gebhart/patrepeval huggingface dataset:
Urinary candidate biomarker discovery in a rat unilateral ureteral obstruction model (2015)

Urine has the potential to become a better source of biomarkers. Urinary proteins are affected by many factors; therefore, differentiating between the variables associated with any particular pathophysiological condition in clinical samples is challenging. To circumvent these problems, simpler systems, such as animal models, should be used to establish a direct relationship between disease progression and urine changes. In this study, a unilateral ureteral obstruction (UUO) model was used to observe tubular injury and the eventual development of renal fibrosis, as well as to identify differential urinary proteins in this process. Urine samples were collected from the residuary ureter linked to the kidney at 1 and 3 weeks after UUO. Five hundred proteins were identified and quantified by LC-MS/MS, out of which 7 and 19 significantly changed in the UUO 1- and 3-week groups, respectively, compared with the sham-operation group. Validation by western blot showed increased levels of Alpha-actinin-1 and Moesin in the UUO 1-week group, indicating that they may serve as candidate biomarkers of renal tubular injury, and significantly increased levels of Vimentin, Annexin A1 and Clusterin in the UUO 3-week group, indicating that they may serve as candidate biomarkers of interstitial fibrosis.
Atomically uniform Sn-rich GeSn semiconductors with 3.0–3.5 <i>μ</i>m room-temperature optical emission (2018)

The simultaneous control of lattice strain, composition, and microstructure is crucial to establish high-quality, direct bandgap GeSn semiconductors. Herein, we demonstrate that multilayer growth with a gradual increase in composition is an effective process to minimize bulk and surface segregation and eliminate phase separation during epitaxy yielding a uniform Sn incorporation up to ∼18 at. %. Detailed atomistic studies using atom probe tomography reveal the presence of abrupt interfaces between monocrystalline GeSn layers with interfacial widths in the 1.5–2.5 nm range. Statistical analyses of 3-D atom-by-atom maps confirmed the absence of Sn precipitates and short-range atomic ordering. Despite the residual compressive strain of −1.3 %, the grown layers show clear room-temperature photoluminescence in the 3.0–3.5 μm wavelength range originating from the upper GeSn layer with the highest Sn content. This finding lays the groundwork to develop silicon-compatible mid-infrared photonic devices.
Emulsion and controlled miniemulsion polymerization of the renewable monomer γ‐methyl‐α‐methylene‐γ‐butyrolactone (2008)

Abstract The kinetics of free‐radical emulsion polymerization of γ‐methyl‐α‐methylene‐γ‐butyrolactone (MeMBL), a renewable monomer related to methyl methacrylate, are presented in detail for the first time, and stable polymer latices are prepared. The effects of different reaction parameters on free‐radical emulsion polymerization of MeMBL are presented. Homogeneous nucleation is asserted to be the dominant path for particle formation. Miniemulsion copolymerization of MeMBL and styrene is also reported. In this case, the homogeneous nucleation process appears limited when using an oil soluble initiator. Both the RAFT miniemulsion polymerizations and RAFT bulk polymerizations are well controlled and narrow polydispersity copolymers are produced. Rate retardation is observed in the RAFT miniemulsion polymerizations compared with the free‐radical polymerization and RAFT bulk polymerizations and the possible causes of the retardation are discussed. The reactivity ratios of MeMBL and styrene in RAFT bulk copolymerization are also determined. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5929–5944, 2008
Yedalog: Exploring Knowledge at Scale (2015)

With huge progress on data processing frameworks, human programmers are frequently the bottleneck when analyzing large repositories of data. We introduce Yedalog, a declarative programming language that allows programmers to mix data-parallel pipelines and computation seamlessly in a single language. By contrast, most existing tools for data-parallel computation embed a sublanguage of data-parallel pipelines in a general-purpose language, or vice versa. Yedalog extends Datalog, incorporating not only computational features from logic programming, but also features for working with data structured as nested records. Yedalog programs can run both on a single machine, and distributed across a cluster in batch and interactive modes, allowing programmers to mix different modes of execution easily.
Nonlinear amplifying loop mirror (1990)

