gebhart/patrepeval huggingface dataset:
Fidaxomicin Preserves the Intestinal Microbiome During and After Treatment of Clostridium difficile Infection (CDI) and Reduces Both Toxin Reexpression and Recurrence of CDI (2012)

The microflora-sparing properties of fidaxomicin were examined during the conduct of a randomized clinical trial comparing vancomycin 125 mg 4 times per day versus fidaxomicin 200 mg twice per day for 10 days as treatment of Clostridium difficile infection (CDI). Fecal samples were obtained from 89 patients (45 received fidaxomicin, and 44 received vancomycin) at study entry and on days 4, 10, 14, 21, 28, and 38 for quantitative cultures for C. difficile and cytotoxin B fecal filtrate concentrations. Additionally, samples from 10 patients, each receiving vancomycin or fidaxomicin, and 10 samples from healthy controls were analyzed by quantitative real-time polymerase chain reaction with multiple group-specific primers to evaluate the impact of antibiotic treatment on the microbiome. Compared with controls, patients with CDI at study entry had counts of major microbiome components that were 2-3-log(10) colony-forming units (CFU)/g lower. In patients with CDI, fidaxomicin allowed the major components to persist, whereas vancomycin was associated with a further 2-4-log(10) CFU reduction of Bacteroides/Prevotella group organisms, which persisted to day 28 of the study, and shorter term and temporary suppression of both Clostridium coccoides and Clostridium leptum group organisms. In the posttreatment period, C. difficile counts similarly persisted in both study populations, but reappearance of toxin in fecal filtrates was observed in 28% of vancomycin-treated patient samples (29 of 94), compared with 14% of fidaxomicin-treated patient samples (13 of 91; P = .03). Similarly, 23% of vancomycin-treated patients (10 of 44) and 11% of fidaxomicin-treated patients (5 of 44) had recurrence of CDI. Whereas vancomycin and fidaxomicin are equally effective in resolving CDI symptoms, preservation of the microflora by fidaxomicin is associated with a lower likelihood of CDI recurrence.
Coding of plenoptic images by using a sparse set and disparities (2015)

A focused plenoptic camera not only captures the spatial information of a scene but also the angular information. The capturing results in a plenoptic image consisting of multiple microlens images and with a large resolution. In addition, the microlens images are similar to their neighbors. Therefore, an efficient compression method that utilizes this pattern of similarity can reduce coding bit rate and further facilitate the usage of the images. In this paper, we propose an approach for coding of focused plenoptic images by using a representation, which consists of a sparse plenoptic image set and disparities. Based on this representation, a reconstruction method by using interpolation and inpainting is devised to reconstruct the original plenoptic image. As a consequence, instead of coding the original image directly, we encode the sparse image set plus the disparity maps and use the reconstructed image as a prediction reference to encode the original image. The results show that the proposed scheme performs better than HEVC intra with more than 5 dB PSNR or over 60 percent bit rate reduction.
Epilogue: When Privacy Rights Encounter First Amendment Freedoms (1991)

THE PHRASE "constitutional right to privacy" is a frequently used over-generalization for a narrow set of rights that are recognized by the federal courts in the context of governmental intrusion on individual decision making regarding peculiarly personal matters.In fact, the "zone of privacy" thus recognized by the courts is the freedom from intrusion by state regulation into those personal decisions, including marriage, procreation, and childrearing.Carving out this niche for peculiarly personal matters does not mean the courts intended to swallow up an entire body of tort law into the Constitution.'Much less does it support any notion that the "right to privacy" is one of constitutional proportions for all purposes.This symposium has raised issues of whether the right of privacy was intended to be or has been elevated to the level of a constitutional right.In this era of increasing news media coverage of daily events, these issues frequently crystallize in the context of the exercise of first amendment freedoms.When this clash occurs, however, the common law derivation of privacy rights becomes apparent: for there is no requirement to balance privacy right factors against first amendment considerations, as there would be in a proceeding that involved competing constitutional rights.The following discussion reflects upon the derivation and evolution of the right to privacy, assesses its development under recognized claims regarding newsgathering activities, and concludes with some observations on constitutional limitations to the honoring of individual privacy rights.When Warren and Brandeis wrote their historic article on the
Antimicrobial susceptibility of Bifidobacterium strains from humans, animals and probiotic products (2006)

