gebhart/patrepeval huggingface dataset:
Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells (2015)

Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competence and changes in subnuclear position. We generated genome-wide RT profiles for 26 distinct human cell types, including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm, and neural crest (NC) development. We identified clusters of RDs that replicate at unique times in each stage (RT signatures) and confirmed global consolidation of the genome into larger synchronously replicating segments during differentiation. Surprisingly, transcriptome data revealed that the well-accepted correlation between early replication and transcriptional activity was restricted to RT-constitutive genes, whereas two-thirds of the genes that switched RT during differentiation were strongly expressed when late replicating in one or more cell types. Closer inspection revealed that transcription of this class of genes was frequently restricted to the lineage in which the RT switch occurred, but was induced prior to a late-to-early RT switch and/or down-regulated after an early-to-late RT switch. Analysis of transcriptional regulatory networks showed that this class of genes contains strong regulators of genes that were only expressed when early replicating. These results provide intriguing new insight into the complex relationship between transcription and RT regulation during human development.
Electrostatic transportation of water droplets on superhydrophobic surfaces (2002)

This article reports electrostatic transportation of water droplets on superhydrophobic alkylketene dimer (AKD) and Teflon AF/sup R/ surfaces. The actuation is based on electrostatic forces generated by metal electrodes placed underneath the surface. By switching the electrode voltages, the droplets moved stepwise along the electrode paths. The lowest voltage which resulted continuous movement was 124 VAC (rms) and the maximum speed was over 1 cm/s which shows great improvement with respect to previously reported electrostatic actuation of water droplets in open air [M. Washizu, "Electrostatic Actuation of Liquid Droplets for microreactor Applications", IEEE Trans. Ind. App. 34, 4 (1998), pp. 732-737].
Deep Fat Frying: Fundamentals and Applications (1999)

Introduction. Fried Product Processing and Characteristics. Frying Oil Characteristics. Fried Product Quality. Introductory Analysis of Frying Systems. Theory and Simulation of Frying. Oil Absorption in Fried Foods. Deep-Fat Frying Systems. Continuous Fryer Control Systems. Low-Fat Tortilla Chips. Packaging Fried Foods. Index.
Marking patients' skin for radiotherapy treatment field alignment. (1988)

From the survey and research, it appears that sterile or non-sterile waterproof Indian ink used for tattooing patients produces few reported side effects and problems considering the number of patients tattooed. Marker pens also seem to be entirely suitable for patients and for radiotherapy centre requirements.
La Acción Tutorial Como Innovación Docente En La Titulación De Enfermería (2006)

La accion tutorial es un nuevo proceso de apoyo y guia para los estudiantes a traves de su recorrido en la Universidad, cuyo fin es favorecer el desarrollo academico, personal, social y profesional del alumnado participante. En este trabajo proponemos el desarrollo de la accion tutorial como un metodo de innovacion docente que trabaje las competencias personales, sociales y academicas subrayadas por el Espiritu de Bolonia. Por otra parte, al centrar la implantacion de esta accion tutorial en la titulacion de enfermeria, se hace necesario detenernos en sus peculiaridades, para lo cual recogemos una serie de aspectos, como la contextualizacion, la deteccion de necesidades, el estudio de los destinatarios, la temporalizacion y los recursos previstos.
Primus (florasulam 50 G/L), a new triazolopyrimidine sulfonanilide herbicide to control broad-leaved weeds in maize when applied in early postemergence (1 to 6 leaf stage of maize). Preliminary results. (2001)

The results of the tests show that it is possible to consider replacing atrazine-based programmes with very low doses of modern herbicides applied at early stages of the maize. A mixture of active substances is vital. Repeated very low doses at the 1/2 and 4/5 leaf stages of the maize were found to be the most effective.
Collagen crosslinking in keratoconus. (1978)