A novel device arrangement for all-optical switching that permits efficient exploitation of waveguide nonlinearities is discussed. It is based on a long optical fiber loop mirror with an integral short asymmetrically located optical amplifier. The device performance is demonstrated by using a Nd(3+)-doped fiber amplifier. Switching is obtained for peak signal powers of less than 1 W and an amplifier pump power of 10 mW.
Self-Reconfigurable Evolvable Hardware System for Adaptive Image Processing (2013)

This paper presents an evolvable hardware system, fully contained in an FPGA, which is capable of autonomously generating digital processing circuits, implemented on an array of processing elements (PEs). Candidate circuits are generated by an embedded evolutionary algorithm and implemented by means of dynamic partial reconfiguration, enabling evaluation in the final hardware. The PE array follows a systolic approach, and PEs do not contain extra logic such as path multiplexers or unused logic, so array performance is high. Hardware evaluation in the target device and the fast reconfiguration engine used yield smaller reconfiguration than evaluation times. This means that the complete evaluation cycle is faster than software-based approaches and previous evolvable digital systems. The selected application is digital image filtering and edge detection. The evolved filters yield better quality than classic linear and nonlinear filters using mean absolute error as standard comparison metric. Results do not only show better circuit adaptation to different noise types and intensities, but also a nondegrading filtering behavior. This means they may be run iteratively to enhance filtering quality. These properties are even kept for high noise levels (40 percent). The system as a whole is a step toward fully autonomous, adaptive systems.
Iterative Cycles of<i>In Vitro</i>Protein Selection for DNA Polymerase Activity (2003)

Isolation of genes encoding catalysts for defined chemical reactions should be facilitated by selection of proteins for catalysis from molecular repertoires. Display of proteins on phage allows the coupling between a protein and its gene. Furthermore, if the reaction product can be linked to the phage enzyme catalyzing the reaction, affinity chromatography for the product yields the protein catalyzing the reaction and its gene. One main advantage of this selection method is that it can be in principle generalized to most chemical reactions.Here, iterative in vitro selections for polymerase activity were used to isolate a single phage-polymerase among more than 108 phage particles. Three to five selection cycles were required depending on the fraction of infectious phage-polymerases in the initial phage population. This is the first report quantifying the enrichment over iterative selection rounds for the isolation of rare catalysts displayed on phage.
Cluster analysis for multivariable process control (2005)

This paper describes the novel use of cluster analysis in the field of industrial process control. The severe multivariable process problems encountered in manufacturing have often led to machine shutdowns, where the need for corrective actions arises in order to resume operation. Production faults which are caused by processes running in less efficient regions may be prevented or diagnosed using reasoning based on cluster analysis. Indeed the internal complexity of a production machinery may be depicted in clusters of multidimensional data points which characterise the manufacturing process. The application of a mean-tracking cluster algorithm to field data acquired from a high-speed machinery is discussed. The objective of such an application is to illustrate how machine behaviour can be studied, in particular how regions of erroneous and stable running behaviour can be identified.
Claudin‐derived peptides are internalized via specific endocytosis pathways (2012)

Claudin proteins are involved in the paracellular tightening of epithelia and endothelia. Their internalization, which can be modulated by extracellular stimuli, for example, proinflammatory cytokines, is a prerequisite for the regulation of the paracellular barrier to allow, for instance, cell migration or drug delivery. The internalization of peptide sequences of claudins is completely unknown. Here, we studied the internalization of two peptides, TAMRA-claudin-1 and TAMRA-claudin-5, derivatives of the extracellular loop of claudin-1 and -5, respectively, in either epithelial or endothelial cells. The cellular uptake of the claudin-1 peptide follows the clathrin-mediated endocytosis as indicated by inhibitors and respective tracers for colocalization. In addition, macropinocytosis and caveolae-mediated endocytosis of the peptide was observed. In contrast, the claudin-5 peptide is mainly internalized via the caveolae-mediated endocytosis evidenced by the colocalization with respective tracers and vesicle markers, whereas the nonselective macropinocytosis seems to be involved in a less effective manner. In conclusion, the assumption is supported that claudin peptides can be internalized by specific and nonspecific pathways.
An integrated environment to visually construct 3D animations (1995)