The use of the LSM + cysteine medium allowed us to discriminate between intrinsic and atypical resistance properties of bifidobacteria and sets the scene for future definition of epidemiological cut-off values for all important Bifidobacterium species. The presence of an acquired tet(W) gene in several probiotic product isolates stresses the need for a minimal safety evaluation during the selection of Bifidobacterium strains for probiotic use.
Forecasting private consumption: survey-based indicators vs. Google trends (2011)

In this study we introduce a new indicator for private consumption based on search query time series provided by Google Trends. The indicator is based on factors extracted from consumption-related search categories of the Google Trends application Insights for Search. The forecasting performance of the new indicator is assessed relative to the two most common survey-based indicators: the University of Michigan Consumer Sentiment Index and the Conference Board Consumer Confidence Index. The results show that in almost all conducted in-sample and out-of-sample forecasting experiments the Google indicator outperforms the survey-based indicators. This suggests that incorporating information from Google Trends may offer significant benefits to forecasters of private consumption. Copyright © 2011 John Wiley & Sons, Ltd.
Learning, Mutation and Long Run Equilibria in Games (1991)

An evolutionary model with a finite number of players and with stochastic mutations is analyzed. The expansion and contraction of strategies is linked to their current relative success, but mutuation, perturbing the system from its deterministic evolution, are present as well. The focus is on the long run implications of ongoing mutations, which drastically reduce the set of equilibria. For 2 by 2 symmetric games with two symmetric strict Nash equilibria the risk dominant equilibrium is selected. In particular, if both strategies have equal security levels, the Pareto dominant Nash equilibrium is selected. In particular, if both strategies have equal security levels, the Pareto dominant Nash equilibrium is selected, even though there is another strict Nash equilibrium. Copyright 1993 by The Econometric Society.
Engineered RNA Nanodesigns for Applications in RNA Nanotechnology (2013)

Nucleic acids have emerged as an extremely promising platform for nanotechnological applications because of their unique biochemical properties and functions. RNA, in particular, is characterized by relatively high thermal stability, diverse structural flexibility, and its capacity to perform a variety of functions in nature. These properties make RNA a valuable platform for bio-nanotechnology, specifically RNA Nanotechnology, that can create <b><i>de novo</i></b> nanostructures with unique functionalities through the design, integration, and re-engineering of powerful mechanisms based on a variety of existing RNA structures and their fundamental biochemical properties. This review highlights the principles that underlie the rational design of RNA nanostructures, describes the main strategies used to construct self-assembling nanoparticles, and discusses the challenges and possibilities facing the application of RNA Nanotechnology in the future.
Survival and Growth in the Presence of Elevated Copper: Transcriptional Profiling of Copper-Stressed Pseudomonas aeruginosa (2006)

Transcriptional profiles of Pseudomonas aeruginosa exposed to two separate copper stress conditions were determined. Actively growing bacteria subjected to a pulse of elevated copper for a short period of time was defined as a "copper-shocked" culture. Conversely, copper-adapted populations were defined as cells actively growing in the presence of elevated copper. Expression of 405 genes changed in the copper-shocked culture, compared to 331 genes for the copper-adapted cultures. Not surprisingly, there were genes identified in common to both conditions. For example, both stress conditions resulted in up-regulation of genes encoding several active transport functions. However, there were some interesting differences between the two types of stress. Only copper-adapted cells significantly altered expression of passive transport functions, down-regulating expression of several porins belonging to the OprD family. Copper shock produced expression profiles suggestive of an oxidative stress response, probably due to the participation of copper in Fenton-like chemistry. Copper-adapted populations did not show such a response. Transcriptional profiles also indicated that iron acquisition is fine-tuned in the presence of copper. Several genes induced under iron-limiting conditions, such as the siderophore pyoverdine, were up-regulated in copper-adapted populations. Interesting exceptions were the genes involved in the production of the siderophore pyochelin, which were down-regulated. Analysis of the copper sensitivity of select mutant strains confirmed the array data. These studies suggest that two resistance nodulation division efflux systems, a P-type ATPase, and a two-component regulator were particularly important for copper tolerance in P. aeruginosa.
Ubiquitin in Motion: Structural Studies of the Ubiquitin-Conjugating Enzyme∼Ubiquitin Conjugate (2011)

