gebhart/patrepeval huggingface dataset:
Ribosome Display for Rapid Protein Evolution by Consecutive Rounds of Mutation and Selection (2010)

Directed evolution experiments are performed to improve the properties of proteins by creating a library of mutated genes of interest and selecting those genes that encode proteins exhibiting desired properties. Here, we present one of the methods to carry out an evolutionary experiment called ribosome display. Ribosome display allows this process to be carried out entirely in vitro, and it is therefore a rapid and robust method for protein evolution.
Understanding and guiding the phase inversion process for synthesis of solvent resistant nanofiltration membranes (2015)

ABSTRACT Since its introduction in membrane technology in the 1960's, phase inversion by means of immersion precipitation has been widely studied for the preparation of membranes to be applied in the fields of microfiltration (MF) and ultrafiltration (UF). However, much less knowledge is available about this process in terms of integrally skinned asymmetric nanofiltration membranes, especially for more hydrophobic polymers applied in solvent resistant nanofiltration (SRNF). This review focuses on the preparation aspects of integrally skinned asymmetric membranes to be applied in the field of SRNF via phase inversion. It starts with the explanation of the basic principles of the phase inversion process, covering both thermodynamic and kinetic aspects. Further, it summarizes the parameters that significantly influence final membrane performance and morphology, including polymer type and concentration, casting solvent, additives, evaporation time, and temperature, humidity, membrane thickness, composition, and temperature of coagulation bath and post‐treatment. Literature contained within this review constitutes the core references in the field of SRNF, but also several references on preparation of MF, UF, aqueous NF, and reverse osmosis (RO) membranes have been included to better clarify or illustrate certain aspects of the process. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132 , 42130.
Wear behavior and tribo-surface characteristics of nano magnesium composites (2023)

A nano magnesium composite was synthesized with the addition of 5.6 wt.% of titanium, 3 wt.% of aluminum and 2.5 wt.% of nano boron carbide particles through the disintegrated metal deposition process. To validate the metallurgical features of the synthesized magnesium composite, the samples were exposed to X-ray diffraction study and scanning electron microscopic analysis with dispersive spectroscopy analysis. Wear behavior of the nano magnesium composite was studied through pin-on-disc dry sliding wear experiments by changing the load and sliding velocity over a sliding distance of 3000 m. Further, wear rate of the produced material was analyzed for varied wear parameters. Wear behavior of the magnesium composite revealed an adverse effect with an increased load and a positive effect with increased sliding velocity. The microscopic analysis of the worn surface and the collected debris revealed the characteristics of the wear surface of the nano magnesium composite. Adhesion, abrasion, delamination, oxidation and thermal softening were the mechanisms observed in the post-failure analysis.
Blended local planning for generating safe and feasible paths (2008)

Many planning approaches adhere to the two-tiered architecture consisting of a long-range, low fidelity global planner and a short-range high fidelity local planner. While this architecture works well in general, it fails in highly constrained environments where the available paths are limited. These situations amplify mismatches between the global and local plans due to the smaller set of feasible actions. We present an approach that dynamically blends local plans online to match the field of global paths. Our blended local planner generates paths from control commands to ensure the safety of the robot as well as achieve the goal. Blending also results in more complete plans than an equivalent unblended planner when navigating cluttered environments. These properties enable the blended local planner to utilize a smaller control set while achieving more efficient planning time. We demonstrate the advantages of blending in simulation using a kinematic car model navigating through maps containing tunnels, cul-de-sacs, and random obstacles.
Reproduction and environment (2011)