In this paper, we present an expressive 3D animation environment that enables users to rapidly and visually prototype animated worlds with a fully 3D user-interface. A 3D device allows the specification of complex 3D motion, while virtual tools are visible mediators that live in the same 3D space as application objects and supply the interaction metaphors to control them. In our environment, there is no intrinsic difference between user-interface and application objects. Multi-way constraints provide the necessary tight-coupling among components that makes it possible to seamlessly compose interactive and animated behaviors. By recording the effects of manipulations, all the expressive power of the 3D user-interface is exploited to define animations. Effective editing of recorded manipulations is made possible by compacting all continuous parameter evolutions with an incremental data-reduction algorithm, designed to preserve both geometry and timing. The automatic generation of editable representations of interactive performances overcomes one of the major limitations of current performance animation systems. Novel interactive solutions to animation problems are made possible by the tight integration of all system components. In particular, animations can be synchronized by using constrained manipulation during playback. The accompanying video tape illustrates our approach with interactive sequences showing the visual construction of 3D animated worlds. All the demonstrations were recorded live and were not edited.
Lack of matrix metalloproteinase-9 worsens ventilator-induced lung injury (2008)

Matrix metalloproteinase-9 (MMP-9) is released by neutrophils at the sites of acute inflammation. This enzyme modulates matrix turnover and inflammatory response, and its activity has been found to be increased after ventilator-induced lung injury. To clarify the role of MMP-9, mice lacking this enzyme and their wild-type counterparts were ventilated for 2 h with high- or low-peak inspiratory pressures (25 and 15 cmH2O, respectively). Lung injury was evaluated by gas exchange, respiratory mechanics, wet-to-dry weight ratio, and histological analysis. The activity of MMP-9 and levels of IL-1beta, IL-4, and macrophage inflammatory protein (MIP-2) were measured in lung tissue and bronchoalveolar lavage fluid (BALF). Cell count and myeloperoxidase activity were measured in BALF. There were no differences between wild-type and Mmp9-/- animals after low-pressure ventilation. After high-pressure ventilation, wild-type mice exhibited an increase in MMP-9 in tissue and BALF. Mice lacking MMP-9 developed more severe lung injury than wild-type mice, in terms of impaired oxygenation and lung mechanics, and higher damage in the histological study. These effects correlated with an increase in both cell count and myeloperoxidase activity in the BALF, suggesting an increased neutrophilic influx in response to ventilation. An increase in IL-1beta and IL-4 in the BALF only in knockout mice could be responsible for the differences. There were no differences between genotypes in MMP-2, MMP-8, or tissue inhibitors of metalloproteinases. These results show that MMP-9 protects against ventilator-induced lung injury by decreasing alveolar neutrophilic infiltration, probably by modulation of the cytokine response in the air spaces.
The influence of cadence and power output on the biomechanics of force application during steady‐rate cycling in competitive and recreational cyclists (1991)

The intent of this study was two-fold. The first aim was to investigate how cyclists orient forces applied by the feet to the pedals in response to varying power output and cadence demands, and the second was to assess whether competitive riders responded differently from recreational riders to such variations. One group consisted of US Cycling Federation category II licensed competitive cyclists (n = 7) and the second group consisted of recreational cyclists with no competitive experience (n = 38). The subjects rode an instrumented stationary 10-speed geared bicycle mounted on a platform designed to provide rolling and inertial resistance for six pedal rate/power output conditions for a minimum of 2 min for each ride. The pedalling rates were 60, 80 and 100 rev min-1 and the power outputs 100 and 235 W. All rides were presented in random order. The forces applied to the pedals, the pedal angle with respect to the crank and the crank angle were recorded for the final 30 s of each ride. From these data, a number of variables were computed including peak normal and tangential forces, crank torque, angular impulse, proportion of resultant force perpendicular to the crank, and pedal angle. Both the competitive and recreational groups responded similarly to increases in cadence and power output. There was a decrease in the peak normal forces, whereas the tangential component remained almost constant as cadence was increased. Regardless of cadence, the riders responded to increased power output demands by increasing the amount of positive angular impulse. All the riders had a reduced index of effectiveness as cadence increased. This was found to be the result of the large effect of the forces during recovery on this calculation. There were no significant differences between the two groups in each of these variables over all conditions. It was concluded that the lack of difference between the groups was a combined consequence of the limited degrees of freedom associated with the bicycle and that the relatively low power output for the competitive riders was insufficient to discriminate or highlight superior riding technique.
Molecular evidence that homologous recombination occurs in proliferating human somatic cells. (1990)

