gebhart/patrepeval huggingface dataset:
Potential for Prebiotics as Feed Additives to Limit Foodborne Campylobacter Establishment in the Poultry Gastrointestinal Tract (2019)

<i>Campylobacter</i> as an inhabitant of the poultry gastrointestinal tract has proven to be difficult to reduce with most feed additives. In-feed antibiotics have been taken out of poultry diets due to the negative reactions of consumers along with concerns regarding the generation of antibiotic resistant bacteria. Consequently, interest in alternative feed supplements to antibiotics has grown. One of these alternatives, prebiotics, has been examined as a potential animal and poultry feed additive. Prebiotics are non-digestible ingredients by host enzymes that enhance growth of indigenous gastrointestinal bacteria that elicit metabolic characteristics considered beneficial to the host and depending on the type of metabolite, antagonistic to establishment of pathogens. There are several carbohydrate polymers that qualify as prebiotics and have been fed to poultry. These include mannan-oligosaccharides and fructooligosaccharides as the most common ones marketed commercially that have been used as feed supplements in poultry. More recently, several other non-digestible oligosaccharides have also been identified as possessing prebiotic properties when implemented as feed supplements. While there is evidence that prebiotics may be effective in poultry and limit establishment of foodborne pathogens such as <i>Salmonella</i> in the gastrointestinal tract, less is known about their impact on <i>Campylobacter</i>. This review will focus on the potential of prebiotics to limit establishment of <i>Campylobacter</i> in the poultry gastrointestinal tract and future research directions.
Blockers of the Kv1.5 Channel for the Treatment of Atrial Arrhythmias [1] (2003)

Atrial arrhythmias are a common problem in cardiological practice. Despite the availability of several antiarrhythmic drugs, there is a medical need for safer and more efficient antiarrhythmic treatment. Compounds that act atrial selectively without prolonging the QTc-time and without negative inotropy to terminate and/or prevent atrial arrhythmias would be of high interest. In this context, the voltage-gated potassium channel Kv1.5 is regarded as a promising target to achieve atrial selectivity, which in turn would be associated with fewer side effects than classical antiarrhythmics. This review summarizes patents and other publications on compounds which show this novel mode of action. The chemistry, selectivity and structure-activity data disclosed in the literature are discussed in light of recent work demonstrating the antiarrhythmic efficacy of Kv1.5 blockers in vivo. Several studies in pig, dog or goat models have confirmed their proposed atrial selective antiarrhythmic effect in vivo. Most of the more intensively characterized Kv1.5 blockers have turned out not to be selective but also block other ion channels. Based on the currently available data it seems that additional inhibition of Kv4.3 and KACh is beneficial for the desired antiarrhythmic effect or at least does not hamper the atrial selectivity of a Kv1.5 blocker. Significant block of IK1, HERG or sodium channels, however, clearly leads to loss of atrial selectivity and increases the risk of lethal ventricular proarrhythmia.
Towards a theory of biological robustness (2007)

Mol Syst Biol. 3: 137

Robustness is one of the fundamental characteristics of biological systems. Numerous reports have been published on how robustness is involved in various biological processes and on mechanisms that give rise to robustness in living systems (Savageau, 1985a, 1985b, 1998; Barkai and Leibler, 1997; Alon et al , 1999; von Dassow et al , 2000; Bhalla and Iyengar, 2001; Csete and Doyle, 2002, 2004; Kitano et al , 2004, 2004a, 2004b; Stelling et al , 2004; Kitano and Oda, 2006; Kitano, 2007a). With increasing interest in systems biology, properties at the system level such as robustness have attracted serious scientific research. Nevertheless, a mathematical foundation that provides a unified perspective on robustness is yet to be established. For systems biology to mature into a solid scientific discipline, there must be a solid theoretical and methodological foundation. Often, systems biology is equated with computer simulation of cells and organs. Although computer simulation is a powerful technique for clarifying the complex dynamics of biological systems, it is also a useful tool for exploring the foundation of biological systems. While investigation on the dynamic properties of specific aspects of organisms is scientifically significant and can be widely applied, it is a study on specific instances of design within a design space that is shaped by fundamental principles, structural, environmental, and evolutionary constraints. The scientific goal of systems biology is not merely to create precision models of cells and organs, but also to discover fundamental and structural principles behind biological systems that define the possible design space of life (Figure 1). The value of understanding fundamental and structural theories is that they provide deeper insights into the governing principles that complex evolvable systems including biological …
PIK3CA/AKT1 Mutations in Breast Carcinoma: a Comprehensive Review of Experimental and Clinical Studies (2012)

