gebhart/patrepeval huggingface dataset:
Bandwidth-Aware Scheduling with SDN in Hadoop: A New Trend for Big Data (2014)

Software Defined Networking (SDN) is a revolutionary network architecture that separates out network control functions from the underlying equipment and is an increasingly trend to help enterprises build more manageable data centers where big data processing emerges as an important part of applications. To concurrently process large-scale data, MapReduce with an open source implementation named Hadoop is proposed. In practical Hadoop systems one kind of issue that vitally impacts the overall performance is know as the NP-complete minimum make span problem. One main solution is to assign tasks on data local nodes to avoid link occupation since network bandwidth is a scarce resource. Many methodologies for enhancing data locality are proposed such as the HDS and state-of-the-art scheduler BAR. However, all of them either ignore allocating tasks in a global view or disregard available bandwidth as the basis for scheduling. In this paper we propose a heuristic bandwidth-aware task scheduler BASS to combine Hadoop with SDN. It is not only able to guarantee data locality in a global view but also can efficiently assign tasks in an optimized way. Both examples and experiments demonstrate that BASS has the best performance in terms of job completion time. To our knowledge, BASS is the first to exploit talent of SDN for big data processing and we believe it points out a new trend for large-scale data processing.
Analysis of the clonal relationships between strains of Neisseria meningitidis by pulsed field gel electrophoresis (1992)

Fingerprint patterns were generated from strains of Neisseria meningitidis by digestion of chromosomal DNA samples with 'rare-site' restriction endonucleases and resolution of the resultant fragments by pulsed field gel electrophoresis (PFGE). The potential of this technique for the rapid establishment of the clonal relationships between different isolates of the meningococcus was investigated. The fingerprint patterns from various serogroup A strains, previously assigned to clonal subgroups on the basis of their electrophoretic types (ETs), were compared. Fingerprints generated with the endonucleases SfiI, SpeI and NheI each gave distinctive patterns for the clonal subgroups I-IV of serogroup A. Further, the endonucleases SpeI and, particularly, NheI were capable of resolving differences between various subgroup III strains isolated at different times and geographical locations. Strains isolated during the 'new wave' pandemic, which was associated with the Haj, from Europe, America, and Africa, had a characteristic fingerprint pattern and appeared to be distinct from 'old wave' pandemic strains. The PFGE technique is a relatively rapid and sensitive method for establishing clonal relationships among epidemic strains of N. meningitidis.
Inorganic-Organic Composite Solid Polymer Electrolytes (2000)

Inorganic‐organic composite solid polymer electrolytes (CSPEs) have been prepared from the poly(ethylene oxide) (PEO)‐like electrolytes of the general formula polyvinylidene fluoride‐hexafluoropropylene and ceramic powders. In the PEO‐like electrolytes, PVdF‐HFP is the copolymer of PVdF and HFP, is a nonvolatile oligomeric polyethylene oxide of ∼400 g/mol molecular weight, and LiX is lithium bis(trifluoroethylsulfonyl) imide. Two types of inorganic oxide ceramic powders were used: a highly material of the composition 14 mol % , and the poorly Li‐silicates where M is Ca or Mg and x is 0 or 0.05. The composite electrolytes can be prepared as thin membranes in which the conductivity and good mechanical strength of the inorganic ceramics are complemented by the structural flexibility and high conductivity of organic polymer electrolytes. Excellent electrochemical and thermal stabilities have been demonstrated for the electrolyte films. Li//composite electrolyte// rechargeable cells have been fabricated and cycled at room temperature and 50°C. © 2000 The Electrochemical Society. All rights reserved.
Conclusive Evidence That the Major T-cell Antigens of theMycobacterium tuberculosis Complex ESAT-6 and CFP-10 Form a Tight, 1:1 Complex and Characterization of the Structural Properties of ESAT-6, CFP-10, and the ESAT-6·CFP-10 Complex (2002)

