gebhart/patrepeval huggingface dataset:
PDZ Domain Proteins: Plug and Play! (2003)

Protein-protein interactions are key elements in building functional protein complexes. Among the plethora of domains identified during the last 10 years, PDZ domains are one of the most commonly found protein-protein interaction domains in organisms from bacteria to humans. Although they may be the sole protein interaction domain within a cytoplasmic protein, they are most often found in combination with other protein interaction domains (for instance, SH3, PTB, WW) participating in complexes that facilitate signaling or determine the localization of receptors. Diversity of PDZ-containing protein function is provided by the large number of PDZ proteins that Mother Nature has distributed in the genome and implicates this protein family in the wiring of a huge number of molecules in molecular networks from the plasma membrane to the nucleus. Although at first sight their binding specificity appeared rather monotonous, involving only binding to the carboxyl-terminus of various proteins, it is now recognized that PDZ domains interact with greater versatility through PDZ-PDZ domain interaction; they bind to internal peptide sequences and even to lipids. Furthermore, PDZ domain-mediated interactions can sometimes be modulated in a dynamic way through target phosphorylation. In this review, we attempt to describe the structural basis of PDZ domain recognition and to give some functional insights into their role in the scaffolding of protein complexes implicated in normal and pathological biological processes.
Hinweise zur Gestaltung von Lageplänen (1998)

ZusammenfassungEs ist aktueller Stand der Technik, Entwürfe EDV-gestützt zu bearbeiten. Die nachfolgenden Hinweise sollen helfen, falls Kleinigkeiten „von Hand“ erledigt werden sollen.
Pitch and Plasticity: Insights from the Pitch Matching of Chords by Musicians with Absolute and Relative Pitch (2013)

Absolute pitch (AP) is a form of sound recognition in which musical note names are associated with discrete musical pitch categories. The accuracy of pitch matching by non-AP musicians for chords has recently been shown to depend on stimulus familiarity, pointing to a role of spectral recognition mechanisms in the early stages of pitch processing. Here we show that pitch matching accuracy by AP musicians was also dependent on their familiarity with the chord stimulus. This suggests that the pitch matching abilities of both AP and non-AP musicians for concurrently presented pitches are dependent on initial recognition of the chord. The dual mechanism model of pitch perception previously proposed by the authors suggests that spectral processing associated with sound recognition primes waveform processing to extract stimulus periodicity and refine pitch perception. The findings presented in this paper are consistent with the dual mechanism model of pitch, and in the case of AP musicians, the formation of nominal pitch categories based on both spectral and periodicity information.
Reduced polarization decay due to electron-hole in-scattering in a semiconductor active medium (1996)

Summary form only given. The electron-hole in-scattering processes, which reduce the decay of the active medium polarization, should be included in a consistent treatment of semiconductor laser gain. The in-scattering processes affect the laser gain by decreasing the influence of the high k states, which contribute absorption to the spectrum. A theory, based on the semiconductor-Bloch equations with the effects of carrier-carrier scattering treated at the level of the quantum kinetic equations in the Markov limit, predicts gain spectra that do not exhibit absorption below the renormalized band gap, in agreement with experiment.
Synthetic Methods in Step‐Growth Polymers (2003)

Synthetic Methods in Step-Growth Polymers provides a concise source of information on synthetic techniques, purification, and characterization methods for step-growth polymers and also addresses future synthetic trends.
Effect of cerebral dopamine metabolism genetic polymorphism on patient-reported quality-of-life (QOL): An analysis of the E3805 CHAARTED trial. (2023)

