gebhart/patrepeval huggingface dataset:
A Sagittal Plane Model of the Knee and Cruciate Ligaments With Application of a Sensitivity Analysis (1996)

In this investigation the complex multi-bundle structure of the cruciate ligaments and their interaction with the tibiofemoral joint was modeled analytically by representing the different regions of the cruciates with ligament elements. A sensitivity analysis was then performed to describe the effect that variations of the model input parameters had on the model variables (outputs). The effect that the cruciate ligament bundles had in controlling joint kinematics was dependent on knee flexion angle, and the load applied to the tibiofemoral joint. For passive range of knee motion with the thigh in the horizontal plane (a common rehabilitation activity), all cruciate ligament bundles were strained with the joint positioned between 0 and 10 deg of knee flexion, between 10 and 50 deg only the anterior bundle of the posterior cruciate ligament A-PCL was strained, and from 50 to 90 deg both the anteromedial portion of the anterior cruciate ligament A-ACL and the A-PCL were strained. This finding indicates that a strain distribution about a transverse cross section of the cruciates exists, and demonstrates the importance of differentiating between the strained and unstrained (unloaded) states of these ligaments. The strain value of a cruciate ligament bundle was an indication of how the bundle controls joint kinematics, while the unstrained values describe how much the ligament bundle must deform before it becomes strained and a restraint to tibiofemoral joint motion. In response to anterior and posterior directed loads, applied parallel to the tibial plateau, the respective, ACL and PCL load values were larger in magnitude. The sensitivity of the model outputs to the input parameters was highly dependent on knee flexion angle. The geometrical input parameters of the model (including the ligament insertion site locations and articular surface geometry) had the most pronounced effect on the model output quantities, while the stiffness and initial strain conditions of the ligament bundles had less of an effect on the model outputs. When loaded, the strain values of the ligament bundles were sensitive to the ligament insertion site position. The greatest sensitivity of the model outputs was the femoral insertion of the ACL; supporting clinical impressions and previous experimental findings. Changes in the anterior-posterior dimension of the femoral articular surface did not produce a substantial effect on the model outputs, while changes in the proximal-distal dimension created a large effect; similar results were found for the tibial surface dimensions. These findings indicate that rigid body contact between the articular surfaces may not be a realistic assumption particularly with application to the prediction of tibiofemoral compressive loading and the force/strain values of the cruciate ligament elements. This also has important implications for the design and clinical application of total knee replacements (that function as rigid bodies), particularly those that spare the PCL.
Optical Sensors Based on Hybrid DNA/Conjugated Polymer Complexes (2004)

Single-stranded DNA (ss-DNA) can specifically bind to various targets, including a complementary ss-DNA, ions, proteins, drugs, and so forth. When binding takes place, the oligonucleotide probe often undergoes a conformational transition. This conformational change of the negatively charged ss-DNA can be detected by using a water-soluble, cationic polythiophene derivative, which transduces the complex formation into an optical (colorimetric or fluorometric) signal without any labeling of the probe or the target. This simple and rapid methodology has enabled the specific and sensitive detection of nucleic acids and human thrombin. This new biophotonic tool can easily be applied to the detection of various other biomolecules and is also useful in the high-throughput screening of new drugs.
Single-molecule studies of DNA transcription using atomic force microscopy (2012)

Atomic force microscopy (AFM) can detect single biomacromolecules with a high signal-to-noise ratio on atomically flat biocompatible support surfaces, such as mica. Contrast arises from the innate forces and therefore AFM does not require imaging contrast agents, leading to sample preparation that is relatively straightforward. The ability of AFM to operate in hydrated environments, including humid air and aqueous buffers, allows structure and function of biological and biomolecular systems to be retained. These traits of the AFM are ensuring that it is being increasingly used to study deoxyribonucleic acid (DNA) structure and DNA-protein interactions down to the secondary structure level. This report focuses in particular on reviewing the applications of AFM to the study of DNA transcription in reductionist single-molecule bottom-up approaches. The technique has allowed new insights into the interactions between ribonucleic acid (RNA) polymerase to be gained and enabled quantification of some aspects of the transcription process, such as promoter location, DNA wrapping and elongation. More recently, the trend is towards studying the interactions of more than one enzyme operating on a single DNA template. These methods begin to reveal the mechanics of gene expression at the single-molecule level and will enable us to gain greater understanding of how the genome is transcribed and translated into the proteome.
Factors Affecting Heart Rate Variability in Preterm Infants (1980)

