gebhart/patrepeval huggingface dataset:
Melanoregulin regulates a shedding mechanism that drives melanosome transfer from melanocytes to keratinocytes (2012)

Mammalian pigmentation is driven by the intercellular transfer of pigment-containing melanosomes from the tips of melanocyte dendrites to surrounding keratinocytes. Tip accumulation of melanosomes requires myosin Va, because melanosomes concentrate in the center of melanocytes from myosin Va-null (dilute) mice. This distribution defect results in inefficient melanosome transfer and a dilution of coat color. Dilute mice that simultaneously lack melanoregulin, the product of the dilute suppressor locus, exhibit a nearly complete restoration of coat color, but, surprisingly, melanosomes remain concentrated in the center of their melanocytes. Here we show that dilute/dsu melanocytes, but not dilute melanocytes, readily transfer the melanosomes concentrated in their center to surrounding keratinocytes in situ. Using time-lapse imaging of WT melanocyte/keratinocyte cocultures in which the plasma membranes of the two cells are marked with different colors, we define an intercellular melanosome transfer pathway that involves the shedding by the melanocyte of melanosome-rich packages, which subsequently are phagocytosed by the keratinocyte. Shedding, which occurs primarily at dendritic tips but also from more central regions, involves adhesion to the keratinocyte, thinning behind the forming package, and apparent self-abscission. Finally, we show that shedding from the cell center is sixfold more frequent in cultured dilute/dsu melanocytes than in dilute melanocytes, consistent with the in situ data. Together, these results explain how dsu restores the coat color of dilute mice without restoring intracellular melanosome distribution, indicate that melanoregulin is a negative regulator of melanosome transfer, and provide insight into the mechanism of intercellular melanosome transfer.
Atmospheric Radiation: Theoretical Basis (1989)

Introduction 1. Theory of Radiative Transfer 2. Vibration-Rotation Spectra of Gaseous Molecules 3. Band Models 4. Absorption by Atmospheric Gases 5. Radiation Calculations in a Clear Atmosphere 6. Extinction by Molecules and Droplets 7. Radiative Transfer in a Scattering Atmosphere 8. Atmospheres in Radiative Equilibrium 9. Evolution of a Thermal Disturbance Appendix 1: Physical constants Appendix 2: Spectroscopic units Appendix 3: A model atmosphere Appendix 4: Properties of water vapor Appendix 5: The Planck function Appendix 6: The exponential integrals Appendix 7: The Ladenburg and Reiche function Appendix 8: The Elsasser function Appendix 9: The physical state of the sun
The magical Fibonacci number (1990)

Fibonacci numbers are explained, and some of the many manifestations of the Fibonacci series in nature are described. These range from the so-called golden spiral to the Penrose tiling patterns that describe the structure of quasicrystals.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Covalent structure, disulfide bonding, and identification of reactive surface and active site residues of human prostatic acid phosphatase (1991)

The pairing of the half-cysteine residues of human prostatic acid phosphatase was established by proteolytic digestion and analysis of the resulting peptide mixtures by fast atom bombardment mass spectrometry (FAB-MS). An independently derived, full length cDNA clone was used as the basis for the interpretation of the FAB-MS data. The sequence of the native protein is that predicted from the present cDNA sequence, except for the carboxyl-terminal end and some possible post-translational deamidations. Isolated human prostatic acid phosphatase was found to have multiple carboxyl-terminal ends, terminating in Thr, Glu, and Asp, corresponding to residues 349-351 of the 354-residue protein that is predicted from the cDNA sequence after removal of a leader peptide. The protein contains no free sulfhydryl groups. The identical monomer chains of the dimeric native enzyme are found to contain three disulfide bonds, specifically Cys-129 to Cys-340, Cys-183 to Cys-281, and Cys-315 to Cys-319. In view of the conserved positions of cysteines in the homologous human and rat liver lysosomal acid phosphatases, an identical disulfide bonding pattern may be predicted for those proteins. The location of a potential antigenic site was established by selective labeling of proximate tyrosine residues predicted to be on the surface. A conserved RHGXRXP sequence is present in the prostatic, lysosomal, Escherichia coli, and yeast acid phosphatases and is predicted to be of mechanistic significance. In addition, residue Arg-54 is shown to be an active site residue by reaction of the enzyme with phenylglyoxal. Interestingly, this residue is present in a sequence RXRY (R,H) that is also present in lysosomal phosphatase and in recently described protein tyrosine phosphatases.
Cytostatic 6-Arylpurine Nucleosides. 6. SAR in Anti-HCV and Cytostatic Activity of Extended Series of 6-Hetarylpurine Ribonucleosides (2005)