123 Background: QOL outcomes have been associated with specific genetic variants in neurotransmitter metabolism. One such variant associated with reduced symptoms in placebo studies is in the rs4680 SNP of Carboxy-O-Methyltransferase (COMT). This variant is associated with reduced COMT enzymatic activity, higher cerebral dopamine levels, and improved mood. The interaction between this germline variant and cancer-directed treatment on QOL is undefined. A priori, we hypothesized that the COMT rs4680 SNP would be associated with better pain and QOL patient reported outcomes (PROs), than wildtype (WT) COMT within the E3805 CHAARTED Trial. Methods: E3805 compared docetaxel + androgen deprivation therapy (ADT+D) vs ADT in patients with metastatic hormone sensitive prostate cancer (mHSPC). PROs were collected at baseline, 3, 6, 9, and 12 months. Blood samples were genotyped prior to treatment. We compared PROs between patients with COMT WT vs rs4680 SNP within treatment arms longitudinally. PROs include Brief Pain Inventory (BPI) classified as: no (0), minimal (1), or more (≥2) pain, and BPI interference (range 0-10, 0= no pain or interference), and the Functional Assessment of Cancer Therapy-Prostate (FACT-P, higher score= better QOL, clinically important difference (CID)= 6). Descriptive statistics were used to characterize QOL over time. Fisher’s exact test, Wilcoxon rank sum test and mixed effects models were used to evaluate the associations between SNP and QOL in each arm. Results: Of 790 participants, 550 with SNP data were included. In the ADT+D arm, SNPs were not associated with PROs at any time point. In contrast, in the ADT alone arm, when compared to WT, rs4680 was associated with less pain at 3 months, less interference at 3, 6 and 9 months, and better QOL at 6 months (met criteria for CID). Conclusions: The rs4680 SNP, often associated with higher cerebral dopamine levels and improved QOL, was associated with less pain and superior QOL among patients with mHSPC treated with ADT, but not chemohormonal therapy. This is the first hypothesis driven genotyping study to demonstrate that genetics are associated with QOL in patients with cancer, especially when treatment does not cause profound symptoms. Clinical trial information: NCT00309985 . [Table: see text]
Reactivity of Titanium Oxo Ethoxo Cluster [Ti16O16(OEt)32]. Versatile Precursor of Nanobuilding Block-Based Hybrid Materials (2005)

Oxo alcoxo metallic clusters can be employed as inorganic nanobuilding blocks to obtain well-defined organic-inorganic hybrid materials. A better understanding of the surface reactivity of the clusters should allow optimization of the elaboration of hybrid materials through a better control of the hybrid interface. The oxo alcoxo cluster Ti(16)O(16)(OEt)32 presents a shell of labile ethoxy groups that can be selectively transalcoholyzed with preservation of the titanium oxo core, leading to new oxo alcoxo clusters Ti(16)O(16)(OEt)32-x(OR)x (R: alkyl, phenyl, styrenic, etc. groups). The reactivity of the Ti(16)O(16)(OEt)32 cluster toward aliphatic and aromatic alcohols is investigated to determine both the kinetics and the number of substituted titanium atoms, which are strongly dependent on the nature of the alcohol. Characterization of the organic modification of the cluster is performed in situ by liquid (13)C NMR measurements, using the molecular structures of two new clusters, Ti(16)O(16)(OEt)28(OnPr)4 and Ti(16)O(16)(OEt)(24)(OnPr)(8) (OnPr = propoxy groups), as references. The structures of these clusters have been established using single-crystal X-ray diffraction. Moreover, a complete spectroscopic assignment of each ethoxy group is proposed after combining crystallographic data, (13)C NMR T(1) relaxation measurements, and (1)H-(1)H, (1)H-(13)C 2D NMR experiments. Finally, the cluster is functionalized with polymerizable ligands via transalcoholysis and transesterification reactions using hydroxystyrene and acetoxystyrene.
A machine learning calibration model using random forests to improve sensor performance for lower-cost air quality monitoring (2018)