The examination of reducible collagen crosslinks in keratoconus cornea revealed the presence of lysinonorleucine in amounts far greater than in normal age-matched corneas. There was no indication of decreased hydroxylysine levels in keratoconus, and there were no clinical indications of a generalized connective tissue disorder. The abnormal levels of dehydrolysinonorleucine in the tissue may represent a change in hydroxylation of selected lysyl residues of normal collagen or the synthesis of abnormal collagen, perhaps an unusual type.
HLA-DR15 (DR2) is overrepresented in myelodysplastic syndrome and aplastic anemia and predicts a response to immunosuppression in myelodysplastic syndrome (2002)

The extent and importance of autoimmune mechanisms in myelodysplastic syndrome (MDS) and the role of immunosuppression in the treatment of this disease are not well defined. We report overrepresentation of HLA-DR2 and its serologic split HLA-DR15 in both MDS and aplastic anemia (AA). Four clinically and ethnically defined patient groups were analyzed. The HLA-DR15 antigen frequencies among North American white MDS patients (n = 72) and AA patients (n = 59), who received immunosuppressive treatment at the National Institutes of Health (NIH), were 36% and 42%, respectively. These antigen frequencies were significantly higher than that of the control population of 240 North American white NIH blood donors typed for HLA antigens by the same molecular technique (HLA-DR15, 21.3%, P =.01 for MDS, P <.001 for AA). Among North American white patients reported in the International Bone Marrow Transplant Registry (IBMTR), 30% of 341 MDS patients and 33% of 364 AA patients were positive for HLA-DR2. These antigen frequencies were higher than those reported for the general North American white population (HLA-DR2, 25.3%, P =.089 for MDS, P =.01 for AA). The DR15 and DR2 frequencies were significantly increased in MDS refractory anemia (RA) (P =.036 and P =.01, respectively) but not MDS refractory anemia with excess blasts. In the NIH MDS patients, HLA-DR15 was significantly associated with a clinically relevant response to antithymocyte globulin (ATG) or cyclosporine immunosuppression (multivariate analysis, P =.008). In MDS with RA, DR15 may be useful as a guide to pathophysiology, prognosis, and treatment.
Management Styles (1986)

Management style is too general a concept and must be extended by the consideration of both level and type of capability in the assessment of current competence and the prediction of potential. Context and its significance for the expression of different capabilities must be understood if more subtle and accurate typologies are to be developed. These would make it possible to match people's strengths at any given time to appropriate areas of work. Studies on style are summarised, and a model of individual differences which discriminates two separate dimensions of style is described. A model of organisational structure is presented which allows the direct matching of person and task and future matching as the person's capabilities grow.
Modern Perspectives on Epilepsy in Relation to Psychiatry: Behavioral Disturbances of Epilepsy (1988)

In this paper, the second of a two-part series on current psychiatric aspects of epilepsy, the authors consider the classification and management of the various kinds of psychoses and other behavior disturbances associated with some cases of epilepsy. After discussing the common aspects of epilepsy and schizophrenia, they describe attempts to categorize epileptic psychoses, focusing on a classification of ten kinds of psychoses that they believe has broadest application. They present guidelines for psychopharmacological management of epilepsy accompanied by behavior disturbance, with emphasis on anticonvulsant monotherapy, and they discuss possibly related seizure disorders and possible etiologies of behavioral symptoms of epilepsy.
Prospective Evaluation of Reader Performance on MDCT in Characterization of Cystic Pancreatic Lesions and Prediction of Cyst Biologic Aggressiveness (2011)

Morphologic features of pancreatic cystic lesions on MDCT allow reliable characterization into mucinous and nonmucinous subtypes and enable prediction of biologic aggressiveness.
Computational methods for predicting coiled-coil protein-protein interactions (2005)