Significant anti-HCV activity of 6-hetarylpurine ribonucleosides has been discovered and is reported here for the first time and compared with cytostatic effect. An extended series of 6-hetarylpurine nucleosides has been prepared by heterocyclizations in position 6 of purine nucleosides or by cross-couplings of 6-chloropurine nucleosides with hetarylboronic acids, -stannanes, or -zinc halides. The most anti-HCV active were purine ribonucleosides bearing pyrrol-3-yl or 2-furyl groups exerting EC(90) = 0.14 and 0.4 microM, respectively.
KNIME - the Konstanz information miner (2009)

The Konstanz Information Miner is a modular environment, which enables easy visual assembly and interactive execution of a data pipeline. It is designed as a teaching, research and collaboration platform, which enables simple integration of new algorithms and tools as well as data manipulation or visualization methods in the form of new modules or nodes. In this paper we describe some of the design aspects of the underlying architecture, briey sketch how new nodes can be incorporated, and highlight some of the new features of version 2.0.
Analysis of Actinobacillus pleuropneumoniae and Related Organisms by DNA-DNA Hybridization and Restriction Endonuclease Fingerprinting (1991)

The objective of this study was to determine the degree of genetic relatedness of Actinobacillus pleuropneumoniae to selected members of the family Pasteurellaceae, with particular emphasis on species commonly associated with swine. Free-solution DNA-DNA hybridization studies revealed that representative strains of all 12 serotypes of A. pleuropneumoniae formed a homogeneous group, sharing 74 to 90% sequence homology with A. pleuropneumoniae serotype 1. All serotypes of A. pleuropneumoniae tested demonstrated a high degree of genetic relatedness (66 to 79%) to the type species of the genus Actinobacillus, A. lignieresii. Little homology (less than 20%) was detected between A. pleuropneumoniae strains and selected Haemophilus spp. and Pasteurella spp. Since free-solution hybridization methods are technically demanding and require large amounts of highly purified DNA, restriction endonuclease fingerprinting (REF) was examined to determine whether it could be a useful taxonomic tool for classification of members of the family Pasteurellaceae. REF profiles were compared, and the degree of similarity between organisms was quantitated by calculating Jaccard similarity coefficients. There was a significant positive relationship between the REF Jaccard coefficients and the DNA homology values determined from free-solution hybridization experiments.
Studies of Photochemical Reactions of 7,8-Digermabicyclo[2.2.2]octadienes by Steady-State and Laser Flash Photolysis Techniques (2000)

The photochemistry of 1,4-diphenyl-2,3-benzo-7,7,8,8-tetraalkyl-7,8-digermabicyclo[2.2.2]octadienes in solution has been studied in detail by steady-state, nanosecond laser flash photolysis, and matrix isolation techniques. Photolysis of 7,8-digermabicyclo[2.2.2]octadienes in solution resulted mainly in the formation of tetraalkyldigermenes and 1,4-diphenylnaphthalene in the triplet excited state. The 7,8-digermabicyclo[2.2.2]octadiene also photochemically isomerized to 1,4-diphenyl-2,3-benzo-6,6,7,7-tetraalkyl-6,7-digermatricyclo[3.3.0.0]octane as minor product. The reactions of tetraalkyldigermenes with butadienes (2,3-dimethylbuta-1,3-diene and 2-methylbuta-1,3-diene), carbon tetrachloride, and methanol gave the corresponding digermene trapped products: 1,2-digermacyclohex-4-enes, 1,2-dichlorodigermanes together with hexachloroethane, and methoxydigermanes, respectively, in good yields. The transient bands of tetraalkyldigermenes using nanosecond laser flash photolysis appeared at ca. 380 nm. The rate constants for the quenching reactions of the digermene with oxygen, polyhalomethanes, alcohols, 2,3-dimethylbuta-1,3-diene, 1-hexyne, and triethylsilane were also measured under various conditions. The quenching reactions of digermenes with carbon tetrachloride and ethanol (k = ∼107 M-1 s-1) are 100 times faster than that with 1,3-butadiene (k = ∼105 M-1 s-1). The digermenes were very rapidly quenched with oxygen (k = ∼108 M-1 s-l), but very slowly with 1-hexyne and triethylsilane (k < 104 M-1 s-l) under reaction conditions. The UV absorption bands of tetraalkyldigermenes generated from 7,8-digermabicyclo[2.2.2]octadienes in matrix at 77 K were also observed at 370−380 nm. The mechanism of digermene formation was also discussed.
Determination of Optimal SVM Parameters by Using GA/PSO (2010)