Ubiquitination of proteins provides a powerful and versatile post-translational signal in the eukaryotic cell. The formation of a thioester bond between ubiquitin (Ub) and the active site of a ubiquitin-conjugating enzyme (E2) is critical for the transfer of Ub to substrates. Assembly of a functional ubiquitin ligase (E3) complex poised for Ub transfer involves recognition and binding of an E2∼Ub conjugate. Therefore, full characterization of the structure and dynamics of E2∼Ub conjugates is required for further mechanistic understanding of Ub transfer reactions. Here we present characterization of the dynamic behavior of E2∼Ub conjugates of two human enzymes, UbcH5c∼Ub and Ubc13∼Ub, in solution as determined by nuclear magnetic resonance and small-angle X-ray scattering. Within each conjugate, Ub retains great flexibility with respect to the E2, indicative of highly dynamic species that adopt manifold orientations. The population distribution of Ub conformations is dictated by the identity of the E2: the UbcH5c∼Ub conjugate populates an array of extended conformations, and the population of Ubc13∼Ub conjugates favors a closed conformation in which the hydrophobic surface of Ub faces helix 2 of Ubc13. We propose that the varied conformations adopted by Ub represent available binding modes of the E2∼Ub species and thus provide insight into the diverse E2∼Ub protein interactome, particularly with regard to interaction with Ub ligases.
Attaching Proteins to Carbon Nanotubes via Diimide-Activated Amidation (2002)

Carbon nanotubes are functionalized by bovine serum albumin (BSA) proteins via diimide-activated amidation under ambient conditions. The nanotube-BSA conjugates thus obtained are highly water-soluble, forming dark-colored aqueous solutions. Results from characterizations using atomic force microscopy (AFM), thermal gravimetric analysis, Raman, and gel electrophoresis show that the conjugate samples indeed contain both carbon nanotubes and BSA proteins and that the protein species are intimately associated with the nanotubes. Bioactivities of the nanotube-bound proteins are evaluated using the total protein micro-determination assay (the modified Lowry procedure). The results show that the overwhelming majority (∼90%) of the protein species in the nanotube-BSA conjugates remain bioactive.
Proteome-scale purification of human proteins from bacteria (2002)

The completion of the human genome project and the development of high-throughput approaches herald a dramatic acceleration in the pace of biological research. One of the most compelling next steps will be learning the functional roles of all proteins. Achievement of this goal depends in part on the rapid expression and isolation of proteins at large scale. We exploited recombinational cloning to facilitate the development of methods for the high-throughput purification of human proteins. cDNAs were introduced into a master vector from which they could be rapidly transferred into a variety of protein expression vectors for further analysis. A test set of 32 sequence-verified human cDNAs of various sizes and activities was moved into four different expression vectors encoding different affinity-purification tags. By means of an automatable 2-hr protein purification procedure, all 128 proteins were purified and subsequently characterized for yield, purity, and steps at which losses occurred. Under denaturing conditions when the His6 tag was used, 84% of samples were purified. Under nondenaturing conditions, both the glutathione S-transferase and maltose-binding protein tags were successful in 81% of samples. The developed methods were applied to a larger set of 336 randomly selected cDNAs. Sixty percent of these proteins were successfully purified under denaturing conditions and 82% of these under nondenaturing conditions. A relational database, FLEXProt, was built to compare properties of proteins that were successfully purified and proteins that were not. We observed that some domains in the Pfam database were found almost exclusively in proteins that were successfully purified and thus may have predictive character.
A rapid antimicrobial susceptibility test based on single-cell morphological analysis (2014)

