surrounded by a lipid membrane, we investigated the effects of these mutations on EV structure, composition, and biological activity. The cho1Δ/Δ mutant releases EVs comparable in size to wild-type EVs, but EVs from the psd1Δ/Δ psd2Δ/Δ strain are much larger than those from the wild type, including a population of >100-nm EVs not observed in the EVs from the wild type. Proteomic analysis revealed that EVs from both mutants had a significantly different protein cargo than that of EVs from the wild type. EVs were tested for their ability to activate NF-κB in bone marrow-derived macrophage cells. While wild-type and psd1Δ/Δ psd2Δ/Δ mutant-derived EVs activated NF-κB, the cho1Δ/Δ mutant-derived EV did not. These studies indicate that the presence and absence of these C. albicans genes have qualitative and quantitative effects on EV size, composition, and immunostimulatory phenotypes that highlight a complex interplay between lipid metabolism and vesicle production.
The influence of oxygen at epitaxial Si/Si substrate interface for 0.1 μm epitaxial Si channel N-MOSFETs grown by UHV-CVD (2002)

Very high gm values of intrinsic doped epitaxial channel MOSFETs compared with those of bulk MOSFETs has been experimentally confirmed for the first time. It has been found that preheating of the wafer before the UHV-CVD epitaxial growth is critically important to improve the crystal quality of the epitaxial layer and thus to obtain the high gm values. By adopting 700/spl deg/C 5 minutes preheating, a very high gm value of 630 mS/mm was obtained for a 0.1 /spl mu/m epitaxial channel n-MOSFET.
Principal Component Analysis (2018)

However, in some scenarios, such as clinical trials, the number of data points is limited (given the difficulty in collecting samples from many individuals), and the amount of information collected is high (think of how much information labs give us based on small samples of collected blood).
Enhancing colour image quality in television displays (1999)

A general framework and first experimental results are presented for a computational model for achieving optimal colour appearance of natural images on television displays. The image quality framework includes: (a) analysis of relationships between overall image quality and quality-related attributes; (b) analysis of relationships between the quality-related attributes and their psychometric correlates; (c) analysis of relationships between the psychometric correlates and the physical parameters of a display; and (d) development of an adaptive algorithm for optimal image appearance by manipulation of the display’s parameters. In the psychophysical experiments, observers viewed a series of colour images on high-end consumer television display, to investigate the relationships between overall image quality and four quality-related attributes: brightness rendering, chromatic rendering, visibility of details and overall naturalness. The results of the experiments suggest that these attributes are interrelated. Some subjects can more easily separate the quality-related attributes than other subjects. The overall image quality can be modelled as a linear combination of the brightness rendering and chromatic rendering judgements with different weights, which are subject dependent. The optimal value of the overall image quality judgements is slightly skewed towards the darker end of the lightness scale and towards the more colourful end of the chroma scale. The degree of skewedness depends on image content.
Flow of microgel capsules through topographically patterned microchannels (2007)

We investigated the flow dynamics of microgel capsules in topographically patterned microfluidic devices. For microgels flowing through channel constrictions, or orifices, we observed three phenomena: (i) the effect of confinement, (ii) the role of interactions between the microgels and the channel surface, and (iii) the effect of the velocities of microgels prior to their passage through an orifice. We studied negatively charged alginate microgels and positively charged alginate microgels coated with N-(2-hydroxy)propyl-3-trimethylammonium chitosan chloride (HTCC). Aqueous dispersions of microgels were driven through poly(dimethyl siloxane) microchannels carrying a weak negative surface charge. The velocity of the continuous phase, and hence, the velocity of the microgels increased as they passed through topographically patterned orifices. Alginate microgels were observed to have a larger increase in velocity relative to HTCC-coated alginate microgels. This effect, which was attributed to electrostatic attraction or repulsion, was found to be strongest for orifices with dimensions close to the microgel diameter. For example, when 75 microm-diameter microgels flowed through a 76 microm orifice, alginate gels (negatively charged) experienced a 2x greater increase in velocity than HTCC-coated (positively charged) microgels. This effect was exaggerated at lower initial flow rates. For example, when 75 microm-diameter microgels flowed through an 80 microm orifice, a two-fold difference in the velocity changes of the two microgel types was observed when the initial flow rate was 275 microm s(-1), while a three-fold difference in velocity changes was observed when the initial flow rate was 130 microm s(-1). We speculate that these studies will be useful for modeling the flow of suspensions of cells or other biologically relevant particles for a wide range of applications.
Gender Differences in the Quality of Life of Patients with Liver Cirrhosis Related to Hepatitis C after Liver Transplantation (2013)