Abstract. Low-cost sensing strategies hold the promise of denser air quality monitoring networks, which could significantly improve our understanding of personal air pollution exposure. Additionally, low-cost air quality sensors could be deployed to areas where limited monitoring exists. However, low-cost sensors are frequently sensitive to environmental conditions and pollutant cross-sensitivities, which have historically been poorly addressed by laboratory calibrations, limiting their utility for monitoring. In this study, we investigated different calibration models for the Real-time Affordable Multi-Pollutant (RAMP) sensor package, which measures CO, NO2, O3, and CO2. We explored three methods: (1) laboratory univariate linear regression, (2) empirical multiple linear regression, and (3) machine-learning-based calibration models using random forests (RF). Calibration models were developed for 16–19 RAMP monitors (varied by pollutant) using training and testing windows spanning August 2016 through February 2017 in Pittsburgh, PA, US. The random forest models matched (CO) or significantly outperformed (NO2, CO2, O3) the other calibration models, and their accuracy and precision were robust over time for testing windows of up to 16 weeks. Following calibration, average mean absolute error on the testing data set from the random forest models was 38 ppb for CO (14 % relative error), 10 ppm for CO2 (2 % relative error), 3.5 ppb for NO2 (29 % relative error), and 3.4 ppb for O3 (15 % relative error), and Pearson r versus the reference monitors exceeded 0.8 for most units. Model performance is explored in detail, including a quantification of model variable importance, accuracy across different concentration ranges, and performance in a range of monitoring contexts including the National Ambient Air Quality Standards (NAAQS) and the US EPA Air Sensors Guidebook recommendations of minimum data quality for personal exposure measurement. A key strength of the RF approach is that it accounts for pollutant cross-sensitivities. This highlights the importance of developing multipollutant sensor packages (as opposed to single-pollutant monitors); we determined this is especially critical for NO2 and CO2. The evaluation reveals that only the RF-calibrated sensors meet the US EPA Air Sensors Guidebook recommendations of minimum data quality for personal exposure measurement. We also demonstrate that the RF-model-calibrated sensors could detect differences in NO2 concentrations between a near-road site and a suburban site less than 1.5 km away. From this study, we conclude that combining RF models with carefully controlled state-of-the-art multipollutant sensor packages as in the RAMP monitors appears to be a very promising approach to address the poor performance that has plagued low-cost air quality sensors.
A specific role of MutT protein: to prevent dG.dA mispairing in DNA replication. (1989)

Occurrence of the transversion mutation A.T to C.G is specifically enhanced in Escherichia coli mutT mutants. With the aid of the cloned mutT gene, the MutT protein, which has a molecular mass of 15 kilodaltons, was overproduced and purified to near homogeneity. The protein catalyzes hydrolysis of dGTP to dGMP. dGDP and GTP were also hydrolyzed by the protein, but at a lower rate than seen with dGTP. No other deoxynucleoside triphosphates were hydrolyzed. Using poly(dA).(dT)20 as a template-primer, we investigated the misincorporation of dGMP, dCMP, and dAMP by the alpha subunit and the core of E. coli DNA polymerase III. When the polymerization reaction was performed with the alpha subunit, both dCMP and dGMP were misincorporated. The core, composed of alpha, epsilon, and theta subunits, misincorporated only dGMP. This would imply that the proofreading function of the epsilon subunit of DNA polymerase III may correct the dC.dA mispair but not the dG.dA mispair. Misincorporation of dAMP was not observed in reactions with the alpha subunit or core. The misincorporation of dGMP, but not dCMP, was almost completely suppressed by adding purified MutT protein to the reaction mixture. Under these conditions, only a portion of dGTP present in the reaction mixture was degraded. It is therefore likely that the MutT protein may prevent dGMP misincorporation by degrading a specific form of dGTP, probably the syn form, which can pair with deoxyadenosine.
SORT-SGM: Subpixel Optimized Real-Time Semiglobal Matching for Intelligent Vehicles (2012)

The suitability of stereo algorithms for intelligent vehicle applications is conditioned by their ability to compute dense accurate disparity maps in real time. In this paper, an original stereo reconstruction system that is designed for automotive applications is presented. The system is based on the semiglobal matching algorithm (SGM), which is widely known for its high quality and potential for real-time implementation. Several improvements that target the matching, disparity optimization, and disparity refinement steps are proposed. Pixel-level matching uses the census transform because of its invariance to intensity differences due to camera bias or gain that affects the images. The huge memory bandwidth requirements for the SGM disparity optimization step are reduced through a new integration strategy. At the subpixel level, accuracy is increased by devising a new methodology for generating dedicated subpixel interpolation functions. Using this methodology, two novel subpixel interpolation functions for the SGM algorithm are implemented and evaluated. The proposed algorithm has been implemented on a graphics processing unit in the Compute Unified Device Architecture (CUDA). The result is an increased speed and accuracy algorithm profiled for complex real-traffic scenarios. The proposed algorithm has been evaluated at a large scale, and evidence that was collected from both standard benchmarks and real-world images confirm the findings and show a significant improvement over existing solutions.
A robust failure detection and isolation algorithm (2002)