The use of support vector machine (SVM) for function approximation has increased over the past few years. Unfortunately, the practical use of SVM is limited because the quality of SVM models heavily depends on a proper setting of SVM hyper-parameters and SVM kernel parameters. Therefore, it is necessary to develop an automated, reliable, and relatively fast approach to determine the values of these parameters that lead to the lowest generalization error. This paper presents two SVM parameter optimization approaches, i.e. GA-SVM and PSO-SVM. Both of them adopt a objective function which is based on the leave-one-out cross-validation, and the SVM parameters are optimized by using GA (genetic algorithm) and PSO ( particle swarm optimization) respectively. From experiment results, it can be concluded that both approaches, especially PSO-SVM, can solve the problem of estimating the optimal SVM parameter settings at a reasonable computational cost. Further, we point out the importance of a proper population size for GA/PSO-SVM, and present the recommended population size for GA-SVM and PSO-SVM.
A Review of Wearable Technologies for Elderly Care that Can Accurately Track Indoor Position, Recognize Physical Activities and Monitor Vital Signs in Real Time (2017)

Rapid growth of the aged population has caused an immense increase in the demand for healthcare services. Generally, the elderly are more prone to health problems compared to other age groups. With effective monitoring and alarm systems, the adverse effects of unpredictable events such as sudden illnesses, falls, and so on can be ameliorated to some extent. Recently, advances in wearable and sensor technologies have improved the prospects of these service systems for assisting elderly people. In this article, we review state-of-the-art wearable technologies that can be used for elderly care. These technologies are categorized into three types: indoor positioning, activity recognition and real time vital sign monitoring. Positioning is the process of accurate localization and is particularly important for elderly people so that they can be found in a timely manner. Activity recognition not only helps ensure that sudden events (e.g., falls) will raise alarms but also functions as a feasible way to guide people's activities so that they avoid dangerous behaviors. Since most elderly people suffer from age-related problems, some vital signs that can be monitored comfortably and continuously via existing techniques are also summarized. Finally, we discussed a series of considerations and future trends with regard to the construction of "smart clothing" system.
Sources of Error in Joint Surveys (1965)

Synopsis Because of the significant influence of joints on important engineering properties of hard un-weathered rock, a description of such rock is inadequate for engineering purposes unless it includes reasonably complete and accurate information concerning the spacing and orientation of the joints. Such information can be obtained by means of a joint survey based on the examination of outcrops, of tunnel walls, and of borehole photographs, provided that adequate precautions are taken to eliminate the serious errors likely to occur in the interpretation of the results of such a joint survey. These errors arise from failure to take account of the fact that the orientation of drill holes and of tunnels, as well as that of exposed rock surfaces within a small area, commonly lack sufficient variety to ensure a reliable estimate of the relative abundance of joints of the several sets present in the area. The errors can generally be reduced to a tolerable level by correcting for the effects of non-random orientation of exposed rock surfaces, by making observations in an adequate number of appropriately orientated boreholes, and by plotting the results of the survey in polar diagrams which are corrected for the effect of the angle of intersection between the joints and the drill holes or exposed rock faces. A cause de l'influence importante des joints sur les propriétés mécaniques de la roche dure intacte, une description de ces roches est insuffisante à des fins techniques à moins qu'elle comprenne des renseignements asses complets et précis sur l'espacement et l'orientation des joints. Ces renseignements peuvent s'obtenir par une etude de joints basée sur l'examen des affleurements, des murs de tunnels, et des photographies de trou de sondage, pourvu qu'on prenne des précautions suffisantes pour éliminer les erreurs sérieuses se produisant vraisemblablement dans l'interprétation d'une telle étude de joints. Ces erreurs se produisent parce qu'on ne tient pas compte du fait que l'orientation des trous de forage et des tunnels, ainsi que de celles des surfaces de roches exposées sur un petit territoire, n'est souvent pas asses variée pour permettre une évaluation sûre de l'abondance relative de joints des divers groupes présents sur le territoire. Les erreurs peuvent généralement être réduites à un niveau tolérable par des corrections pour les effets d'orientation non aléatoires des surfaces de roches exposées, en faisant des observations dans un nombre suffisant de trous de forage à peu prés orientés, et en tracant les resultats de l'étude sur des diagrammes polaires qui sont corrigés pour l'effet de l'angle d'intersection entre les joints, et les trous de forage ou les faces de roches exposées.
Disability and Need for Rehabilitation among Patients with Inflammatory Bowel Disease (1992)