The phosphatidylinositol-3-kinase (PI3K) pathway is an important nexus for integration of extracellular and intracellular signals, and there are very frequent perturbations of this pathway in breast cancer, making it an attractive target for therapeutic manipulation. Hotspot mutations in PIK3CA or AKT1 are found in nearly 30% of breast cancers, especially estrogen receptor-positive and Her-2/neu-positive subgroups. This review will emphasize experimental models, clinical characterization and implications of PIK3CA/AKT1 mutations in breast cancer. In vitro studies have demonstrated that these mutations are kinase-activating and can confer cellular transforming properties in the correct context. Further, overexpression of PIK3CA H1047R in a variety of murine models results in mammary proliferation and carcinomas, and established carcinomas may become PIK3CA H1047R-independent. Data from human breast carcinomas regarding the clinicopathologic significance of PIK3CA/AKT1 mutations were contradictory at first, yet trends are beginning to emerge. PIK3CA mutation seems to impart a favorable prognosis in estrogen-receptor positive breast cancers, and mutations are seen early, in pre-invasive breast lesions. Although larger studies are needed, PIK3CA mutations may not confer selective advantage in the metastatic setting. Numerous pharmacologic compounds targeting the PI3K pathway are in development. The complexity of PI3K crosstalk with other signaling cascades, negative feedback regulation, and the myriad of other genotypic and phenotypic deviations in breast cancers argues for thorough molecular characterization of tumors in cancer trials.
LPV models for jet-printed heightmap control (2019)

The technological development of microscale additive manufacturing requires automated control of material deposition to build a desired 3D structure. This paper considers 3D structures as heightmaps and presents a novel, linear parameter-varying (LPV) model of heightmap evolution for control. Three model identification methods are proposed, each using numerical simulations of liquid drop wetting on nonflat surfaces to obtain the model's time- and space-varying impulse response. First, a method using online numerical simulations is developed for high accuracy at high computational expense. Second, a method using regression to a precomputed dataset of numerical simulations is developed for computationally constrained applications. Third, a spatially invariant version of the second method is developed for compatibility with methods of fast, frequency domain, control computation. For fast numerical simulations, the solver Surface Evolver is used. In simulation, the LPV models identified by the three proposed methods show improved accuracy and precision over a standard linear model. The fast-to-identify and more accurate LPV heightmap evolution models improve the foundation for automated control of microscale additively manufactured structures.
The National Lung Screening Trial: Results stratified by demographics, smoking history, and lung cancer histology (2013)

A benefit of LDCT did not appear to vary substantially by age or smoking status; there was weak evidence of a differential benefit by sex. A differential benefit across lung cancer histologies may exist.
Time course of conscious and unconscious semantic brain activation (2000)

Event-related brain potentials (ERPs) were used to investigate the neurophysiological correlates of conscious and unconscious semantic processing. Masked words, which do not enter consciousness, as well as visible words, were shown to modulate the N400 ERP potential to subsequently presented, meaningfully related target words. The N400 is known as an electrophysiological index of semantic processing. However, for unconsciously perceived words semantic brain activation decays fast within 200 ms, but increases with time for consciously perceived words. Thus, conscious and unconscious semantic activation involves similar brain areas, but both forms of processes exhibit distinct, qualitatively different time courses.
Technique for Measurement of Specific Volume of Liquids at High Pressures and Temperatures (1959)