These results show a significant effect of the gender variable on QoL in HCV patients.
Lowering Error Floors Using Dithered Belief Propagation (2010)

We propose dithered belief propagation decoding algorithms to reduce the number of decoding failures of a belief propagation decoder and lower the error floor. The random nature of the algorithms enables a low hardware complexity compared to previously reported techniques. We introduce two dithering methods that target check node operations and channel input values, respectively. We present simulation results that confirm the error rate gains in the floor region, and that relate those gains with the maximum number of decoding iterations. The results show that the first algorithm can achieve good error rate gains with a low iteration limit. For the second algorithm, results show that with a large iteration limit, high FER gains are possible. Furthermore the average time complexity remains the same as that of a standard belief propagation algorithm.
<title>Data handling and validation from Wisconsin's remote vehicle emissions sensing studies</title> (1995)

The Wisconsin Department of Natural Resources and Department of Transportation (WDOT) are conducting a joint study to determine the effectiveness of applying optical sensing techniques to vehicular emission monitoring. Two field studies using Remote Sensing Technologies, Inc. remote sensing equipment was conducted in 1993 and 1994. This paper describes the data handling and data validation activities of these studies, including identification of data elements. Data handling was performed by the same people who conducted the 180,000 vehicle emissions tests. A contemporary commercial spreadsheet from Borland International, Inc. was used to import the raw data from the remote sensor. The data was reviewed with the spreadsheet then moved into a Borland relational database product. The relational database permitted structured queries against databases of vehicle inspection/maintenance (I/M) data from WDOT, National Insurance Crime Bureau, and EnviroTest. We determined effective cut points for vehicles of different ages which delineated high-polluting vehicles (gross emitters) from vehicles in compliance. The I/M data was also used to intercompare the remote sensing results with traditional testing results. Remote sensing test results were then compared for errors of commission and omission with respect to I/M test. Ultimately, this remote sensing database technique could serve as a means for identifying gross emitters who would be required to visit an I/M facility for an out-of-cycle emissions test.
Changes in conjunctival clusterin expression in severe ocular surface disease. (2002)

Clusterin expression is markedly reduced in the pathologic, keratinized ocular surface epithelium, suggesting its importance in maintaining the ocular surface epithelium as a nonkeratinizing epithelium.
The role of minor groove functional groups in DNA hydration (2003)

Here we describe the crystal structure of modified [d(CGCGAATTCGCG)]2 refined to 2.04 A. The modification, which affects only the two thymines at the central ApT step, involves isosteric removal of the 2-keto oxygen atoms and substitution of the N1 nitrogen with carbon. The crystal structure reveals the ability of this modified thymine to effectively base pair with adenine in [d(CGCGAAtTCGCG)]2. The structure also suggests that the minor groove 'spine of hydration' is destabilized but essentially intact.
232: THE COMPENSATORY RESERVE INDEX IN CONGENITAL CARDIAC INTENSIVE CARE: PRELIMINARY DATA AND UTILITY (2018)