A robust failure detection and isolation (RFDI) algorithm for linear dynamic systems that is insensitive to failure mode, noise, and plant model uncertainties is presented. For robustness to failure mode uncertainties, the algorithm assumes that the failure is the output of a shaping filter, or specifically, a Gauss-Markov model. Such a model embraces a large class of failures. For robustness to noise and plant model uncertainties, the algorithm relies on either a robust risk sensitive (exponential Gaussian) or a robust H/sub /spl infin// filter for the synthesis of failure residuals. It is shown that the algorithm is a generalization of likelihood ratio tests for failure detection and isolation in dynamic systems. Numerical results are presented for an underwater vehicle application, demonstrating that the RFDI algorithm can provide good performance over the desired range of model uncertainties. By contrast, the performance of the nominally optimal likelihood ratio test can considerably degrade in the presence of the same uncertainties.
Purification and Some Properties of Cytosine Deaminase from Bakers’ Yeast (1989)

Journal Article Purification and Some Properties of Cytosine Deaminase from Bakers’ Yeast Get access Tohoru Katsuragi, Tohoru Katsuragi Laboratory of Fermentation Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai-shi, Osaka 591, Japan Search for other works by this author on: Oxford Academic Google Scholar Toshihiro Sonoda, Toshihiro Sonoda Laboratory of Fermentation Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai-shi, Osaka 591, Japan Search for other works by this author on: Oxford Academic Google Scholar Kin’ya Matsumoto, Kin’ya Matsumoto Laboratory of Fermentation Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai-shi, Osaka 591, Japan Search for other works by this author on: Oxford Academic Google Scholar Takuo Sakai, Takuo Sakai Laboratory of Fermentation Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai-shi, Osaka 591, Japan Search for other works by this author on: Oxford Academic Google Scholar Kenzo Tonomura Kenzo Tonomura Laboratory of Fermentation Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai-shi, Osaka 591, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 53, Issue 5, 1 May 1989, Pages 1313–1319, https://doi.org/10.1080/00021369.1989.10869490 Published: 01 May 1989 Article history Received: 24 November 1988 Published: 01 May 1989
Partitioning routing area into zones with distinct pins (2002)

Topological routing has gained importance in state-of-the-art layout synthesis. This paper poses the problem of partitioning the routing area of a given placement into a minimum set of zones such that in each zone, no two pins belong to the same net. Thus, topological routing can be completed among the zones whereas within a zone the only wires are from a pin to the boundary of the zone. Hence, such partitioning may accelerate routing by reducing the problem size. The related problem of identifying a zone with maximum number of distinct pins is also considered here. Both problems are observed to be NP-hard. A genetic algorithm for the first one and a greedy heuristic for the second problem are proposed. Experimental results are observed to be near optimal in most of the cases.
Carpal-Tunnel Syndrome Associated with Vasospasm (1967)

Twenty-eight patients with concurrent carpal-tunnel syndrome and Raynaud's phenomenon or acrocyanosis were studied. Fifteen had a definite diagnosis or presumptive evidence of a systemic disease. Thirteen patients were treated conservatively and fifteen had decompression of the transverse carpal ligament. All patients treated surgically had an excellent result in regard to the carpal-tunnel symptoms, whereas in the group treated conservatively only three showed improvement. Six patients treated surgically had excellent or good results in regard to their vascular symptoms and nine had fair or poor results; in the group conservatively treated, one noted improvement and ten were unchanged or worse. Early surgical treatment of these combined syndromes appears warranted.
Preserved Versus Preservative-Free Latanoprost for the Treatment of Glaucoma and Ocular Hypertension: A Post Hoc Pooled Analysis (2021)

This post hoc pooled analysis confirmed the findings of the individual studies that PFL is as efficacious at reducing IOP as PCL but better tolerated. After switching to PFL, there was twice the improvement in the OSD composite score. PFL was twice as effective at reducing ocular hyperemia and other ocular signs. These findings suggest that PFL has features that may improve patient compliance, thereby potentially improving the IOP-lowering efficacy on a long-term basis.
ESTIMATION OF LANE WIDTH REQUIREMENTS FOR HEAVY VEHICLES ON STRAIGHT PATHS (1999)