Knowing which proteins interact is essential for learning about biological processes and functions, as almost every process in the cell involves a protein interaction. Determining protein-protein interactions is one of the most well-studied yet difficult problems in biology. The large amount of genomic data—20,000+ genes in human alone—and the combinatorial number of possible interactions make it impossible to test all proteins in the laboratory in a short time, even using high-throughput techniques, and motivates the study of efficient computational methods. We focus on protein interactions mediated by two-stranded, parallel coiled-coil, one of the most common structural motifs. Coiled coils are involved in many cellular processes, including transcription, oncogenesis, cell structure, and cell fusion events. We present several computational methods for predicting coiled-coil protein interactions. 
First, we describe a learning method that represents coiled coils in terms of their interhelical interactions and derives, from sequence and experimental data, a weight that indicates how favorable each residue-residue interaction is. When tested on interactions between human and yeast bZIP transcription factor proteins, our method identifies 70% of strong interactions while maintaining that 92% of predictions are correct. Showing its usefulness outside this protein class, we apply our method to predict novel bZIP interactions in Arabidopsis and to computationally identify all coiled-coil interactions in the yeast proteome. While unable to identify coiled coils with high confidence at the proteomic scale, our method makes inroads towards this more challenging problem. Finally, we integrated three successful predictors using a probabilistic framework. The combined method is demonstrated to perform better than any individual method, on average. 
Our work is the first to predict protein-protein interactions with such high confidence. While developed for coiled coils, the techniques can also be applied towards other structural domains and general protein-protein interactions.
Amino acid derivatization and analysis in five minutes (1991)

A convenient method permits acid separation by capillary gas chromatography in minutes — the suitable analytic forms are prepared in seconds.
Estimation of instantaneous air temperature above vegetation and soil surfaces from Landsat 7 ETM+ data in northern Germany (2011)

The temperature–vegetation index method (TVX method, also called contextual method) for the area-wide mapping of instantaneous air temperature is adopted for use with Landsat 7 Enhanced Thematic Mapper Plus (ETM+) data. The method requires multispectral data consisting of bands in the red, near-infrared and thermal spectral regions, and no additional data. The approach is complemented with an iterative filtering routine for eliminating outliers and an interpolation algorithm for filling data gaps. The adopted method is applied to a multi-temporal dataset of nine ETM+ scenes, covering large parts of north-eastern Germany including the Durable Environmental Multidisciplinary Monitoring Information Network (DEMMIN) test site. Thus, for the first time the TVX method is applied to fine spatial resolution data and a central European region. The satellite-derived air temperatures (60 m spatial resolution) are compared with in situ measurements, showing an average error of about 3 K (root mean square, RMS), whereas the mean error in land surface temperature (LST) estimation is about 2 K. The results compare well with the in situ values throughout all seasons. The accuracy of about 3 K is in line with previously reported results for the TVX method (employing medium spatial resolution data) as well as for physically based approaches (ecosystem- or energy-balance models). Only remote sensing models incorporating in situ air temperature (as training data for neural networks or in multiple regression analysis) are reported to perform better in terms of RMS deviations. In the past, overestimation of air temperature by the TVX method was repeatedly observed. It is shown that the remote sensing approach tends to under- or overestimate the in situ air temperatures, depending on the in situ measurement heights. In conjunction with the attempt to assign the satellite-derived air temperature to a certain height above ground, the possibility of a simple correction for reference height is investigated. Over- and underestimations larger than 2 K seem to reflect existing differences in temperature rather than calculation errors. Furthermore, the dependence of the derived air temperature spatial pattern on different moving window sizes is shown. Possible sources of errors and limitations of the approach are discussed in detail.
Proactive Fiber Damage Detection in Real-time Coherent Receiver (2017)

We develop an algorithm extension for a coherent receiver, coupled with machine learning to monitor mechanical stress to an optical fiber, for recognizing fiber breaks before they occur. We demonstrate event classification with 95% accuracy over a real-time PDM-QPSK testbed.
Integrating Web 2.0 in e-learning environments: a socio-technical approach (2007)

The great diffusion of Web 2.0 is having a tremendous effect and change on the way people search, find, collaboratively develop and consume information and knowledge. Education and learning are not an exception of Web 2.0 trends, as the number of Web 2.0 empowered e-learning environments are booming. Although research in Web 2.0 applications in learning is rising, the studies tend to be very descriptive failing to identify and discuss the pedagogical theories and models that support and enhance the exploitation of Web 2.0 tools in (e)-learning environments. This paper aims to first discuss the use of Web 2.0 in (e)-learning and the new skills that they enable, and then, debate the pedagogical theories that support the exploitation of Web 2.0 for creating personalised and collaborative learning environments. To achieve that, a socio-technical approach is suggested.
Toughening of epoxy resin using synthesized polyurethane prepolymer based on hydroxyl-terminated polyesters (1998)