Physicians who manage patients with inflammatory bowel disease (IBD) as well as the patients themselves need to know about the prospects of disability and the demand for rehabilitation associated with this chronic disease. The present study uses German social security statistics to characterize IBD patients undergoing a rehabilitation or having a disability and their employment status before and after rehabilitation. Each year, about 9 and 3% of all German employees with IBD underwent a rehabilitation or were granted a disability pension, respectively. In comparison with other diseases, IBD patients tended to be young, female and employed in white-collar occupations. Although they had significantly longer sick leaves, 87% were still employed before entering rehabilitation. The majority, i.e. 72%, improved under rehabilitation. Compared with other diseases, however, rehabilitation of patients with IBD was less successful, i.e. less patients improved, and more patients remained unchanged or even worsened during rehabilitation. After rehabilitation, continuation of the last employment was recommended in 82% of the cases, in 94% after additional medical or vocational measures. Overall, failed rehabilitation led to a similar rate of disability in IBD as in other diseases. Within the IBD population, however, female sex and white-collar occupations were associated with an increased risk, while male sex and blue-collar occupations were associated with a reduced risk for disability. These data reflect the underlying epidemiology of IBD as well as its natural history. Despite its severity and chronicity, the overwhelming majority of patients with IBD manage to stay in the work force and succeed in overcoming the obstacles posed by their disease.
Rapid detection of point mutations of the Neisseria gonorrhoeae gyrA gene associated with decreased susceptibilities to quinolones (1996)

Mutations in the gyrA gene resulting in amino acid changes at Ser-91 and Asp-95 are significantly associated with decreased susceptibilities to quinolones in Neisseria gonorrhoeae. To detect these mutations, we developed a rapid and simple assay based on amplification of the region of the gyrA gene containing the mutation sites by PCR and digestion of the PCR product with a restriction enzyme. A naturally occurring HinfI restriction site was present in the region containing the Ser-91 codon, and an artificial HinfI restriction site was created in the region containing the Asp-95 codon by the method of primer-specified restriction site modification. The mutations generating alterations at Ser-91 and Asp-95 were detected as restriction fragment length polymorphisms of the PCR products digested with HinfI. Fifty-five clinical strains of N. gonorrhoeae were examined for mutations in the gyrA gene by this method. Mutations at Ser-91 and/or Asp-95 were detected in all the 31 strains in which the mutations had been confirmed by DNA sequencing. Our method allows simultaneous testing of a large number of strains and provides results within 8 h. This rapid and simple assay could be a useful screening device for genetic alterations associated with decreased susceptibilities to quinolones in N. gonorrhoeae and could facilitate epidemiological studies on clinical isolates of N. gonorrhoeae with decreased susceptibilities to quinolones.
A Facile Synthesis of 4-(3β -Methoxy-5α-androstan-17β-YL)-3-pyrrolin-2-one (1993)

Abstract The title compound was prepared in 4 steps from 3β-methoxy-21-hydroxy-5α-pregnan-20-one (1). The required intermediate (4) was obtained using lithium enolate derived from t-butyl acetate. Interesting enough, p-tosyl chloride in pyridine quantitatively converted compound 1 into the α-chloro ketone derivative (2).
Vibrational Circular Dichroism Analysis Reveals a Conformational Change of the Baccatin III Ring of Paclitaxel:  Visualization of Conformations Using a New Code for Structure−Activity Relationships (2008)