A strategy has been developed to detect and characterize certain heritable genomic alterations that occur as cells proliferate in vitro. Multiple subclones of cells were isolated from two clonal lymphoblastoid cell lines--one from a boy with Bloom's syndrome (BS), a cancer-predisposing condition known to feature excessive somatic mutation, the other from a normal man. The DNAs from the cell lines were hybridized to a panel of probes that can detect restriction fragment length polymorphisms, and the patterns of polymorphism in the primary clones were compared with that in each of the secondary clones. In one of the BS secondary clones three loci, positioned distally on the long arm of chromosome 3 and that are heterozygous in the donor and all other cell lines derived from the primary clone, had lost heterozygosity and apparently had become homozygous; in contrast, heterozygous loci more proximal on 3q had retained their heterozygosity, as had those on 3p. Taking into account the pattern of chromosome instability uniquely characteristic of BS, the most plausible explanation for the alterations in the altered clone is that somatic recombination had occurred in vitro, via homologous chromatid interchange. Such spontaneous recombinational events in nonneoplastic, nonmutagenized cells may contribute to the high cancer incidence in BS and, by analogy, to cancer that arises in the general population.
Studies on the .BETA.-1,3-glucanase system of Streptomyces. Part I. Enzymatic preparation of crystalline laminaribiose from curdlan. (1984)

The enzymatic preparation of laminaribiose was investigated in this research. Whencurdlan was hydrolyzed with the β-l, 3-glucanase system of Streptomyces sp. K27-4, the hydrolyzate mainly consisted of glucose and laminaribiose in an approximate ratio of 1 : 1 by weight. Yeast strains selected in this study, effectively and selectively metabolized all of the glucose in the hydrolyzate, without any degradation of laminaribiose. By successive treatment of curdlan with the glucanase system and glucose-metabolizable yeast, 31g of crystalline laminaribiose was obtained from 1OOg of curdlan.
Novel optical isolator consisting of a YIG spherical lens and PANDA-fibre polarisers (1985)

A novel optical isolator consisting of an yttrium-iron-garnet (YIG) sphere and two PANDA-fibre polarisers is reported. The YIG sphere functions not only as a Faraday rotator but also as an efficient coupling lens. The extinction ratio of the PANDA-fibre polariser was 37 dB when the 3 m-long fibre was coiled by the diameter D = 21 cm. The isolation ratio was 34.7 dB at 1.3 μm wavelength with the insertion loss of 4.1 dB through the PANDA-fibre polariser to the analyser.
Development of a Real‐Time Polymerase‐Chain‐Reaction Assay for Quantitative Detection of<i>Enterocytozoon bieneusi</i>DNA in Stool Specimens from Immunocompromised Patients with Intestinal Microsporidiosis (2003)

A new real-time polymerase chain reaction (PCR) method was developed for quantitation of Enterocytozoon bieneusi DNA in sequential stool specimens from immunocompromised patients with intestinal microsporidiosis. Patients were treated with fumagillin (n=6) or with placebo (n=6), in a randomized comparative trial. At baseline, mean E. bieneusi DNA levels were not significantly different in stool specimens from the placebo group, compared with those from the fumagillin group (5.9+/-0.4 vs. 5.9+/-0.6 log(10) copies/microL of stool suspension, respectively; P=.96). In the placebo group, parasitic burden remained stable during follow-up (P=.46), whereas, in the fumagillin group, E. bieneusi DNA levels dropped below the lower limit of detection in all patients (mean reduction from baseline, -4.7 log(10) copies; P<.0001). Real-time PCR performed better than did semiquantitative assessments by microscopy, to measure parasitic burden. In conclusion, this real-time PCR assay is a reliable tool for quantitation of E. bieneusi DNA in stool specimens and for the monitoring of treatment efficacy.
Energy Levels and Crystal-Field Calculations of Europium and Terbium in Yttrium Aluminum Garnet (1964)