Two factors play an important part in determining the optimum number of offspring that any species should produce each pregnancy, the optimum number for the fetuses to develop normally in the uterus, and the ability of the mother to adequately suckle the newborn to the point where they are able to survive the rigors of the environment. The first is of prime importance and is determined by a relatively tight control over the number of pre-ovulatory follicles that develop and ovulate, while the second is determined by when the offspring are born, and how frequently births occur in relation to the development of the young. In some species time of year of birth is not necessarily a major consideration, e.g. where seasonal variations in food supply are not great, but in more extreme climates timing of birth is of crucial importance as there must be sufficient time for the young to be able to withstand harsh climates and variations in food supply. In these situations the time of breeding needs to be controlled to limit the periods of fertility, so that if conception occurs birth can still take place at an optimum time of year. In most species reproduction is very efficient and usually ovulations will result in pregnancy.
Permeability of fractures created by triaxial direct shear and simultaneous X-ray imaging (2024)

Rock fractures in the subsurface have the potential to act as fluid flow pathways but the permeability of existing, new, or future in-situ rock fractures is difficult to characterize.We perform triaxial direct shear experiments to evaluate the permeability potential of freshly created fractures as a function of stress/depth using specimens of carbonate-rich Marcellus Shale.Applied confining stress ranged from 2 to 30 MPa, specimens were 25 mm diameter and 25 mm length, shearing displacement of at least 2 mm was imposed, and measured permeability ranged between 10 -3 and 10 4 mD as dependent on stress and fracture conditions.Simultaneous X-ray video and computed tomography were used to directly measure fracture displacement and apertures.Results show that the stress at which fractures form is likely the most significant factor controlling fracture permeability, with higher stresses causing significant 2 to 4 orders of magnitude permeability reduction.The effect of creating fractures at high stress on permeability reduction was significantly stronger than the effect of increasing the confining stress on an existing fracture.Results included analysis of transient fracture permeability following renewed shear displacement, a process which resulted in rapid permeability enhancement followed by a slower decay in permeability.
Moving Between Contexts - A User Evaluation of a Transitional Interface (2008)

Navigating between different virtual worlds, interface&#13;\nscales or task contexts has emerged as an interesting research area for Augmented and Virtual Reality interfaces. We have developed a transitional interface which allows users to smoothly move between exocentric Augmented Reality and egocentric Virtual Reality views. In this paper we report on the first user study to investigate performance, usability, presence and awareness issues with transitional interfaces. The results of this explorative study provide initial guidelines for future research and development of multicontext-navigation environments and raise interesting&#13;\nquestions for future research.
Graph Kernels (2010)

We present a unified framework to study graph kernels, special cases of which include the random walk (Gartner et al., 2003; Borgwardt et al., 2005) and marginalized (Kashima et al., 2003, 2004; Mahet al., 2004) graph kernels. Through reduction to a Sylvester equation we improve the time complexity of kernel computation between unlabeled graphs with n vertices from O(n6) to O(n3). We find a spectral decomposition approach even more efficient when computing entire kernel matrices. For labeled graphs we develop conjugate gradient and fixed-point methods that take O(dn3) time per iteration, where d is the size of the label set. By extending the necessary linear algebra to Reproducing Kernel Hilbert Spaces (RKHS) we obtain the same result for d-dimensional edge kernels, and O(n4) in the infinite-dimensional case; on sparse graphs these algorithms only take O(n2) time per iteration in all cases. Experiments on graphs from bioinformatics and other application domains show that these techniques can speed up computation of the kernel by an order of magnitude or more. We also show that certain rational kernels (Cortes et al., 2002, 2003, 2004) when specialized to graphs reduce to our random walk graph kernel. Finally, we relate our framework to R-convolution kernels (Haussler, 1999) and provide a kernel that is close to the optimal assignment kernel of kernel of Frohlich et al. (2006) yet provably positive semi-definite.
Multiple Large Gel Two-dimensional Electrophoresis for Proteomics. (2003)

A fundamental concern about proteomics is improving the coverage of detection of a cellular proteome using our technology. In the case of two-dimensional gel electrophoresis (2-DE), a core technology of proteomics, enlargement of the gel size appears a straightforward and effective strategy for increasing the number of detected proteins. We utilized fourteen large 2-DE gels (twelve 24cm×7cm gels) which were assembled into a 93cm×103cm cybergel. Our data suggested that the cyber gel can display more than 11, 000 protein spots expressed in a 1-105 dynamic range in cells.
Titelbild: Crystal Structure of Tricolorin A: Molecular Rationale for the Biological Properties of Resin Glycosides Found in Some Mexican Herbal Remedies (Angew. Chem. 44/2004) (2004)

