gebhart/patrepeval huggingface dataset:
Study on porous silk fibroin materials. I. Fine structure of freeze dried silk fibroin (2001)

Silk fibroin solution was prepared by dissolving the silk fibroin in triad solvent CaCl2 · CH3CH2OH · H2O. In this article we tested and analyzed the state of frozen silk fibroin solution and fine structure of freeze dried porous silk fibroin materials. The results indicated that the glass transition temperature of frozen silk fibroin solution ranges from −34 to −20°C, and the initial melting temperature of ice in frozen solution is about −8.5°C. When porous silk fibroin materials are prepared by means of freeze drying, if freezing temperature is below −20°C, the structure of silk fibroin is mainly amorphous with a little silk II crystal structure, and if freezing temperature is above −20°C, quite a lot of silk I crystal structure forms. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 79: 2185–2191, 2001
Comparison of Training Methods for Deep Neural Networks (2015)

This report describes the difficulties of training neural networks and in particular deep neural networks. It then provides a literature review of training methods for deep neural networks, with a focus on pre-training. It focuses on Deep Belief Networks composed of Restricted Boltzmann Machines and Stacked Autoencoders and provides an outreach on further and alternative approaches. It also includes related practical recommendations from the literature on training them. In the second part, initial experiments using some of the covered methods are performed on two databases. In particular, experiments are performed on the MNIST hand-written digit dataset and on facial emotion data from a Kaggle competition. The results are discussed in the context of results reported in other research papers. An error rate lower than the best contribution to the Kaggle competition is achieved using an optimized Stacked Autoencoder.
Identification of MUC5B, MUC5AC and small amounts of MUC2 mucins in cystic fibrosis airway secretions (1999)

To investigate the genetic identities of the mucins secreted in cystic fibrosis (CF) airways, sputum was collected from five individuals. Samples were separated into gel and sol phases by high-speed centrifugation and the gel phase was extracted in 6 M guanidinium chloride. The 'insoluble' residue remaining after extraction of the gel phase was brought into solution by reduction/alkylation. Density-gradient centrifugation in CsCl revealed polydisperse distributions of sialic acid-containing mucins in the gel phase, insoluble residue and sol phase fractions and the degree of variation between the different individuals was low. Antibodies recognizing MUC5AC and MUC5B identified these mucins in each of the fractions. MUC2, however, was present only as a component of the insoluble residue from the gel which accounted for less than 4% by mass of the total mucins. MUC5B and MUC5AC from the gel phase were large oligomeric species composed of disulphide-bond linked subunits and MUC5B was present as two populations with different charge densities which are likely to correspond to MUC5B 'glycoforms'. The sol phase contained, in addition to MUC5AC and MUC5B, mainly smaller mucins which did not react with the antisera and which were probably degraded. MUC5AC appeared to be enriched in the sol, suggesting that this mucin may be more susceptible to proteolytic degradation than MUC5B. The mucins present in sputum remained broadly similar during acute exacerbation and following antibiotic treatment, although the relative amount of an acidic MUC5B glycoform was decreased during infection.
The role of perspective effects and accelerations in perceived three-dimensional structure-from-motion. (2000)

It has been suggested that perceived three-dimensional (3D) structure-from-motion can be accounted for by a 2-frame orthographic approximation of the flow field. This study investigated the extent to which higher order cues (perspective and acceleration) are used in addition to first-order flow. Participants matched the 3D dihedral angle of a hinged plane (probe) defined by multiple-depth cues to one defined by motion only, for stimulus sizes of 8 and 33 degrees, using perspective and orthographic projection. The results show that perspective effects can be important even for relatively small stimuli (8 degrees) and that accelerations contribute to perceived shape. In all conditions, large biases were found. These are well accounted for by a model in which all relevant flow measurements (first-order, perspective, and acceleration) are used together with estimates of the noise in each. The model has no built-in bias toward particular 3D shapes. Instead, the visual system may act as an optimal estimator of 3D structure-from-motion.
Bacterial synthesis of N-hydroxycinnamoyl phenethylamines and tyramines (2015)