Ehrmann, Daniel; Leopold, David; Chopra, Tavishi; Moulton, Steven; Kim, John Author Information
Cure-PROs: Next-generation targeted protein degraders. (2023)

e15101 Background: Many proteins, including transcription factors and scaffolding proteins, are not amenable to targeting by traditional small molecule inhibitors due to the lack of a well-defined binding pocket or active site. Proteolysis-Targeting Chimeras (PROTACs) are a new class of hetero-bifunctional molecules that bind both a target protein and an E3 ubiquitin ligase, bringing the two into proximity for appending ubiquitin, and subsequently marking the target protein for proteasomal degradation. Currently, thirteen PROTACs are in clinical trials for oncology indications. However, the clinical utility of PROTACs is challenged by their large size and long development timelines. Also, resistance mutations in the E3 ligase or transporter overexpression inevitably evolve. Thus, a new platform for small-molecule degraders that enables ultra-rapid drug development timelines, efficient cellular uptake, and can be developed to overcome innate and acquired drug resistance is needed. Methods: Coferons, developed in our laboratory, are small molecules that self-assemble upon binding to a target, where they form reversible covalent dimers through bio-orthogonal linker chemistries. We have combined features of the Coferon platform and PROTACs to generate CURE-PROs (Combinatorial Ubiquitination REal-time PROteolysis), consisting of one target protein ligand and one E3 ligase ligand that form reversible heterodimers that lead to targeted protein degradation within cells. By modifying known ligands for BRD4, and the E3 ubiquitin ligases Cereblon, VHL, and MDM2, with linkers able to reversibly join the BRD4 to the ligase ligands, we synthesized libraries of CURE-PRO monomers that can be combined to create thousands of CURE-PRO dimer combinations. We explored whether this platform could yield meaningful BRD4 degradation in vitro and in vivo. Results: Rapid combinatorial cell-based screening identified several BRD4-E3 ligase CURE-PRO combinations that induced greater than 50% BRD4 degradation, with the most promising CURE-PRO pairs achieving more than 95% protein degradation. Consistent with a PROTAC mechanism-of-action, successful CURE-PRO combinations confirmed significant protein degradation which was inhibited by proteasome inhibitors or competition with parent ligands. Significant BRD4 degradation was also observed in mice bearing bilateral human xenograft tumors, confirming CURE-PRO proof-of-mechanism in vivo. Conclusions: The combinatorial nature of our platform has the potential to significantly reduce synthesis time and effort to identify the optimal linker length and E3 ligase for each target protein. The CURE-PRO platform consists of expanding libraries of monomers for both additional oncoprotein targets as well as E3 ligases, which can be redeployed to shorten lead development timelines.
LONG-TERM PERFORMANCE OF HOLLOW FIBRE MEMBRANE SOLVENT EXTRACTION MODULES USED FOR Cr(VI) RECOVERY FROM ELECTROPLATING RINSE WATER (2000)

ABSTRACT The long-term performance of a hollow fibre membrane solvent extraction unit has been investigated for the recovery of Cr(VI) from plating rinse water. A pilot scale experiment was performed in a local electro-plating plant using-membrane modules with an area of 0·17 m2. The separation of Cr(VI) from the rinse liquor was carried out in two hollow fibre membrane modules, and is compared with a single module supported liquid membrane (SLM) which was also used in the same service. The Cr(VI) flux declined gradually to half the initial value after 25 days. This was found to be due to the membrane fouling combined with the degradation of organic solvent. The loss of organic solution was initially severe but stabilized after a few days and became negligible. The flux in the SLM mode appeared similar but the life time was very short, less than a day, however continuous operation was attainable by periodic replenishment of the membrane. Using both designs, it has been shown that Cr(VI) could be extracted from dilute feed into the stripping solution with an enrichment factor of 10 – 20 times using this technique.
Mild and Robust Redox‐Neutral Pd/C‐Catalyzed Lignol β‐O‐4′ Bond Cleavage Through a Low‐Energy‐Barrier Pathway (2015)

A Pd/C catalyzed redox neutral C¢O bond cleavage of 2-aryloxy-1-arylethanols has been developed. The reactions are carried out at 80 °C, in air, using a green solvent system to yield the aryl ketones in near quantitative yields. Addition of catalytic amounts of a hydrogen source to the reaction mixture activates the catalyst to proceed through a low energy barrier pathway. Initial studies support a transfer hydrogenolysis reaction mechanism that proceeds through an initial dehydrogenation followed by an enol adsorption to Pd/C and a reductive C¢O bond cleavage.
Infrared probe of the bulk insulating response inBi2−xSbxTe3−ySeytopological insulator alloys (2015)