The proteins ESAT-6 and CFP-10 have been shown to be secreted by Mycobacterium tuberculosis and Mycobacterium bovis cells, to be potent T-cell antigens, and to have a clear but as yet undefined role in tuberculosis pathogenesis. We have successfully overexpressed both ESAT-6 and CFP-10 in Escherichia coli and developed efficient purification schemes. Under in vivo-like conditions, a combination of fluorescence, circular dichroism, and nuclear magnetic resonance spectroscopy have shown that ESAT-6 contains up to 75% helical secondary structure, but little if any stable tertiary structure, and exists in a molten globule-like state. In contrast, CFP-10 was found to form an unstructured, random coil polypeptide. An exciting discovery was that ESAT-6 and CFP-10 form a tight, 1:1 complex, in which both proteins adopt a fully folded structure, with about two-thirds of the backbone in a regular helical conformation. This clearly suggests that ESAT-6 and CFP-10 are active as the complex and raises the interesting question of whether other ESAT-6/CFP-10 family proteins (22 paired genes in M. tuberculosis) also form tight, 1:1 complexes, and if so, is this limited to their genome partner, or is there scope for wider interactions within the protein family, which could provide greater functional flexibility?
Transmission of Equine Influenza Virus to English Foxhounds (2008)

We retrospectively demonstrated that an outbreak of severe respiratory disease in a pack of English foxhounds in the United Kingdom in September 2002 was caused by an equine influenza A virus (H3N8). We also demonstrated that canine respiratory tissue possesses the relevant receptors for infection with equine influenza virus.
Construction of a Semisynthetic Human VH Single-Domain Antibody Library and Selection of Domain Antibodies against α-Crystalline of Mycobacterium tuberculosis (2015)

The use of human variable heavy (VH) domain antibodies has been on the rise due to their small scaffold size and simple folding mechanism. A highly diverse library is largely dependent on the diversity introduced within the complementarity-determining region (CDR) cassettes. Here we introduced diversity with the use of a single framework diversifying all three CDRs using tailored codons consisting of degenerate trinucleotides (NNK). The length of the degeneracy in the CDRs was also taken into consideration based on the most frequently occurring length of CDRs and the canonical confirmation for each antibody subfamily. The semisynthetic human VH domain genes were assembled in a single pot using a temperature cascading process. The affinity selection process with Mycobacterium tuberculosis (MTb) α-crystalline was done using a semiautomated process. Enrichment of target-specific clones was observed with successful identification of monoclonal VH domain antibodies for MTb α-crystalline. In short, the semisynthetic library generated was able to select monoclonal VH domain antibodies against full MTb α-crystalline protein with complete semisynthetic CDRs displayed on a single scaffold. The library has the potential to be applied for the isolation of antibodies against other pathogenic proteins.
Primordial germ cells in the mouse embryo during gastrulation (1990)

With the aid of a whole-mount technique, we have detected a small cluster of alkaline phosphatase (ALP)-positive cells in whole mounts of mid-primitive-streak-stage embryos, 7-7 1/4 days post coitum (dpc). Within the cluster, about 8 cells contain a small cytoplasmic spot, intensely stained for ALP activity and possibly associated with an active Golgi complex. The cluster lies just posterior to the definitive primitive streak in the extraembryonic mesoderm, separated from the embryo by the amniotic fold. Towards the end of gastrulation, the number of cells containing the ALP-positive spot rises to between 50 and 80. Thereafter the number of cells in the extraembryonic cluster declines, and similar cells start to be seen in the mesoderm of the primitive streak and then in the endoderm. At 8 dpc, about 125 ALP-stained cells are found, mainly in the hindgut endoderm and also at the base of the allantois, their appearance and location at this stage agreeing closely with previous reports on primordial germ cells (PGCs). Embryos from which the cluster area has been removed at the 7-day stage are devoid of PGCs after culture for 48 h, whereas the excised tissue is rich in PGCs. We argue that the cells in the cluster are indeed primordial germ cells, at a stage significantly earlier than any reported previously. This would indicate that the PGC lineage in the mouse is set aside at least as early as 7 dpc, possibly as one of the first 'mesodermal' cell types to emerge, and that its differentiation, as expressed by ALP activity, is gradual.
A tool for integrating conceptual schemas and user views (2003)