We reconstructed the metabolic pathways for synthesis of N-HC tyramines and N-HC phenethylamines by expressing several genes including 4CL, TST or SHT, PDC or TDC, and TAL (encoding tyrosine ammonia lyase) and engineering the shikimate metabolic pathway to increase endogenous tyrosine concentration in E. coli. Approximately 101.9 mg/L N-(p-coumaroyl) phenethylamine and 495.4 mg/L N-(p-coumaroyl) tyramine were synthesized from p-coumaric acid. Furthermore, 152.5 mg/L N-(p-coumaroyl) phenethylamine and 94.7 mg/L N-(p-coumaroyl) tyramine were synthesized from glucose.
Optimization of Nonconventional Well Type, Location, and Trajectory (2003)

Summary The determination of the optimal type, location, and trajectory of a nonconventional well is extremely challenging. The problem is more complicated than other well optimization problems because of the wide variety of possible well types (i.e., number, location, and orientation of laterals) that must be considered. In this paper, a general methodology for the optimization of nonconventional wells is presented. The optimization procedure entails a Genetic Algorithm (GA) applied in conjunction with several acceleration routines that include an artificial neural network, a hill climber, and a near-well upscaling technique. The overall methodology is then applied to a number of problems involving different reservoir types and fluid systems. It is shown that the objective function (cumulative oil produced or net present value of the project) is always increased relative to its value in the first generation of the optimization, in some cases by 30% or more. The optimal well type is found to vary depending on the reservoir model and objective function. The effects of reservoir uncertainty are also included in some of the optimizations. It is shown that the optimal type of well can differ, depending on whether single or multiple realizations of the reservoir geology are considered.
Biosynthesis of cis‐Jasmone: a pathway for the inactivation and the disposal of the plant stress hormone jasmonic acid to the gas phase? (1997)

Abstract Flowers of Jasminum rincospernum convert deuterium‐labeled jasmonic acid [ 2 H 5 ]‐ 4a and methyl 1,2‐didehy‐drojasmonate [ 2 H 4 ]‐ 8 into labeled cis ‐jasmone [ 2 H 4 ]‐ 1. The labeling pattern of the resulting cis ‐jasmone ( 1 ) is consistent with a Grob fragmentation of the didehydrojasmonic acid 8a by decarboxylation after protonation of the keto group. The pathway is also operative in leaves of several higher plants, including mono‐ and dicotyledonous specimens. In Lima beans besides cis‐jasmone ( 1 ) an equimolar mixture of trans ‐ and cis ‐isomers of methyl jasmonate ( 4 ) and epi ‐ 4 , is emitted after treatment with Jasmonic acid ( 4a ). The relative ratio of 1 and 4 / epi ‐ 4 is critically dependent on the concentration of the administered jasmonic acid ( 4a ) and the ambient temperature of the plant. Unlike 4a , the 1,2‐didehydrojasmonic acid ( 8a ) is not able to induce volatile biosynthesis. Therefore, the transformation of 4a via 8 a into 1 appears to have a special importance for the irreversible inactivation and disposal of the plant stress hormone jasmonic acid to the gas phase and may serve, besides other modes of inactivation, as a shunt in case of high internal of the stress hormone 4a. The conversion of the biologically active jasmonic acid ( 4a ) into the inactive and volatile cis ‐jasmone (1) is the first example of a disposal of an inactive metabolite of a phytohormone to the gas phase as an infinite sink.
The Parkinson's disease genes pink1 and parkin promote mitochondrial fission and/or inhibit fusion in Drosophila (2008)