Neonatal heart rate variability (NHRV) was studied in 92 preterm infants (birth weight, 750 to 2,500 gm; gestational age, 28 to 36 weeks). Each infant was monitored continuously during the first 6 hours and for one hour at 24, 48, and 168 hours of life. During each hour NHRV was quantified and related to the following parameters: sex, gestational age, postnatal age, heart rate, and the presence and severity of respiratory distress syndrome (RDS). NHRV in healthy preterm infants was inversely related to heart rate level and directly related to the infant's postnatal age. In healthy babies with gestations of 30 to 36 weeks there was no significant correlation between NHRV and gestation. Decrease in NHRV was significantly related to the severity of RDS, and the reappearance of NHRV in infants with RDS was associated with a good prognosis. Decreased NHRV significantly differentiated the infants with RDS who survived after the fifth hour of life. The data reveal that NHRV (1) should be corrected for heart rate level and postnatal age; (2) is decreased in RDS; and (3) can be used as an indicator of morbidity and mortality in preterm infants with RDS.
The computational complexity of nonlinear compensators based on the Volterra inverse (2002)

The performance of many analogue and digital signal processing systems is limited by nonlinear distortion mechanisms which can be modelled with a Volterra series. The nonlinear distortion can be compensated by the application of post (or pre)-distortion based on a Volterra inverse. The computational complexity associated with this type of compensation can be very high, particularly for systems with high nonlinearity order and long memory. We determine the 3rd and 5th order analytical Volterra inverses, and examine their associated computational complexity. We show how the analytical Volterra inverse can be used to determine the memory span of the kernels of an adaptive Volterra inverse, leading to computational complexity expressions. We then compare the computational complexity of the analytical and adaptive Volterra inverse. The results show that the analytical inverse has a much lower complexity than the adaptive inverse.
A Spatio-Temporal Analysis Approach for Short-Term Forecast of Wind Farm Generation (2014)

In this paper, short-term forecast of wind farm generation is investigated by applying spatio-temporal analysis to extensive measurement data collected from a large wind farm where multiple classes of wind turbines are installed. Specifically, using the data of the wind turbines' power outputs recorded across two consecutive years, graph-learning based spatio-temporal analysis is carried out to characterize the statistical distribution and quantify the level crossing rate of the wind farm's aggregate power output. Built on these characterizations, finite-state Markov chains are constructed for each epoch of three hours and for each individual month, which accounts for the diurnal non-stationarity and the seasonality of wind farm generation. Short-term distributional forecasts and a point forecast are then derived by using the Markov chains and ramp trend information. The distributional forecast can be utilized to study stochastic unit commitment and economic dispatch problems via a Markovian approach. The developed Markov-chain-based distributional forecasts are compared with existing approaches based on high-order autoregressive models and Markov chains by uniform quantization, and the devised point forecasts are compared with persistence forecasts and high-order autoregressive model-based point forecasts. Numerical test results demonstrate the improved performance of the Markov chains developed by spatio-temporal analysis over existing approaches.
A Short Step Synthesis of AV-toxin D (1988)

Abstract AV-toxin D(1) is the most active phytotoxic component among AV-toxins isolated from the cultural medium of Acrospermum viticola which cause the zonate leave spot disease, and is the sole natural product having methoxy groups on phenoxazone skeleton. By using the nitrene annulation reaction, we succeeded in the short step synthesis of 1.
Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases (2008)

Gene knockout is the most powerful tool for determining gene function or permanently modifying the phenotypic characteristics of a cell. Existing methods for gene disruption are limited by their efficiency, time to completion, and/or the potential for confounding off-target effects. Here, we demonstrate a rapid single-step approach to targeted gene knockout in mammalian cells, using engineered zinc-finger nucleases (ZFNs). ZFNs can be designed to target a chosen locus with high specificity. Upon transient expression of these nucleases the target gene is first cleaved by the ZFNs and then repaired by a natural-but imperfect-DNA repair process, nonhomologous end joining. This often results in the generation of mutant (null) alleles. As proof of concept for this approach we designed ZFNs to target the dihydrofolate reductase (DHFR) gene in a Chinese hamster ovary (CHO) cell line. We observed biallelic gene disruption at frequencies >1%, thus obviating the need for selection markers. Three new genetically distinct DHFR(-/-) cell lines were generated. Each new line exhibited growth and functional properties consistent with the specific knockout of the DHFR gene. Importantly, target gene disruption is complete within 2-3 days of transient ZFN delivery, thus enabling the isolation of the resultant DHFR(-/-) cell lines within 1 month. These data demonstrate further the utility of ZFNs for rapid mammalian cell line engineering and establish a new method for gene knockout with application to reverse genetics, functional genomics, drug discovery, and therapeutic recombinant protein production.
A Variational Method for Multiple-Image Blending (2011)