Epoxy resins are increasingly finding applications in the field of structural engineering. A wide variety of epoxy resins are available, and some of them are characterized by a relatively low toughness. One approach to improve epoxy resin toughness includes the addition of either a rigid phase or a rubbery phase. A more recent approach to toughen brittle polymers is through interpenetrating network (IPN) grafting. It has been found that the mechanical properties of polymer materials with an IPN structure are fairly superior to those of ordinary polymers. Therefore, the present work deals with epoxy resin toughening using a polyurethane (PU) prepolymer as modifier via IPN grafting. For this purpose, a PU prepolymer based on hydroxyl-terminated polyester has been synthesized and used as a modifier at different concentrations. First, the PU-based hydroxyl-terminated polyester has been characterized. Next, an IPN (Epoxy–PU) has been prepared and characterized using Fourier transform infrared (FTIR) spectroscopy, thin-layer chromatography (TLC), and scanning electron microscopy (SEM) prior to mechanical testing in terms of impact strength and toughness. In this study, a Desmophen 1200-based PU prepolymer was used as a modifier at different concentrations within the epoxy resin. The results also showed that, further to the IPN formation, the epoxy and the PU prepolymer reacted chemically (via grafting). Compared to virgin resin, the effect on the mechanical properties was minor. The impact strength varies from 3–9 J/m and Kc from 0.9–1.2 MPa m1/2. Furthermore, the incorporation of a chain extender with the PU prepolymer as a modifier into the mixture caused a drastic improvement in toughness. The impact strength increases continuously and reaches a maximum value (seven-fold that of virgin resin) at a modifier critical concentration (40 phr). Kc reaches 2.5 MPa m1/2 compared to 0.9 MPa m1/2 of the virgin resin. Finally, the SEM analysis results suggested that internal cavitation of the modifier particles followed by localized plastics shear yielding is probably the prevailing toughening mechanism for the epoxy resin considered in the present study. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 70: 2603–2618, 1998
Growth hormone- and prolactin-binding proteins in mammalian serum (1992)

The present study was undertaken to characterize the species specificity and diversity of lactogenic and somatogenic binding to serum among mammals and to classify GH-binding protein (GH-BP) in this group of species. Animal sera were characterized on the basis of human (h) GH and bovine (b) PRL binding levels, binding specificity toward GHs and PRLs, binding affinity constant (Ka), and the ability of a monoclonal antirabbit GH receptor antibody (MAb-7) to inhibit the binding to serum. Analyses of the results yielded a classification of the mammalian sera into five types of GH binding, which we elected to call GH-BP. The guinea pig had undetectable levels of GH-BP and was labeled type 0. Type I GH-BP was found in the mouse and the rat. hGH binding to GH-BP of type I serum was of low affinity (1.2-3.9 x 10(8) M-1) with high IC50 (approximately 100 ng/tube) and was purely somatogenic in nature. Type II GH-BP was found in the goat, sheep, and cow. Their IC50 of hGH binding was approximately 4-fold lower than that of type I GH-BP. Their binding of hGH was relatively specific and only marginally displaced by the PRLs. Type III GH-BP was found in the rabbit, horse, cat, dog, and pig. These animals' sera had high affinity binding toward hGH (4.7-9.2 x 10(9) M-1), with low IC50 (approximately 2 ng/tube) and dominant lactogenic binding. The great similarity of type III GH-BPs was further stressed by the ability of MAb-7 to inhibit [125I]hGH binding to all type III sera, but not to the other mammalian sera tested. Type IV GH-BP was found in the human and rhesus monkey sera. These were characterized by binding affinities that were intermediate between those for types II and III GH-BP and by the inability of nonprimate GHs to compete with hGH binding. To directly confirm the potent effect of the lactogenic hormones in type III GH-BP, the specific binding of bPRL to sera of type III animals was studied. [125I]bPRL-specific binding was determined under optimized assay conditions and was the highest in rabbit serum, with the following rank order being observed: rabbit >> horse = dog = pig > cat. Scatchard analysis of [125I]bPRL binding revealed linear plots with similar affinity constants (Ka) of 1.7-3.3 x 10(9) M-1.
Virulence control in group A<i>Streptococcus</i>by a two-component gene regulatory system: Global expression profiling and<i>in vivo</i>infection modeling (2002)