Mutations in PTEN-induced kinase 1 (pink1) or parkin cause autosomal-recessive and some sporadic forms of Parkinson's disease. pink1 acts upstream of parkin in a common genetic pathway to regulate mitochondrial integrity in Drosophila. Mitochondrial morphology is maintained by a dynamic balance between the opposing actions of mitochondrial fusion, controlled by Mitofusin (mfn) and Optic atrophy 1 (opa1), and mitochondrial fission, controlled by drp1. Here, we explore interactions between pink1/parkin and the mitochondrial fusion/fission machinery. Muscle-specific knockdown of the fly homologue of Mfn (Marf) or opa1, or overexpression of drp1, results in significant mitochondrial fragmentation. Mfn-knockdown flies also display altered cristae morphology. Interestingly, knockdown of Mfn or opa1 or overexpression of drp1, rescues the phenotypes of muscle degeneration, cell death, and mitochondrial abnormalities in pink1 or parkin mutants. In the male germline, we also observe genetic interactions between pink1 and the testes-specific mfn homologue fuzzy onion, and between pink1 and drp1. Our data suggest that the pink1/parkin pathway promotes mitochondrial fission and/or inhibits fusion by negatively regulating mfn and opa1 function, and/or positively regulating drp1. However, pink1 and parkin mutant flies show distinct mitochondrial phenotypes from drp1 mutant flies, and flies carrying a heterozygous mutation in drp1 enhance the pink1-null phenotype, resulting in lethality. These results suggest that pink1 and parkin are likely not core components of the drp1-mediated mitochondrial fission machinery. Modification of fusion and fission may represent a novel therapeutic strategy for Parkinson's disease.
SubtiList: the reference database for the Bacillus subtilis genome (2002)

SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome project, SubtiList provides a curated dataset of DNA and protein sequences, combined with the relevant annotations and functional assignments. Information about gene functions and products is continuously updated by linking relevant bibliographic references. Recently, sequence corrections arising from both systematic verifications and submissions by individual scientists were included in the reference genome sequence. SubtiList is based on a generic relational data schema and a World Wide Web interface developed for the handling of bacterial genomes, called GenoList. The World Wide Web interface was designed to allow users to easily browse through genome data and retrieve information according to common biological queries. SubtiList also provides more elaborate tools, such as pattern searching, which are tightly connected to the overall browsing system. SubtiList is accessible at http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at http://genolist.pasteur.fr/.
Variable-rate tree-structured vector quantizers (1995)

In general, growth algorithms for optimal tree-structured vector quantizers do not exist. In this paper we show that if the source satisfies certain conditions; namely, that of diminishing marginal returns; optimal growth algorithms do exist. We present such an algorithm and compare its performance with that of other tree growth algorithms. Even for sources that do not meet the necessary conditions for the growth algorithm to be optimal, such as for speech with unknown statistics, it is seen by simulation that the algorithm outperforms other known growth algorithms, For sources that do not satisfy the required conditions, the algorithm presented here can also be used to grow the initial tree for the pruning process. The performance of such pruned trees is superior to that of trees pruned from full trees of the same rate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Species-Specific High Molecular Weight Forms of Basic Fibroblast Growth Factor (1990)

bFGF was extracted from either mouse, rat and human cell lines or mouse, rat bovine and human brain tissue and partially purified by cation exchange chromatography and heparin-affinity chromatography. When the heparin-affinity purified proteins were probed on Western blots with antisera against either a highly conserved internal bFGF sequence or recombinant 18 kDa bFGF, species-specific forms of bFGF were detected. bFGF proteins from rat and mouse sources were of apparent molecular weight 18,000, 21,500 and 22,000 whereas those from human sources were of 18,000, 22,500 and 24,000. Bovine bFGF proteins were similar to the multiple human bFGFs. The 22.5 kDa and 24 kDa proteins from human cells were also recognized by an antibody specific for the N-terminally extended forms of human bFGF, whereas this antibody failed to detect 18 kDa bFGF. We showed that the differences in molecular weight between human and rat bFGFs are consistent with the predicted ATG (methionine) or alternative CTG (leucine) translational start sites in the 5' upstream sequences of bFGF cDNAs. In addition we show that, irrespective of the species of origin, the larger bFGF proteins may be separated from 18 kDa bFGF by Mono S chromatography.
A novel Aurora-A kinase inhibitor MLN8237 induces cytotoxicity and cell-cycle arrest in multiple myeloma (2010)