A rapid antibiotic susceptibility test (AST) is desperately needed in clinical settings for fast and appropriate antibiotic administration. Traditional ASTs, which rely on cell culture, are not suitable for urgent cases of bacterial infection and antibiotic resistance owing to their relatively long test times. We describe a novel AST called single-cell morphological analysis (SCMA) that can determine antimicrobial susceptibility by automatically analyzing and categorizing morphological changes in single bacterial cells under various antimicrobial conditions. The SCMA was tested with four Clinical and Laboratory Standards Institute standard bacterial strains and 189 clinical samples, including extended-spectrum β-lactamase-positive Escherichia coli and Klebsiella pneumoniae, imipenem-resistant Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococci from hospitals. The results were compared with the gold standard broth microdilution test. The SCMA results were obtained in less than 4 hours, with 91.5% categorical agreement and 6.51% minor, 2.56% major, and 1.49% very major discrepancies. Thus, SCMA provides rapid and accurate antimicrobial susceptibility data that satisfy the recommended performance of the U.S. Food and Drug Administration.
Melanoma Progression Despite Infiltration by In Vivo-primed TRP-2–specific T Cells (2009)

Many antigens recognized by tumor-reactive cytotoxic CD8+ T cells are self-antigens. Tyrosinase-related protein 2 (TRP-2) is a melanogenic enzyme expressed by both melanocytes and melanomas that is reported to be a candidate melanoma rejection antigen. To study the role of self-reactive CD8+ T cells in tumor immunity and autoimmunity, we generated mice that bear a T-cell receptor transgene (TCR Tg) specific for the TRP-2(180-188) epitope. TRP-2 TCR Tg mice did not spontaneously develop depigmentation despite systemic expression of TRP-2 in the skin. Peripheral T cells from these TCR Tg mice exhibited a naive phenotype and proliferated in response to TRP-2 in vitro. In addition, transfer of in vitro-activated Tg T cells reduced B16 pulmonary tumor burden, but not subcutaneous tumors. We next sought to determine the in vivo responses of the Tg T cells to endogenous and tumor-derived TRP-2. Adoptive transfer of naive TCR Tg T cells into wild-type C57BL/6 mice, in combination with a TRP-2-pulsed dendritic cell vaccine, induced proliferation of the Tg T cells and resulted in migration of the Tg T cells into a subcutaneous B16 melanoma tumor. Although these tumor-infiltrating Tg T cells remained reactive against TRP-2, they did not reduce growth of the primary subcutaneous tumor; similarly, these in vivo-primed effector cells had no significant effect on the growth of pulmonary nodules. These data demonstrate that despite in vivo priming, tumor-infiltrating T cells may fail to reduce tumor burden. Determining the basis for the inability of the tumor microenvironment to sustain effective antitumor responses will be critical for designing newer, more potent antitumor immunotherapies.
Tracking from optical flow (2004)

In this paper, we present an observation model based on the Lucas and Kanade algorithm for computing optical flow, to track objects using particle filter algorithms. Although optical flow information enables us to know the displacement of objects present in a scene, it cannot be used directly to displace an object model since flow calculation techniques lack the necessary precision. In view of the fact that probabilistic tracking algorithms enable imprecise or incomplete information to be handled naturally, this model has been used as a natural means of incorporating flow information into the tracking.
TADDOLs, Their Derivatives, and TADDOL Analogues: Versatile Chiral Auxiliaries (2001)