Two-component gene regulatory systems composed of a membrane-bound sensor and cytoplasmic response regulator are important mechanisms used by bacteria to sense and respond to environmental stimuli. Group A Streptococcus, the causative agent of mild infections and life-threatening invasive diseases, produces many virulence factors that promote survival in humans. A two-component regulatory system, designated covRS (cov, control of virulence; csrRS), negatively controls expression of five proven or putative virulence factors (capsule, cysteine protease, streptokinase, streptolysin S, and streptodornase). Inactivation of covRS results in enhanced virulence in mouse models of invasive disease. Using DNA microarrays and quantitative RT-PCR, we found that CovR influences transcription of 15% (n = 271) of all chromosomal genes, including many that encode surface and secreted proteins mediating host-pathogen interactions. CovR also plays a central role in gene regulatory networks by influencing expression of genes encoding transcriptional regulators, including other two-component systems. Differential transcription of genes influenced by covR also was identified in mouse soft-tissue infection. This analysis provides a genome-scale overview of a virulence gene network in an important human pathogen and adds insight into the molecular mechanisms used by group A Streptococcus to interact with the host, promote survival, and cause disease.
The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter (2016)

ATP-binding cassette exporters use the energy of ATP hydrolysis to transport substrates across membranes by switching between inward- and outward-facing conformations. Essentially all structural studies of these proteins have been performed with the proteins in detergent micelles, locked in specific conformations and/or at low temperature. Here, we used luminescence resonance energy transfer spectroscopy to study the prototypical ATP-binding cassette exporter MsbA reconstituted in nanodiscs at 37 °C while it performs ATP hydrolysis. We found major differences when comparing MsbA in these native-like conditions with double electron-electron resonance data and the crystal structure of MsbA in the open inward-facing conformation. The most striking differences include a significantly smaller separation between the nucleotide-binding domains and a larger fraction of molecules with associated nucleotide-binding domains in the nucleotide-free apo state. These studies stress the importance of studying membrane proteins in an environment that approaches physiological conditions.
An empirical analysis of the co-evolution of schema and code in database applications (2013)

Modern database applications are among the most widely used and complex software systems. They constantly evolve, responding to changes to data, database schemas, and code. It is challenging to manage these changes and ensure that everything co-evolves consistently. For example, when a database schema is modified, all the code that interacts with the database must be changed accordingly. Although database evolution and software evolution have been extensively studied in isolation, the co-evolution of schema and code has largely been unexplored.
Translocatable resistance to mercuric and phenylmercuric ions in soil bacteria (1981)

Of a sample of 42 gram-negative Hg-resistant bacteria, three (a Pseudomonas fluorescens, a Klebsiella sp. and a Citrobacter sp.) contained translocatable elements conferring resistance to Hg2+ (all three) and to Hg2+ and phenylmercuric acetate (P. fluorescens). The discovery of transposable phenylmercuric acetate resistance extends the range of known resistance "transposons" from heavy metals and antibiotics to organometallic compounds.
REAL-TIME FEEDBACK CONTROL OF DROPLET GENERATION FOR EWOD DIGITIAL MICROFLUIDICS (2016)

We report the successful implementation of real-time feedback control of the droplet generation process on the electrowetting-on-dielectric (EWOD) digital microfluidics. Demonstrated in the air environment in this paper, the feedback allows precise (&lt; ±1%) droplet generation and also empowers users to prescribe the volume through software.