A novel method is described for measuring specific volume of liquids at high temperatures and pressures. The displacement of the two ends of a continuous column of the liquid is measured. One end is maintained at high temperature and pressure while the other is at normal conditions.
A New Fungal Lectin Recognizing α(1–6)-linked Fucose in the N-Glycan (2003)

In this report, we describe a new lectin from the fungus Rhizopus stolonifer that agglutinates rabbit red blood cells. Agglutinating activity was detected in the extract of mycelium-forming spores cultured on agar plates but not in the mycelium-forming no spores from liquid medium. This lectin, which we designated R. stolonifer lectin (RSL), was isolated by affinity chromatography with porcine stomach mucin-Sepharose. SDS-polyacrylamide gel electrophoresis and mass spectral analysis showed that RSL is approximately 4.5 kDa, whereas gel filtration indicated a mass of 28 kDa. This indicates that the lectin is a hexamer of noncovalently associated RSL monomers. RSL activity was very stable, since it was insensitive to heat treatment at 70 degrees C for 10 min. Analysis of RSL binding specificity by both microtiter plate and precipitation assays showed that N-glycans with l-fucose linked to the reducing terminal GlcNAc residues are the most potent inhibitors of RSL binding, whereas N-glycans without alpha(1-6)-linked fucose residues are approximately 100-fold weaker inhibitors of binding. Oligosaccharides with alpha(1-2, -3, and -4) linkages showed no inhibition of binding in these assays. In a mirror resonance biosensor assay, high affinity binding was observed between RSL and the glycopeptide of bovine gamma-globulin, which has N-glycans with alpha(1-6)-linked fucose residues. However, RSL showed only a weak interaction with the glycopeptide of quail ovomucoid, which lacks fucose residues. Finally, capillary affinity electrophoresis studies indicated that RSL binds strongly to N-glycans with alpha(1-6)-linked fucose residues. Together, these results show that RSL recognizes the core structure of N-glycans with alpha(1-6)-linked l-fucose residues. This specificity could make RSL a valuable tool for glycobiological studies.
A Novel Dual-Stator Axial-Flux Spoke-Type Permanent Magnet Vernier Machine for Direct-Drive Applications (2014)

This paper proposes a novel double-stator axial-flux spoke-type permanent magnet vernier machine, which has a high torque density feature as well as a high-power factor at low speed for direct-drive systems. The operation principle and basic design procedure of the proposed machine are presented and discussed. The 3-D finite element method (3-D-FEM) is utilized to analyze its magnetic field and transient output performance. Furthermore, the analytical method and a simplified 2-D-FEM are also developed for the machine basic design and performance evaluation, which can effectively reduce the modeling and simulation time of the 3-D-FEM and achieve an adequate accuracy.
Kube-Knots: Resource Harvesting through Dynamic Container Orchestration in GPU-based Datacenters (2019)

Compute heterogeneity is increasingly gaining prominence in modern datacenters due to the addition of accelerators like GPUs and FPGAs. We observe that datacenter schedulers are agnostic of these emerging accelerators, especially their resource utilization footprints, and thus, not well equipped to dynamically provision them based on the application needs. We observe that the state-of-the-art datacenter schedulers fail to provide fine-grained resource guarantees for latency-sensitive tasks that are GPU-bound. Specifically for GPUs, this results in resource fragmentation and interference leading to poor utilization of allocated GPU resources. Furthermore, GPUs exhibit highly linear energy efficiency with respect to utilization and hence proactive management of these resources is essential to keep the operational costs low while ensuring the end-to-end Quality of Service (QoS) in case of user-facing queries.Towards addressing the GPU orchestration problem, we build Knots, a GPU-aware resource orchestration layer and integrate it with the Kubernetes container orchestrator to build Kube- Knots. Kube-Knots can dynamically harvest spare compute cycles through dynamic container orchestration enabling co-location of latency-critical and batch workloads together while improving the overall resource utilization. We design and evaluate two GPU-based scheduling techniques to schedule datacenter-scale workloads through Kube-Knots on a ten node GPU cluster. Our proposed Correlation Based Prediction (CBP) and Peak Prediction (PP) schemes together improves both average and 99 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> percentile cluster-wide GPU utilization by up to 80% in case of HPC workloads. In addition, CBP+PP improves the average job completion times (JCT) of deep learning workloads by up to 36% when compared to state-of-the-art schedulers. This leads to 33% cluster-wide energy savings on an average for three different workloads compared to state-of-the-art GPU-agnostic schedulers. Further, the proposed PP scheduler guarantees the end-to-end QoS for latency-critical queries by reducing QoS violations by up to 53% when compared to state-of-the-art GPU schedulers.
Factors affecting plasma retinol decline during long-term administration of the synthetic retinoid fenretinide in breast cancer patients. (1994)