TADDOLs, which contain two adjacent diarylhydroxymethyl groups in a trans relationship on a 1,3-dioxolane ring, can be prepared from acetals or ketals of tartrate esters by reaction of the latter with aromatic Grignard reagents. They are extraordinarily versatile chiral auxiliaries. Here, a historical review of the subject is followed by discussion of the preparation of TADDOLs and analogous systems, including TADDOLs with N-, P-, O-, and S-heteroatom ligands appropriate for metals. Crystal structure analysis reveals that the heteroatoms on the diarylmethyl groups are almost always in close proximity to each other, joined together by H-bonds, and predisposed to form chelate complexes in which the metallic centers reside in propeller-like chiral environments. Applications of TADDOL derivatives in enantioselective synthesis extend from utilization as stoichiometric chiral reagents or in Lewis acid mediated reactions, to roles in catalytic hydrogenation and stereoregular metathesis polymerization. Derivatives and complexes based on the following metals have so far been investigated: Li, B, Mg, Al, Si, Cu, Zn, Ce, Ti, Zr, Mo, Rh, Ir, Pd, Pt. The number of stereoselective reactions already accomplished with TADDOLs is correspondingly large. It is also easy to prepare TADDOL derivatives that are readily polymerizable and graftable, and to transform them into immobilized solid-phase catalysts. The result is catalysts, simply or dendritically immobilized in polystyrene or on silica gel and characterized by unexpected stability even after multiple use in titanium TADDOLate mediated reactions. TADDOLs show further unusual characteristics that make them useful for applications in material science and supramolecular chemistry: they are the most effective doping agents known for phase transformations of achiral (nematic) into chiral (cholesteric) liquid crystals. The TADDOL OH group that is not involved in intramolecular H-bonding shows a strong tendency to associate intermolecularly with H-bond acceptors. In the process of crystallization this leads, enantioselectively, to the formation of inclusion compounds that lend themselves to the separation of racemic mixtures not otherwise suited to the classical method of crystallization through diastereomeric salts. The high melting points of TADDOLs even make possible the resolution of racemates by distillation! Host-guest compounds formed between TADDOLs and achiral partners can serve as platforms for enantioselective photoreactions. It seems safe to predict that many more applications will be discovered for the TADDOLs and their derivatives. Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author.
Phosphoenolpyruvate Carboxykinase Assayed at Physiological Concentrations of Metal Ions Has a High Affinity for CO2 (2002)

The effect of Mn2+/Mg2+ concentration on the activity of intact, homogeneous phosphoenolpyruvate carboxykinase (PEPCK) from leaves of the C4 grass, Guinea grass (Panicum maximum), have been investigated. Assay conditions were optimized so that PEPCK activity could be measured at concentrations of Mn2+/Mg2+ similar to those found in the cytosol (low micromolar Mn2+ and millimolar Mg2+). PEPCK activity was totally dependent on Mn2+ and was activated at low micromolar concentrations of Mn2+ by millimolar concentrations of Mg2+. Therefore, at physiological concentrations of Mn2+, PEPCK has a requirement for Mg2+. Assay at physiological concentrations of Mn2+/Mg2+ led to a marked decrease in its affinity for ATP and a 13-fold increase in its affinity for CO2. The K m(CO2) was further decreased by assay at physiological ATP to ADP ratios, reaching values as low as 20 μmCO2, comparable with the K m(CO2) of ribulose 1,5-bisphosphate carboxylase-oxygenase. This means that PEPCK will catalyze a reversible reaction and that it could operate as a carboxylase in vivo, a feature that could be particularly important in algal CO2-concentrating systems.
Multimodal chest surface motion data for respiratory and cardiovascular monitoring applications (2017)

Chest surface motion is of significant importance as it contains information of respiratory and cardiac systems together with the complex coupling between these two systems. Chest surface motion is not only critical in radiotherapy, but also useful in personalized systems for continuous cardiorespiratory monitoring. In this dataset, a multimodal setup is employed to simultaneously acquire cardiorespiratory signals. These signals include high-density trunk surface motion (from 16 distinct locations) with VICON motion capture system, nasal breathing from a thermal sensor, respiratory effort from a strain belt and electrocardiogram in lead-II configuration. This dataset contains 72 trials recorded from 11 participants with a cumulative duration of approximately 215 min under various conditions such as normal breathing, breath-hold, irregular breathing and post-exercise recovery. The presented dataset is not only useful for evaluating prediction algorithms for radiotherapy applications, but can also be employed for the development of techniques to evaluate the cardio-mechanics and hemodynamic parameters of chest surface motion.
Quantitative Assessment of Air Trapping in Chronic Obstructive Pulmonary Disease Using Inspiratory and Expiratory Volumetric MDCT (2008)

The densitometric parameter of relative volume change calculated on paired inspiratory and expiratory MDCT using the threshold of -860 H in limited lung correlated closely with airway dysfunction in COPD regardless of the degree of emphysema.