The main aim of this paper is to develop an algorithm for blending of multiple images in the image-stitching process. Our idea is to propose a variational method containing an energy functional to determine both a stitched image and weighting mask functions of multiple input images for image blending. The existence of the solution of the proposed energy functional is shown. We also present an alternative minimizing algorithm to solve the proposed model numerically and show the convergence of this algorithm. Experimental results show that the proposed model works effectively and efficiently and that the proposed method is competitive with the tested existing methods under noisy conditions.
THE EXCITATION OF 8‐METHOXYPSORALEN WITH VISIBLE LIGHT: REVERSED PHASE HPLC QUANTITATION OF MONOADDUCTS and CROSS‐LINKS (1993)

The formation of 8-methoxypsoralen-DNA monoadducts and cross-links is presumed to be responsible for the efficacy of photochemotherapies that employ 8-methoxypsoralen activated with long-wavelength ultraviolet radiation (UVA, 320-400 nm). In this report it is shown that 8-methoxypsoralen can also be activated with visible light (419 nm). Bovine aorta smooth muscle cells were treated with 8-methoxypsoralen (1,000 ng/mL) and 419 nm light (up to 12 J/cm2). Cellular DNA was isolated, hydrolyzed using nucleolytic enzymes and then analyzed by reversed-phase high-performance liquid chromatography. The primary effect of using visible light instead of long-wavelength ultraviolet radiation is a more than 10-fold reduction in the extent of cross-link formation. Because the extent of monoadduct and cross-link formation has not been routinely measured in experiments in which cellular assays have been performed, it is difficult to correlate cell response to the presence of a particular type of 8-methoxypsoralen photoadduct (monoadduct or cross-link). Thus, the use of visible light allows the study of cells containing nearly 100% monoadducts. In addition, the reduction in cross-link formation when visible light is used to activate the compound may also reduce the mutagenicity of 8-methoxypsoralen and hence enhance its therapeutic efficacy.
Prognostic Relevance of Promoter Hypermethylation of Multiple Genes in Breast Cancer Patients (2009)

Background : Methylation-mediated suppression of detoxification, DNA repair and tumor suppressor genes has been implicated in cancer development. This study was designed to investigate the impact of concurrent methylation of multiple genes in breast tumors on disease prognosis. Methods : Methylation specific PCR was carried out to analyze the methylation status of seven genes in archived breast tissues and determine the effect of aberrant methylation of multiple genes on disease prognosis and patients’ survival. Results : Promoter hypermethylation was observed in PRB 67%, ER α 64%, RASSF1A 63%, p16INK4A 51%, PRBβ 2 22%, GSTP1 25% and BRCA1 27% of the breast cancers, respectively. Concurrent methylation of BRCA1, ER α , GSTP1 and RAR β 2, was observed in a large proportion of breast cancers analyzed, suggesting that these genes do not appear to be methylated alone. Patients with high methylation indices had poor prognosis ( p &lt; 0.001, Hazards ratio = 14.58). Cox regression analysis showed RAR β 2 promoter methylation to be an independent important determinant of breast cancer prognosis. Conclusions : Our results suggest that methylation of multiple genes plays an important role in prognosis of breast cancer. Our study not only describes the association of methylation mediated silencing of multiple genes with the severity of disease, but also drives to speculate the molecular crosstalk between genes or genetic pathways regulated by them individually.
Consistent hashing and random trees (1997)

We describe a family of caching protocols for distrib-uted networks that can be used to decrease or eliminate the occurrence of hot spots in the network. Our protocols are particularly designed for use with very large networks such as the Internet, where delays caused by hot spots can be severe, and where it is not feasible for every server to have complete information about the current state of the entire network. The protocols are easy to implement using existing network protocols such as TCP/IP, and require very little overhead. The protocols work with local control, make efficient use of existing resources, and scale gracefully as the network grows. Our caching protocols are based on a special kind of hashing that we call consistent hashing. Roughly speaking, a consistent hash function is one which changes minimally as the range of the function changes. Through the development of good consistent hash functions, we are able to develop caching protocols which do not require users to have a current or even consistent view of the network. We believe that consistent hash functions may eventually prove to be useful in other applications such as distributed name servers and/or quorum systems.
Progress in the use of biochemical and biological markers for evaluation of rheumatoid arthritis (2000)