We have investigated the electronic structure and carrier dynamics of the topological insulator $\mathrm{Bi}{}_{2\ensuremath{-}x}\mathrm{Sb}{}_{x}\mathrm{Te}{}_{3\ensuremath{-}y}\mathrm{Se}{}_{y}$, for $x=0.5,y=1.3$ and $x=1,y=2$, using infrared spectroscopy. Our results show that both of these BSTS alloys are highly insulating in the bulk, with analysis of the infrared data indicating an upper limit to the carrier density of $4.4\ifmmode\times\else\texttimes\fi{}{10}^{17}$ ${\mathrm{cm}}^{\ensuremath{-}3}$. Furthermore, analysis of the interband transitions of $\mathrm{Bi}{}_{1.5}\mathrm{Sb}{}_{0.5}\mathrm{Te}{}_{1.7}\mathrm{Se}{}_{1.3}$ revealed distinct band-structure critical points, which suggest high crystallographic order of our crystals. Motivated by the low carrier density and crystallographic order identified in these compounds, we searched for the Landau level transitions associated with the surface states through magneto-optical measurements in the far infrared range. We failed to observe any indications of the Landau level resonances at fields up to 8 T in sharp contrast with our earlier finding for a related $\mathrm{Bi}{}_{1\ensuremath{-}x}\mathrm{Sb}{}_{x}$ alloy. We discuss factors that may be responsible for suppressed magneto-optics response of these single crystals.
Effects of Load on Emissions and NOx Trap/Catalyst Efficiency for a Direct Injection Spark Ignition Engine (1999)

&lt;div class="htmlview paragraph"&gt;A 1998 Toyota Corona passenger car with a direct injection spark ignition (DISI) engine was tested at constant engine speed (2000 rpm) over a range of loads. Engine-out and tailpipe emissions of gas phase species were measured each second. This allowed examination of the engine-out emissions for late and early injection. Regeneration of the lean NOx trap/catalyst was also examined, as was the efficiency of NOx reduction. NOx stored in the trap/catalyst is released at the leading edge of regenerations, such that the tailpipe NOx is higher than the engine-out NOx for a brief period. The efficiency of NOx reduction was &amp;lt;50% for the lowest loads examined. As the load increased, the efficiency of NOx reduction decreased to near 0% due to excessive catalyst temperatures. Loads sufficiently high to require a rich mixture produce high NOx reduction efficiencies, but in this case the NOx reduction occurs via the three-way catalysts on this vehicle. The Emissions Index for engine-out hydrocarbons (EIHCs) decreases with increasing load for late injection and is independent of load for early injection. The EIHCs for early injection is four times lower than that for late injection at the lowest load examined, which is representative of a high speed cruise on the FTP driving cycle. The EIHCs for a comparable port fuel injected (PFI) vehicle is lower at all loads than that for the DISI vehicle. For the lowest load examined, the EIHCs for the DISI vehicle is six times that for the PFI vehicle. In contrast, the Emissions Index for engine-out NOx (EINOx) is lower for the DISI vehicle than for the PFI vehicle at all loads examined. At the lowest load examined, the EINOx is four times higher for the PFI vehicle. For the DISI vehicle, the EINOx is decreases slightly with increasing load for low loads, then increases as the load increases further and peaks for a slightly lean mixture.&lt;/div&gt;
Efficacy of a predictive display, steering device, and vehicle body representation in the operation of a lunar vehicle (1996)

No abstract available.
Investigation of Acoustic Modeling Techniques for LVCSR Systems (2006)