Aurora-A is a mitotic kinase that regulates mitotic spindle formation and segregation. In multiple myeloma (MM), high Aurora-A gene expression has been correlated with centrosome amplification and proliferation; thus, inhibition of Aurora-A in MM may prove to be therapeutically beneficial. Here we assess the in vitro and in vivo anti-MM activity of MLN8237, a small-molecule Aurora-A kinase inhibitor. Treatment of cultured MM cells with MLN8237 results in mitotic spindle abnormalities, mitotic accumulation, as well as inhibition of cell proliferation through apoptosis and senescence. In addition, MLN8237 up-regulates p53 and tumor suppressor genes p21 and p27. Combining MLN8237 with dexamethasone, doxorubicin, or bortezomib induces synergistic/additive anti-MM activity in vitro. In vivo anti-MM activity of MLN8237 was confirmed using a xenograft-murine model of human-MM. Tumor burden was significantly reduced (P = .007) and overall survival was significantly increased (P < .005) in animals treated with 30 mg/kg MLN8237 for 21 days. Induction of apoptosis and cell death by MLN8237 were confirmed in tumor cells excised from treated animals by TdT-mediated dUTP nick end labeling assay. MLN8237 is currently in phase 1 and phase 2 clinical trials in patients with advanced malignancies, and our preclinical results suggest that MLN8237 may be a promising novel targeted therapy in MM.
Effects of Vascular Endothelial Growth Factor and Basic Fibroblast Growth Factor:Application with Corneal Grafts on the Chorioallantoic Membrane (1993)

The corneae of 17- to 19-day-old chick embryos were dissected and grafted on the chorioallantoic membrane (CAM) of 10- to 14-day-old embryos with reincubation periods of 3-9 days. After fixation, serial semithin or paraffin sections were made. Furthermore, two growth factors were applied together with the corneae. The 165-amino-acid vascular endothelial growth factor (VEGF165) or basic fibroblast growth factor (bFGF) was either pipetted onto the corneae, or pieces of shell membrane were soaked in a factor solution, dried and inserted into an incision in the corneae. After a reincubation of 4-6 days, serial paraffin sections were made. The controls show that the viability of the grafts decreases with increasing age of the host CAM. Furthermore, with prolonged reincubation, the viable corneae become more and more spherical. Due to this movement, necrotic tissue of the CAM is shifted into the center of the sphere. After 9 days, blood vessels can be seen growing in the direction of the necrosis. bFGF pipetted onto the grafts induces marked proliferation of the stroma of the CAM beneath the corneae. Additionally, bFGF carriers inserted into the corneae induce fibrocyte ingrowth in the grafts together with a few blood vessels. VEGF165 specifically induces vascular growth in the CAM beneath the cornea but did not induce blood vessel growth into the grafts. The pros and cons of the method are discussed.
Specificity and diagnostic implications of the reactivity pattern of a panel of monoclonal antibodies against myeloid leukemia cells (1986)

The immunological phenotypes of leukemia cell samples from 60 patients, of whom 54 had acute myeloid leukemia (AML), were assessed with a panel of monoclonal antibodies (Mabs) with specificity for the following epitopes: Epitopes associated with myeloid leukemia cells, Epitopes expressed only on immature myeloid cells (or subsets) and on monocytes, Epitopes only expressed on granulocytes or on granulocytes and mature myeloid cells (promyelocytes, myelocytes and monocytes), Epitopes on HLA-class II (DR) and HLA-class I molecules and on insulin receptors. This panel of Mabs proved useful to identify leukemia cells in blood and to assess their myeloid origin. The panel of Mabs was found also to be useful for immunophenotyping of leukemia cells. Furthermore, the analysis revealed considerable variations in the immunological phenotype of AML cells, reflecting antigenic heterogeneity within the individual leukemia cell population as well as abnormal or no expression of histocompatibility antigens and insulin receptors in some samples. Some of the Mabs bound preferentially to subgroups in the French-American-British (FAB) classification.
Infection in Xenotransplantation (2001)