In traditionellen mexikanischen Rezepten kommt die himmelblaue Trichterwinde ( Ipomea tricolor Cav.) als Deckfrucht vor. Tricolorin A ist eines von mehreren in ihr vorhandenen phytotoxischen Harzglycosiden. R. Pereda‐Miranda, A. Imberty et al. berichten in ihrer Zuschrift auf S. 6044 ff. über seine kristallographisch ermittelte Struktur, die erste eines natürlichen Harzglycosids. Das einen Makrolactonring enthaltende Lipopolysaccharid bildet Kanalstrukturen, die mit seiner biologischen Aktivität in Beziehung gesetzt werden könnten.
<title>Difficulties in superresolving synthetic aperture radar images</title> (2002)

The ability to resolve Synthetic Aperture Radar (SAR) images to finer resolutions than the system bandwidths classically allow is a tantalizing prospect. Seemingly superresolution offers something for nothing, or at least something better than the system was designed for if only we process enough or right. Over the years this has proved to be a rather popular area of investigation, generating a wide variety of algorithms and corresponding claims of performance. Nevertheless, the literature on the fundamental underlying principles of superresolution as applied to SAR has been rather anemic. This paper addresses the following questions: What exactly is superresolution? and What is not really superresolution, but perhaps more aptly described as image enhancement? Is true superresolution possible? and to what degree? What constrains superresolution? and very importantly, How should we objectively test whether an image is in fact superresolved? Whereas superresolution concepts offer the potential of resolution beyond the classical limit, this great promise has not generally been realized. That is not to say that many reported algorithms have no useful effect on images. True superresolution is defined herein as the recovery of true scene spectrum, that allows more accurate scene rendering. The analytical basis for superresolution theory is outlined, and the application to SAR is then investigated as an operator inversion problem, which is generally ill posed. Noise inherent in radar data tends to severely inhibit significant enhancement of image resolution. A criterion for judging superresolution processing of an image is presented.
Characteristics of Self-driven Magnet Wheel and Maglev Test Car Using the Wheels (2000)

The authors have proposed the electromagnetic device called the “magnet wheel” with the rotator attached strong permanent magnets and the conducting plate. This has the functions of induction repulsive type magnetic lift force and thrust which are obtained by using the rotator over the conducting plate as the “partial overlap” or the “tilt” method.This paper presents the performance of self-driven magnet wheel integrated own drive equipment, which is composed by addition of the three-phase armature winding in the place between the permanent magnets and the yoke. As the results for the partial overlap type magnet wheel, the following facts were cleared. The power factor in the input of the self-driven magnet wheel unit is nearly 1.0 in spite of induction repulsive levitation. From the experimental results of the test maglev car mounted four magnet wheel units, it is confirmed that the magnet wheel has the sufficiently large lift force against the own weight and then the half of driving power required for the levitation can be converted into the thrust. By using four wheels, the component of torque is canceled, and the lift force and thrust of the test maglev car are obtained respectively by the summation of those of one unit. The stable levitation was confirmed experimentally.
Coupling-aware Dummy Metal Insertion for Lithography (2007)