The paper describes the use of several advanced acoustic modeling techniques for the 2004 CU-HTK large vocabulary speech recognition systems. These techniques include Gaussianization for speaker normalization, discriminative cluster adaptive training (CAT), subspace for precision and mean (SPAM) modeling of inverse covariances, and discriminative complexity control. Acoustic models featuring these techniques were integrated into a state-of-the-art 10 real-time multi-pass system with sophisticated adaptation for performance evaluation. Experimental results are presented on both broadcast news (BN) and conversational telephone speech (CTS) transcription tasks.
Accelerating Drug Discovery and Repurposing by Combining Transcriptional Signature Connectivity with Docking (2020)

Abstract The development of targeted treatment options for precision medicine is hampered by a slow and costly process of drug screening. While small molecule docking simulations are often applied in conjunction with cheminformatic methods to reduce the number of candidate molecules to be tested experimentally, the current approaches suffer from high false positive rates and are computationally expensive. Here, we present a novel in silico approach for drug discovery and repurposing, dubbed connectivity enhanced Structure Activity Relationship ( ce SAR) that improves on current methods by combining docking and virtual screening approaches with pharmacogenomics and transcriptional signature connectivity analysis. ce SAR builds on the landmark LINCS library of transcriptional signatures of over 20,000 drug-like molecules and ~5,000 gene knock-downs (KDs) to connect small molecules and their potential targets. For a set of candidate molecules and specific target gene, candidate molecules are first ranked by chemical similarity to their ‘concordant’ LINCS analogs that share signature similarity with a knock-down of the target gene. An efficient method for chemical similarity search, optimized for sparse binary fingerprints of chemical moieties, is used to enable fast searches for large libraries of small molecules. A small subset of candidate compounds identified in the first step is then re-scored by combining signature connectivity with docking simulations. On a set of 20 DUD-E benchmark targets with LINCS KDs, the consensus approach reduces significantly false positive rates, improving the median precision 3-fold over docking methods at the extreme library reduction. We conclude that signature connectivity and docking provide complementary signals, offering an avenue to improve the accuracy of virtual screening while reducing run times by multiple orders of magnitude.
Interface reactivity and epitaxial growth of SrTiO3 and other functional oxides on Si and GaAs (2016)

, 4-9 sept 2016
Femtosecond-Lentotomy Treatment: Six Month Follow Up of in vivo treated Rabbit Lenses (2009)

Presbyopia is an age related effect which affects every human at the age of about 40 years. So far reading glasses are the conventional treatment. According to Helmholtz’ theory of accommodation one of the mayor reasons for the development of presbyopia is the increasing sclerosis of the lens. In contrast to that the ciliary muscle and the lens capsule remain mostly active and elastic the whole life. So a possible treatment could be the increase of the flexibility of the lens by creating gliding planes with fs-laser pulses inside the lens tissue.In former studies it was shown that fs-laser pulses were able to increase the flexibility of ex vivo porcine lenses as well as ex vivo human donor lenses. Our current aim was to evaluate the effect of the fs-laser pulses on the crystalline lens of living rabbit eyes due to the fs-lentotomy treatment. The main focus of the evaluation was the exclusion of possible side effects of the treatment like cataract formation or retina damage. The treated eyes were monitored using optical coherence tomography (OCT) and Scheimpflug imaging for localizing and studying the tissue effects of the incisions. Furthermore histological sections of the lens and retina were prepared. The rabbits were investigated pre operatively and up to six months post operatively.The fs-laser induced micro incisions were successfully applied to the left lens of each rabbit. The micro incisions within the crystalline lens were detectable with OCT and Scheimpflug imaging up to six month. The imaging within the lens showed a progressive fading of the incisional opacities generated by the femtosecond laser during the six months and no indication of cataract formation was found. OCT and Scheimpflug images emphasize themselves as necessary tools to monitor the micro incisions over time. Histopathological sections of the lens tissue support the findings of the non invasive imaging techniques. Also the histopathological sections of the retina show no thermal induced change due to the irradiation of the fs-pulses.
Large-area semi-transparent light-sensitive nanocrystal skins (2012)

Large area and semi-transparent highly light sensitive nanocrystal skin is demonstrated via spray-coating nanocrystals on top of polyelectrolyte-polymers based on photogenerated potential buildup where no external bias is applied.