The comparison between measured and conformer-weighted calculated VCD spectra of the baccatin III ring of paclitaxel and visualization of the conformations using the new code for structure-activity relationships are reported for the first time. The VCD spectrum of paclitaxel closely resembles that of the baccatin III ring. The large characteristic nuCO VCD bands with bisignate signs (1732 cm-1, Deltaepsilon = -1.6 x 10(-1); 1715 cm(-1), Deltaepsilon = 2.4 x 10(-1)) strongly reflect the structural property of the family of conformations bacc-ABC32F defined using the new code. The comparison with the conformation of the baccatin III core in the electron micrograph of the crystal structure of tubulin-paclitaxel (1JFF) suggests a conformational change of paclitaxel corresponding to a switch through the binding with beta-tublin and the intermolecular interactions involving the hydroxyl group (D) and carbonyl of acetoxy group (E). The representation of conformational codes allows complicated conformations to be very easily compared and facilitates future computational analyses such as those for the large-molecule calculations as well as genome analysis.
Minimum entropy quantizers and permutation codes (1982)

Amplitude quantization and permutation encoding are two approaches to efficient digitization of analog data. It has been proven that they are equivalent in the sense that their optimum rate versus distortion performances are identical. Reviews of the aforementioned results and of work performed in the interim by several investigators are presented. Equations which must be satisfied by the thresholds of the minimum entropy quantizer that achieves a prescribed mean <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</tex> th power distortion are derived, and an iterative procedure for solving them is developed. It is shown that these equations often have many families of solutions. In the case of the Laplacian distribution, for which we had previously shown that quantizers with uniformly spaced thresholds satisfy the equations when <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r=2</tex> , other families of solutions with nonuniform spacing are exhibited. What had appeared to be a discrepancy between the performances of optimum permutation codes and minimum entropy quantizers is resolved by the resulting optimum quantizers, which span all entropy rates from zero to infinity.
Reliability Estimation for the Generalized Gamma Distribution and Robustness of the Weibull Model (1971)

Two test statistics are suggested for discriminating between the exponential model and the more general Weibull or gamma models, and these are compared to some previously used test statistics by Monte Carlo methods. The results of estimating reliability under an exponential assumption when the true model is Weibull is also investigated. These results as well as the tests mentioned above indicate that the exponential model is often not adequate when the more general models hold. In contrast to this result it was found that the Weibull model was quite robust relative to the generalized gamma distribution with regard to reliability estimation. Some general pivotal function properties are presented for the maximum likelihood estimator of reliability for the generalized gamma distribution and similar results also hold for the Weibull procedure under a generalized gamma assumption. These results made a Monte Carlo study of this problem feasible. Since the maximum likelihood estimators are apparently ill-behaved for smaller sample sizes and since the Weibull model is robust it appears little is gained by using the generalized gamma distribution for samples of size less than 200 to 400.
A recommendation engine for suggesting unexpected thermoelectric chemistries (2015)

The experimental search for new thermoelectric materials remains largely confined to a limited set of successful chemical and structural families, such as chalcogenides, skutterudites, and Zintl phases. In principle, computational tools such as density functional theory (DFT) offer the possibility of rationally guiding experimental synthesis efforts toward very different chemistries. However, in practice, predicting thermoelectric properties from first principles remains a challenging endeavor, and experimental researchers generally do not directly use computation to drive their own synthesis efforts. To bridge this practical gap between experimental needs and computational tools, we report an open machine learning-based recommendation engine (http://thermoelectrics.citrination.com) for materials researchers that suggests promising new thermoelectric compositions, and evaluates the feasibility of user-designed compounds. We show that this engine can identify interesting chemistries very different from known thermoelectrics. Specifically, we describe the experimental characterization of one example set of compounds derived from our engine, RE12Co5Bi (RE = Gd, Er), which exhibits surprising thermoelectric performance given its unprecedentedly high loading with metallic d and f block elements, and warrants further investigation as a new thermoelectric material platform.