An interactive tool has been developed to assist database designers and administrators (DDA) in integrating schemas. It collects the information required for integration from a DDA, performs essential bookkeeping, and integrates schemas according to the semantics provided. The authors present the capabilities of this tool by discussing the integration methodology and the user interface of the tool.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rickettsia Mooseri Infection in the Fleas Leptopsylla Segnis and Xenopsylla Cheopis (1983)

Detailed observations on the acquisition and propagation of experimental Rickettsia mooseri infection in two species of fleas are presented. Rickettsia mooseri infection became detectable by means of the direct fluorescent antibody test about 2 days earlier in Leptopsylla segnis than in the putative vector, Xenopsylla cheopis. By the 6th day after the infective feeding, the entire lining and the lumen of the midgut in L. segnis contained masses of rickettsiae and the agent was being passed in the feces of the flea, whereas in X. cheopis these events did not occur until the 8th day. Basic behavioral differences in the two species of flea may explain these discrepancies and also influence their ability to serve as vectors of murine typhus. As a semisessile flea and sustained feeder, L. segnis only rarely attaches to a second individual and thus has an opportunity to acquire a heavy dose of rickettsiae, if feeding on a rickettsemic host. X. cheopis, in contrast, feeds rapidly and intermittently, even on man, and generally leaves its host soon thereafter, later returning to the same or another host to feed again. While L. segnis may not be as efficient a vector as X. cheopis regarding the intramurine cycle or transmission to man of murine typhus, the dense accumulation of infective feces on certain sites on the fur of the host raises the possibility of air-borne infection to man or rodent. Infection with R. mooseri had no effect on the survival of X. cheopis and L. segnis. Furthermore, no visible cytopathological effect was found in the paraffin-embedded sections of infected fleas.(ABSTRACT TRUNCATED AT 250 WORDS)
MicroRNA expression profiling: A molecular tool for defining the phenotype of hepatocellular tumors (2008)

Two recent conceptual advances have led to an exciting renaissance in genetic regulation of biological processes involved in cell growth, development, and function. The first was the recognition that many portions of the human genome that do not encode conventional protein‐coding genes can encode biologically active RNA species. The second was the identification of mechanisms by which small RNA molecules could regulate gene and protein expression. Consequently, there has been an increasing recognition of the role of genetically encoded regulatory RNA molecules in biological processes. These advances have resulted in several new hypotheses on the mechanistic role of noncoding RNA in physiological processes, and their deregulation in disease. In turn, these hypotheses are beginning to provide new insights into disease classifications and pathogenesis.
Non-Invasive Functional-Brain-Imaging with an OPM-based Magnetoencephalography System (2020)

A non-invasive functional-brain-imaging system based on optically-pumped-magnetometers (OPM) is presented. The OPM-based magnetoencephalography (MEG) system features 20 OPM channels conforming to the subject's scalp. We have conducted two MEG experiments on three subjects: assessment of somatosensory evoked magnetic field (SEF) and auditory evoked magnetic field (AEF) using our OPM-based MEG system and a commercial MEG system based on superconducting quantum interference devices (SQUIDs). We cross validated the robustness of our system by calculating the distance between the location of the equivalent current dipole (ECD) yielded by our OPM-based MEG system and the ECD location calculated by the commercial SQUID-based MEG system. We achieved sub-centimeter accuracy for both SEF and AEF responses in all three subjects. Due to the proximity (12 mm) of the OPM channels to the scalp, it is anticipated that future OPM-based MEG systems will offer enhanced spatial resolution as they will capture finer spatial features compared to traditional MEG systems employing SQUIDs.
Creating Biocompatible Oil–Water Interfaces without Synthesis: Direct Interactions between Primary Amines and Carboxylated Perfluorocarbon Surfactants (2013)