This report presents a method for establishing lane width dimensional limits for heavy vehicles travelling on straight paths that is based on computer modelling. Full-scale tests of the tracking behaviour of an A-double are described that were used to verify and validate the predictions from a computer model of the same vehicle. Separate computer models were then created, and the tracking behaviour and lane width requirements determined for the following range of generic heavy vehicles: 19m prime-mover/semi-trailer; 3-axle truck and 3-axle and 4-axle dog trailer combinations; A-double; A-triple; 19m and 25m B-doubles; B-triple; and rigid-plus-three. These generic heavy vehicle models are worst-case types operating under worst-case conditions to produce maximum lateral displacements. The aim was to determine dimensional limits on tracking for heavy vehicles following straight paths that would cover all possible situations that might occur under the current mass and volume loading schedules. The research found tracking ability was principally dependent on road cross-slope profile, vehicle configuration and length, and speed. All of the vehicles investigated could travel comfortably along roads that have a useable lane width of 3.5m except for the A-triple and the rigid-plus-three operating at the higher of the two speeds investigated (90km/h). The traditional measure of road surface unevenness did not correlate well with tracking performance. A performance-based method of assessing heavy vehicles for route access using state-of-the-art computer modelling techniques has been successfully demonstrated. (a) This report is the result of work commissioned under contract by Austroads as part of its National Strategic Research Program (NSRP)
One-Potp-Toluenesulfonylation of Adenosine and Methyl Glycosides with a Substoichiometric Amount of Organotin Mediators (2000)

ABSTRACT ABSTRACT A substoichiometric amount (10-20 mol%) of dibutyltin dichloride 1 was found to be effective for promoting the regioselective 2'-O-tosylation of adenosine 2 with TsCl in a one-pot manner, wherein a turnover step for tin dichloride 1 was involved. Dibutylchlorotin hydroxide 7, dibutyltin oxide 8, bis(dibutylchlorotin) oxide 10, its hydroxy congener 12, and tributyltin chloride 14 were also effective in a substoichiometric amount for the 2'-O-tosylation of the nucleoside 2. The method was applicable to some methyl glycopyranosides. The tosylation with tin dichloride 1 was not sensitive to the presence of water in the reaction mixture. Possible reaction pathways are discussed.
Lactobacillus rhamnosus GG Inhibits the Toxic Effects of Staphylococcus aureus on Epidermal Keratinocytes (2014)

Few studies have evaluated the potential benefits of the topical application of probiotic bacteria or material derived from them. We have investigated whether a probiotic bacterium, Lactobacillus rhamnosus GG, can inhibit Staphylococcus aureus infection of human primary keratinocytes in culture. When primary human keratinocytes were exposed to S. aureus, only 25% of the keratinocytes remained viable following 24 h of incubation. However, in the presence of 10(8) CFU/ml of live L. rhamnosus GG, the viability of the infected keratinocytes increased to 57% (P = 0.01). L. rhamnosus GG lysates and spent culture fluid also provided significant protection to keratinocytes, with 65% (P = 0.006) and 57% (P = 0.01) of cells, respectively, being viable following 24 h of incubation. Keratinocyte survival was significantly enhanced regardless of whether the probiotic was applied in the viable form or as cell lysates 2 h before or simultaneously with (P = 0.005) or 12 h after (P = 0.01) S. aureus infection. However, spent culture fluid was protective only if added before or simultaneously with S. aureus. With respect to mechanism, both L. rhamnosus GG lysate and spent culture fluid apparently inhibited adherence of S. aureus to keratinocytes by competitive exclusion, but only viable bacteria or the lysate could displace S. aureus (P = 0.04 and 0.01, respectively). Furthermore, growth of S. aureus was inhibited by either live bacteria or lysate but not spent culture fluid. Together, these data suggest at least two separate activities involved in the protective effects of L. rhamnosus GG against S. aureus, growth inhibition and reduction of bacterial adhesion.