As integrated circuits manufacturing technology is advancing into 65nm and 45nm nodes, extensive resolution enhancement techniques (RETs) are needed to correctly manufacture a chip design. The widely used RET called off-axis illumination (OAI) introduces forbidden pitches which lead to very complex design rules. It has been observed that imposing uniformity on layout designs can substantially improve printability under OAI. For metal layers, uniformity can be achieved simply by inserting dummy metal wire segments at all free spaces. Simulation results indeed show significant improvement in printability with such a dummy metal insertion approach. To minimize mask cost, it is advantageous to use dummy metal segments that are of the same size as regular metal wires due to their simple geometry. But these dummy wires are printable and hence increase coupling capacitances and potentially affect yield. The alternative is to use a set of parallel sub-resolution thin wires (which is not printed) to replace a printable dummy wire segment. These invisible dummy metal segments do not increase coupling capacitances but bring a higher lithography cost, which includes mask cost and RET/process expense. This paper presents a strategy for dummy metal insertion that can optimally trade off lithography cost and coupling capacitance. In particular, we present an optimal algorithm that can minimize lithography cost subject to any given coupling capacitance bound. Moreover, this dummy metal insertion achieves a highly uniform density because of the locality of coupling capacitance, which automatically ameliorates chemical mechanical polish (CMP) problem.
Fatigue Life of Nylon Filaments as Fishing Gear Material for Tuna Long-line. (1992)

The fatigue phenomena of nylon filaments which have recently been used as fishing gear material for tuna long-line fishing have been investigated. Fatigue tests were carried out with two nylon filaments (No. 150 monofilament and No. 50×3-ply filament). Results show that there is a great difference in fatigue behavior between the two nylons. Monofilament is found to have high resistance to tension cycling fatigue. In addition the measurement of the residual strength after 104 cycles of fatigue testing at a higher loading level (S/T0=75%) shows no strength loss but rather an increase (5 to 10%). In 3-ply filament, however, a decrease in fatigue life and a marked loss of residual strength after fatigue testing (12 to 27%) are observed. As a result, it can be concluded that the fatigue behavior of nylon filaments depends heavily on the construction of the filaments (number of filaments and twist). In 3-ply filament, fiber-fiber interactions and the twist of filament have a greater influence on the decrease of its fatigue life and the residual strength loss.
Evolutionary Action Score of TP53 Mutations: Integrated Clinico-pathologic And Protein Structural Analysis in Myelodysplastic Syndromes (2020)

ABSTRACT To determine the impact of TP53 mutations on the phenotype and outcome of myelodysplastic syndromes, we quantified the deleterious effects of missense TP53 mutations using the computationally-derived evolutionary action score (higher score indicates worse impact), based on the phylogenetic divergence of the sequence position and amino acid change perturbation, and correlated with clinico-pathologic-genomic features in 270 newly-diagnosed TP53 -mutant patients primarily treated with hypomethylating agents. Using recursive partitioning and regression trees, we identified a subset of patients with low-EAp53 mutations (≤52) with improved overall survival (OS) (n=17, 6%) compared to high-EAp53 (n=253, 94%) [median OS, 48 vs. 10 months; p=0.01]. Compared to high-EAp53, low-EAp53 patients had lower cytogenetic complexity, lower TP53 protein expression, lacked multi-allelic TP53 alterations, but had more somatic mutations in other genes. There was no difference in median TP53 variant allele frequency or distribution of R-IPSS. 3D-protein modeling showed clustering of poor-outcome mutations, indicating structural location influences outcome.
Inteligencia artificial y selección de pruebas en el proceso civil: ¿hacia un proceso más inteligente o hacia un proceso más artificial? (2022)

El presente ensayo contiene un análisis de los principales problemas que puede plantear el uso de la inteligencia artificial aplicada a la selección de pruebas. A partir de una definición básica de inteligencia artificial, el ensayo analiza, en particular, los problemas relativos a los estandardes de pertinencia y de proporcionalidad en la selección de pruebas y las posibles repercusiones sobre el principio de disponibilidad de pruebas.
A Comprehensive Literature Review of JAK Inhibitors in Treatment of Alopecia Areata (2021)