Rheumatoid arthritis (RA) is a chronic systemic inflammatory autoimmune disorder which is predominant in females. The exact etiology remains undefined. Recently, a large number of biochemical and biologic markers, which are useful in the diagnosis, prognosis, and monitoring therapy of RA, have been reported. The new markers include genetic markers, filaggrin, citrulline containing peptides, A2/RA33, cytokines, joint and collagen breakdown products, and bone turnover markers. No laboratory tests in and of themselves are diagnostic of RA. The new markers have been employed in monitoring RA patients during treatment and following the course of the disease. With the development of innovative therapies for RA, many of the biochemical and biologic markers will be useful.
Escherichia coli mutT mutator effect during in vitro DNA synthesis. Enhanced A.G replicational errors. (1987)

The mechanism of the Escherichia coli mutT mutator effect was investigated using single-stranded phage as a mutational target. In vivo experiments showed that two M13mp2 lacZ alpha nonsense mutants reverted at a higher rate on a mutT1 host than on the wild-type host. The specificity of this mutator effect was identical to that observed for E. coli genes: A.T----C.G transversions. The mutT effect was subsequently demonstrated in vitro during DNA replication of M13mp2 DNA in cell-free extracts of E. coli. Replication (the single-stranded----replicative form conversion) in mutT1 extracts proceeded with a higher error rate than in wild-type extracts, and DNA sequence analysis of the in vitro revertants revealed the specific induction of A.T----C.G transversions. On the basis of the template specificity of the mutT effect in vitro, we conclude that the mutT effect involves the aberrant processing of A.G rather than T.C mispairs.
Partial amino acid sequence and molecular cloning of the encoding gene for the major outer membrane protein of Chlamydia trachomatis (1985)

The first 25 N-terminal amino acids of the major outer membrane protein of Chlamydia trachomatis serovar L2 were determined. The amino acid sequence was used to construct an oligonucleotide probe specific for the major outer membrane protein gene. Using this oligonucleotide as a hybridization major outer membrane protein gene. Using this oligonucleotide as a hybridization probe, we discovered one recombinant clone that produced a 15-kilodalton polypeptide which reacted with a monoclonal antibody directed against the major outer membrane protein type-specific epitope. In a separate set of experiments, we uncovered another recombinant clone that produced a 51-kilodalton polypeptide which was reactive with an anti-major outer membrane protein subspecies-specific monoclonal antibody. The expression of these recombinant DNA plasmids in Escherichia coli is discussed.
Preparative Purification of Recombinant Proteins: Current Status and Future Trends (2013)

Advances in fermentation technologies have resulted in the production of increased yields of proteins of economic, biopharmaceutical, and medicinal importance. Consequently, there is an absolute requirement for the development of rapid, cost-effective methodologies which facilitate the purification of such products in the absence of contaminants, such as superfluous proteins and endotoxins. Here, we provide a comprehensive overview of a selection of key purification methodologies currently being applied in both academic and industrial settings and discuss how innovative and effective protocols such as aqueous two-phase partitioning, membrane chromatography, and high-performance tangential flow filtration may be applied independently of or in conjunction with more traditional protocols for downstream processing applications.
Thiamine‐regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch‐like domain in the 5′‐UTR (2003)

Exogenous thiamine regulates Aspergillus oryzae thiA, which is involved in thiamine synthesis. One of the two introns in its 5'-untranslated region (5'-UTR) contains motifs (regions A and B) highly conserved among fungal thiamine biosynthesis genes. Deletion of either region relieved the repression by thiamine and thiamine inhibited intron splicing, suggesting that regions A and B are required for efficient splicing. Furthermore, transcript splicing was essential for thiA gene expression. These observations suggest a novel gene expression regulatory mechanism in filamentous fungi, in which exogenous thiamine controls intron splicing to regulate gene expression. Interestingly, regions A and B constitute a part of a thiamine pyrophosphate-binding riboswitch-like domain that has been quite recently found in the 5'-UTR of thiA.
Anti-GD3 Chimeric sFv-CD28/T-Cell Receptor ζ Designer T Cells for Treatment of Metastatic Melanoma and Other Neuroectodermal Tumors (2010)

As a reagent for clinical development, the second-generation product is shown to have superior properties to warrant its preference for clinical designer T-cell immunotherapy for melanoma and other tumors. Systemic IL2 was required for optimal activity in an established tumor model.
Direct Relationship Between Shape and Size of Template and Synthesis of Copper Metal Particles (1999)

Well-defined surfactant self-assembled microstructures are needed to take full advantage of the templating strategy for the generation of nanoparticles with controlled size and anisometry, as demonstrated here. For example, at a high concentration of Cu(AOT)2 (AOT = bis(ethylhexyl)sulfosuccinate) in isooctane–water the micellar supra-aggregate depicted in the Figure forms, and spherical copper metal particles are produced.
Comparative Genomics of the Eukaryotes (2000)

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.