Advances in transplantation immunology have enhanced the possibility of xenotransplantation as a therapeutic option for end-stage organ failure. The potential spread of animal-derived pathogens to the recipient and to the general population, termed "xenosis," is a potential complication of interspecies transplantation. Recognition of such novel infections may be complicated by infections due to altered microbiologic behavior and clinical symptomatology of these organisms, particularly in the immunocompromised xenograft recipient. Particular concern exists over the activation of latent viruses, including retroviruses, from xenograft tissues. Based on experience with human allogeneic transplantation, those pathogens considered most likely to cause human disease can be excluded prospectively from herds of animals developed for organ donation. Research is needed into the activation and behavior of retroviruses and other potential pathogens in xenotransplantation. Xenotransplantation may also provide unique opportunities not only for the care of patients with organ failure, but in the therapy of individuals with chronic infections to which the xenograft may be resistant. Clinical protocols must be developed so as to enhance the safety of the recipient and of the community-at-large.
Tc17 cells are associated with cigarette smoke‐induced lung inflammation and emphysema (2015)

Long-term cigarette smoke exposure induced Tc17 cell expansion both locally and distally, which was associated with emphysema and deoxyribonucleic acid damage. As an important source of IL-17A, this T cell subset may be a potential target for chronic obstructive pulmonary disease therapy.
The SPARKy (Spring Ankle With Regenerative Kinetics) Project: Design and Analysis of a Robotic Transtibial Prosthesis With Regenerative Kinetics (2007)

Even today’s most sophisticated microprocessor controlled ankle-foot prosthetic devices are passive. They lack internal elements that actively generate power, which is required during the “push-off” phase of normal able-bodied walking gait. Consequently, lower limb amputees expend 20–30% more metabolic power to walk at the same speed as able-bodied individuals. Key challenges in the development of an active ankle-foot prosthetic device are the lack of high power and energy densities in current actuator technology. Human gait requires 250W of peak power and 36 Joules of energy per step (80kg subject at 0.8Hz walking rate). Even a highly efficient motor such as the RE75 by Maxon Precision Motors, Inc. rated for 250W continuous power with an appropriate gearbox would weigh 6.6 Kg. This paper presents the first phase of the Spring Ankle with Regenerative Kinetics (SPARKy 1), a multi-phased project funded by the US Army Military Amputee Research Program, which seeks to develop a new generation of powered prosthetic devices based on the Robotic Tendon actuator, that significantly minimizes the peak power requirement of an electric motor and total system energy requirement while providing the amputee enhanced ankle motion and “push-off” power. This paper will present data to show the kinetic advantages of the Robotic Tendon and the electro-mechanical design and analysis of SPARKy 1 that will provide its users with 100% of required “push-off” power and ankle sagittal plane range of motion comparable to able-bodied gait.
CD80 down-regulation is associated to aberrant DNA methylation in non-inflammatory colon carcinogenesis (2016)

These results indicate that the failure of immune surveillance mechanisms in non-inflammatory colon carcinogenesis may be linked to genomic methylation directly or indirectly affecting CD80 expression.
A practical approach to robotic design for the DARPA Urban Challenge (2008)

Abstract This article presents a practical approach to engineering a robot to effectively navigate in an urban environment. Inherent in this approach is the use of relatively simple sensors, actuators, and processors to generate robot vision, intelligence, and planning. Sensor data are fused from multiple low‐cost, two‐dimensional laser scanners with an innovative rotational mount to provide three‐dimensional coverage with image processing using both range and intensity data. Information is combined with Doppler radar returns to yield a world view processed by a context‐based reasoning control system to yield tactical mission commands forwarded to traditional proportional‐integral‐derivative (PID) control loops. As an example of simplicity and robustness, steering control successfully utilized a relatively simple follow‐the‐carrot guidance approach that has been successfully demonstrated at speeds of 60 mph (97 km/h). The approach yielded a robot that reached the finals of the Urban Challenge and completed approximately 2 h of the event before being forced to withdraw as a result of a global positioning system data failure. © 2008 Wiley Periodicals, Inc.
Heritable Gene Knockout in Caenorhabditis elegans by Direct Injection of Cas9–sgRNA Ribonucleoproteins (2013)

We present a novel method of targeted gene disruption that involves direct injection of recombinant Cas9 protein complexed with guide RNA into the gonad of the nematode Caenorhabditis elegans. Biallelic mutants were recovered among the F1 progeny, demonstrating the high efficiency of this method.