Alopecia areata (AA) is a chronic, immune-mediated form of nonscarring alopecia that is multifactorial and results in localized patches. It is often described as a self-limiting condition that results in the spontaneous regrowth of hair in most cases. However, this regrowth may take several months or years to occur in some patients, leading to the development of psychoemotional trauma in those that are affected. Although several therapies for AA have been developed and tested, there is no specific treatment that has been approved, leading to the availability of many off-label conventional treatment options, with very limited responses. More recently, with the advancement of pre-clinical and genetic studies, a greater understanding of the pathomechanisms involved in the development of AA has been uncovered. This has resulted in the introduction of targeted therapies that use small molecules to block specific pathways involved in AA pathophysiology. As such, the use of janus kinase (JAK) inhibitors for treatment of AA has emerged. JAK inhibitors block the T-cell mediated inflammatory response thought to be the driving factor behind AA pathogenesis, by inhibiting the janus kinase (JAK) signal transducer and activator of transcription (STAT) signaling pathway, leading to a reversal of hair loss in AA patients. Thus, in an effort to demonstrate the efficacy of JAK inhibitors in the treatment of AA, several studies have been published within recent years. However, the question remains, "Are JAK inhibitors effective and safe in the management of Alopecia Areata?". This review aims to provide a comprehensive report on the role, efficacy, and outcomes of using JAK inhibitors in the treatment of AA. To competently answer the research question highlighted, the most recent, quality articles published over a 10-15-year period were sourced using PubMed, NCBI, Research gate, Medline, Cochrane Central Register of Controlled Trials, EMBASE and Google scholar. The literature search was primarily focused on randomized controlled trials (RCTs); however, in the absence of such, only the most recently published case reports, case series, clinical trials and open-label studies published to date were included.
Immunohistochemical Determination of Cytosolic Cytochrome c Concentration in Cardiomyocytes (2005)

Cytochrome c release from the intermembrane space of mitochondria is one of the triggers of apoptosis. There is no histochemical method available to demonstrate cytochrome c in cryostat sections, possibly because small cytosolic proteins diffuse readily into aqueous fixation media. This report shows that it is possible to demonstrate cytochrome c release in cardiomyocytes in failing myocardium using vapor fixation of cryostat sections and immunohistochemistry. The method is calibrated using sections from gelatin blocks containing known concentrations of cytochrome c. The method is applied to the hypertrophied right ventricular wall of rats in which pulmonary hypertension was induced by monocrotaline. Cytochrome c release is found in a fraction of the cardiomyocytes, leading to a mosaic-staining pattern. Cytochrome c release was found in myocytes over the full range of cross-sectional area (from 1 to 3.9 times control) in the hypertrophied myocardium. Cytosolic cytochrome c concentrations up to 0.4-0.5 mM occur frequently.
Synovial fluid biomarker levels predict articular cartilage damage following complete medial meniscectomy in the canine knee (2002)

The purposes of this study were to document the histological changes present in the tibial plateaus 12 weeks after complete medial meniscectomy in dogs and to determine if synovial lavage fluid biomarker levels are predictive of the severity of joint damage. Twelve adult dogs underwent complete unilateral medial meniscectomy and synovial lavage fluid biomarker levels, including cartilage oligomeric matrix protein (COMP), keratan sulfate (5D4). 3B3(-), and 3B3(+), were measured serially at 4-week intervals. The dogs were euthanized 12 weeks after surgery and each medial and lateral tibial plateau from the meniscectomized and contralateral knees was graded histologically. Histological data were analyzed using principal components analysis, which resulted in 4 factors that explained 70% of the variation in the data. Factor 2 (weighted most heavily by subchondral bone thickness) and Factor 3 (representative of articular cartilage damage) were significantly affected by compartmental site (P < 0.01 for both). Both of these factors were highest in the medial tibial plateau of the meniscectomized knee, and Factor 3 was significantly higher in this site than in the medial tibial plateau of the contralateral knee (P < 0.01). Peak levels of all 4 synovial lavage fluid biomarkers occurred at 4 weeks post-meniscectomy and 4-week minus baseline levels of all biomarkers were significantly correlated with the Factor 3 scores. This study demonstrates that significant articular cartilage damage occurs relatively quickly following complete medial meniscectomy in dogs and establishes the content and criterion validity for these synovial fluid lavage biomarkers in canine meniscectomy as surrogate measures of articular cartilage damage.