Experimental and theoretical studies of the trivalent europium and terbium ions in yttrium aluminum garnet are reported in this communication. From crystal-field calculations on the split $^{7}F$ manifolds of ${\mathrm{Eu}}^{3+}$ and ${\mathrm{Tb}}^{3+}$, it is concluded that the crystal field is approximately tetragonal. Agreement between experimental and calculated splitting patterns is satisfactory for those Stark components of $^{7}F$ manifolds which are not far removed from the center of gravity.
LIF and OM Directly Interact with a Soluble Form of gp130, the IL-6 Receptor Signal Transducing Subunit (1994)

Oncostatin M and LIF are related members of a cytokine family that also includes IL-6, CNTF and G-CSF. These proteins exhibit overlapping biological properties and with the exception of G-CSF, they all appear to utilize gp130 as a signaling component of their high affinity receptor complexes. Recently it has been demonstrated that monomeric, membrane bound gp130 can directly bind OM. To further investigate the binding properties of gp130 we generated a soluble form of gp130, sgp130-Rg, to investigate potential gp130 interactions with OM and other members of this cytokine family. Using chemical crosslinking techniques we demonstrate that OM and LIF but not CNTF or IL-6 directly interact with sgp130-Rg. Since OM signaling can be prevented by binding gp130 with anti gp130 mAbs we also investigated the potential of sgp130-Rg to prevent the biological activities of both LIF and OM. Here we demonstrate that sgp130-Rg can bind LIF and OM preventing their biological activities on the TF-1 erythroleukemia cell line. This property suggests that sgp130-Rg may have therapeutic value in the specific prevention of LIF or OM mediated pathologies.
Comprehensive Cardiovascular magnetic resonance of myocardial mechanics in mice using three-dimensional cine DENSE (2011)

Using a 3D cine DENSE sequence tailored for cardiac imaging in mice at 7 T, a comprehensive assessment of 3D myocardial mechanics can be achieved with a scan time of less than 25 minutes and an image analysis time of approximately 1 hour.
In Vitro Regeneration of Style-stigma-like Structure from Stamens of Crocus sativus (2001)

Style_stigma_like structures were regenerated from stamens of Crocus sativus L. The age of the stamen explant has an obvious effect on the induction rate. Auxin NAA has larger effect on the induction of filament style_stigma_like structure. Auxin NAA of higher concentration can lead to higher induction rate. Temperature and light have different effects on the induction of style_stigma_like structure from anther's filament of C. sativus with exogenous hormones at different levels. Ultraviolet tests show that style_stigma_like structure from anther's filament of C. sativus contains crocin, safranal and picrocrocin, contents of which are obviously more than those contained in the style_stigma_like from style. Floral reversion was observed in the induction of style_stigma_like structure from petals, ovaries and styles.
Control of Cell Proliferation by Embryonal‐Origin Factors (1996)

Embryogenesis can be paralleled and contrasted with cancerous cell proliferation; both embryogenesis and cancer are associated with extremely rapid cell proliferation. However, unlike cancer, embryogenesis is characterized by a delicate balance of proliferative and anti-proliferative processes. We have found two chromatographically separated fractions derived from human embryonal neural tissue extracts that significantly suppress the proliferation of human breast cancer cells. The reduction in cell number was time dependent, with maximal inhibition (70%) observed after 4 days of incubation while maintaining cell viability. The anti-proliferative effect was also evidenced by decreased [3H]-thymidine incorporation. Significant inhibition of proliferation of osteosarcoma, fibrosarcoma, and Balb/c 3T3 cell lines was also obtained with a low concentration of the active fractions. Embryonal factors inhibited mouse and rat cell lines, indicating cross-species effectiveness. The SDS-PAGE of the biologically active approximately 10.7 kDa region revealed several protein bands, while the biologically active approximately 4.5 kDa fraction contained only weakly stainable bands. Thus, the embryo contains factors that control the proliferation of malignant cells. These potent and possibly novel compounds should be investigated for their potential therapeutic role in cancer and other proliferative disorders.