Administration of the synthetic retinoid Fenretinide lowers circulating retinol and may thus affect night vision. We have recently shown that plasma retinol levels below 100 ng/ml are associated with moderate alterations of the dark adaptometry test. To identify which patients are more likely to experience a decrease of plasma retinol under this threshold, we measured plasma levels of retinol, Fenretinide, and its metabolite 4-MPR in a cohort of 28 women receiving Fenretinide at the daily dose of 200 mg and studied their relationship with clinical characteristics such as age, menstrual status, body mass index, and time on treatment. Our results show that patients aged over 55 years with a higher percentage of adipose tissue had higher plasma concentrations of 4-MPR, which turned out to be the major determinant of the retinol decrease. This subgroup may thus deserve careful ophthalmological surveillance.
Porous Al[sub 2]O[sub 3] Nanogeometry Sensor Films: Growth and Analysis (2002)

Material studies of thin films of porous anodized have been undertaken to determine their applicability as sensing films for application on surface acoustic wave sensors. We describe the production of these films including their growth parameters and provide an analysis of their crystal morphology. These films were then exposed to various concentrations of analyte and their surface areas determined using Brunauer-Emmett-Teller-type analysis. Finally, the surface area as a function of anodization potential is provided for the films. © 2001 The Electrochemical Society. All rights reserved.
A Bayesian Perspective on Generalization and Stochastic Gradient Descent (2017)

We consider two questions at the heart of machine learning; how can we predict if a minimum will generalize to the test set, and why does stochastic gradient descent find minima that generalize well? Our work responds to Zhang et al. (2016), who showed deep neural networks can easily memorize randomly labeled training data, despite generalizing well on real labels of the same inputs. We show that the same phenomenon occurs in small linear models. These observations are explained by the Bayesian evidence, which penalizes sharp minima but is invariant to model parameterization. We also demonstrate that, when one holds the learning rate fixed, there is an optimum batch size which maximizes the test set accuracy. We propose that the noise introduced by small mini-batches drives the parameters towards minima whose evidence is large. Interpreting stochastic gradient descent as a stochastic differential equation, we identify the "noise scale" $g = ε(\frac{N}{B} - 1) \approx εN/B$, where $ε$ is the learning rate, $N$ the training set size and $B$ the batch size. Consequently the optimum batch size is proportional to both the learning rate and the size of the training set, $B_{opt} \propto εN$. We verify these predictions empirically.
Production of Ethylene Glycol and Its Monoether Derivative from Cellulose (2014)

The efficient usage of lignocellulosic biomass is of great significance for large-scale low-cost biomass conversion to biofuels and other useful chemicals. Here, an interesting catalytic process was reported related to converting cellulose into ethylene glycol (EG) and ethylene glycol monoether (EGME) in methanol over a Ru/NbOPO4 catalyst, with the cleavage of a C–C bond by NbOPO4 and further hydrogenation by supported Ru particles. The influence of reaction temperature, hydrogen pressure, and reaction time was systematically investigated and showed that a 54.5% total yield of EG and EGME could be obtained at 220 °C in 3 M Pa H2, which was an exciting result. Meanwhile, the effect of solvent was also studied in detail. It was shown that methanol played an important role in the production of EG and EGME, especially in the cleavage of the C–C bond. Methanol could protect the C═O bond in glucose produced from cellulose through acetalization, thus prevent its hydrogenation, and led to the production of EG and EGME. Furthermore, the influence of dopants (W, Sn, Ni, Cu) was further investigated, and it was found that only the Ru–Ni/NbOPO4 catalyst was more effective through limiting the further hydrogenolysis of products (EG and EGME) to CO and alkanes, and as high as 64% total yield of EG+EGME was achieved. Moreover, the Ru–Ni/NbOPO4 catalyst showed good reusability, which can be reused at least four times with a little loss in EG and EGME yield.
An intelligent biological information management system (2002)

BioSifter was tested using 500 documents obtained from PubMed database on two biological problems related to genetic polymorphism and extracorporal shockwave lithotripsy. The results indicate that BioSifter is a powerful tool for biological researchers to automatically retrieve relevant text documents from biological literature based on their interest profile. The results also indicate that the first stage of information management process, i.e. data to information transformation, significantly reduces the size of the information space. The filtered data obtained through BioSifter is relevant as well as much smaller in dimension compared to all the retrieved data. This would in turn significantly reduce the complexity associated with the next level transformation, i.e. information to knowledge.
Effect of replacement fluids saline, gelofusine, and blood on biochemical and hematological parameters in rats subjected to repeated blood sampling. (2009)

Blood sample volume had a crucial impact on the measured parameters, which were least affected in the donor blood-treated group. Regardless of the treatment, up to five 250 microl blood samples can be drawn without causing significant changes in a rat's normal condition. However, for a proper determination of PK profile, more than five blood samples are required and therefore drawn blood should be replaced, preferably with donor blood.
ACTION SPECTRA FOR THE INDUCTION OF PYRIMIDINE(6‐4)PYRIMIDONE PHOTOPRODUCTS AND CYCLOBUTANE PYRIMIDINE DIMERS IN NORMAL HUMAN SKIN FIBROBLASTS (1987)

Abstract. Normal human skin fibroblasts were exposed to 265–313‐nm monochromatic UV wavelengths and the yield of pyrimidine(6‐4)pyrimidone photoproducts [(6‐4) photoproducts] and cyclobutane pyrimidine dimers (dimers) measured by radioimmunoassay. The action spectra for the induction of these two types of DNA damage were very similar for wavelengths from 254 to 302 nm. However, the action spectrum value for (6‐4) photoproduct production was less than half the value obtained for dimer induction by 313‐nm UV. Cells were also exposed to the UV produced by a broad‐spectrum fluorescent sunlamp (280–360 nm, peak at 313 nm) under conditions in which various wavelength components were removed from the spectrum. For exposures in which the (6‐4) photoproducts and dimers were induced primarily by wavelengths shorter than 310 nm, their rates of induction, relative to 254‐nm‐irradiated cells, were similar. However, the level of (6‐4) photoproduct production was about three‐fold lower than dimer induction for sunlamp irradiations in which the 315–330‐nm component of this source was primarily responsible for the formation of this damage. These results are consistent with the conclusion that for treatments in which (6‐4) photoproducts are produced by wavelengths in the 310–320‐nm range, which represent the region of absorption peaks for these photoproducts, both the induction and photolysis of (6‐4) photoproducts occur simultaneously during irradiation.
Comparative study of 4 diagnosis criteria sets for mixed connective tissue disease in patients with anti-RNP antibodies. Autoimmunity Group of the Hospitals of Toulouse. (1996)

Alarcón-Segovia's and Kahn's criteria are the best classification criteria to define MCTD.
Hochenantioselektive Alkylierung von Tetrahydroisochinolinen mit einem Valinolderivat als Hilfsreagens: asymmetrische Synthese von (<i>S</i>)‐Isochinolinalkaloiden (1984)

Natürliche Aminosäuren als Chiralitätsquelle bieten enorme Vorteile für enantioselektive Synthesen. Mit einem L ‐Valinolderivat, aus L ‐Valin gut zugänglich, wurde 1 zunächst N ‐alkyliert. Aus dem so erhaltenen 2 ließ sich enantiomerenreines 3 herstellen. magnified image