Currently, one of the most prominent methods used to impart biocompatibility to aqueous-in-oil droplets is to synthesize a triblock copolymer surfactant composed of perfluoropolyether and polyether blocks. The resulting surfactants (EA surfactant, KryJeffa, etc.) allow generation of highly biocompatible droplet surfaces while maintaining the heat stability of the starting material. However, production of these surfactants requires expertise in synthetic organic chemistry, creating a barrier to widespread adoption in the field. Herein, we describe a simple alternative to synthetic modification of surfactants to impart biocompatibility. We have observed that aqueous-in-oil droplet surfaces can be made biocompatible and heat stable by merely exploiting binding interactions between polyetherdiamine additives in the aqueous phase and carboxylated perfluorocarbon surfactants in the oil phase. Droplets formed under these conditions are shown to possess biocompatible surfaces capable of supporting picoliter-scale protein assays, droplet polymerase chain reaction (PCR), and droplet DNA amplification with isothermal recombinase polymerase amplification (RPA). Droplets formed with polyetherdiamine aqueous additives are stable enough to withstand temperature cycling during PCR (30–40 cycles at 60–94 °C) while maintaining biocompatibility, and the reaction efficiency of RPA is shown to be similar to that with a covalently modified surfactant (KryJeffa). The binding interaction was confirmed with various methods, including FT-IR spectroscopy, NMR spectroscopy, electrospray ionization mass spectrometry (ESI-MS), and fluorescence microscopy. Overall, our results suggest that, by simply introducing a commercially-available, polyetherdiamine additive (Jeffamine ED-900) to the aqueous phase, researchers can avoid synthetic methods in generating biocompatible droplet surfaces capable of supporting DNA and protein analysis at the subnanoliter scale.
Dipy, a library for the analysis of diffusion MRI data (2014)

Diffusion Imaging in Python (Dipy) is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments. dMRI is an application of MRI that can be used to measure structural features of brain white matter. Many methods have been developed to use dMRI data to model the local configuration of white matter nerve fiber bundles and infer the trajectory of bundles connecting different parts of the brain. Dipy gathers implementations of many different methods in dMRI, including: diffusion signal pre-processing; reconstruction of diffusion distributions in individual voxels; fiber tractography and fiber track post-processing, analysis and visualization. Dipy aims to provide transparent implementations for all the different steps of dMRI analysis with a uniform programming interface. We have implemented classical signal reconstruction techniques, such as the diffusion tensor model and deterministic fiber tractography. In addition, cutting edge novel reconstruction techniques are implemented, such as constrained spherical deconvolution and diffusion spectrum imaging (DSI) with deconvolution, as well as methods for probabilistic tracking and original methods for tractography clustering. Many additional utility functions are provided to calculate various statistics, informative visualizations, as well as file-handling routines to assist in the development and use of novel techniques. In contrast to many other scientific software projects, Dipy is not being developed by a single research group. Rather, it is an open project that encourages contributions from any scientist/developer through GitHub and open discussions on the project mailing list. Consequently, Dipy today has an international team of contributors, spanning seven different academic institutions in five countries and three continents, which is still growing.
A Computational Model to Predict the Effects of Class I Anti-Arrhythmic Drugs on Ventricular Rhythms (2011)

A long-sought, and thus far elusive, goal has been to develop drugs to manage diseases of excitability. One such disease that affects millions each year is cardiac arrhythmia, which occurs when electrical impulses in the heart become disordered, sometimes causing sudden death. Pharmacological management of cardiac arrhythmia has failed because it is not possible to predict how drugs that target cardiac ion channels, and have intrinsically complex dynamic interactions with ion channels, will alter the emergent electrical behavior generated in the heart. Here, we applied a computational model, which was informed and validated by experimental data, that defined key measurable parameters necessary to simulate the interaction kinetics of the anti-arrhythmic drugs flecainide and lidocaine with cardiac sodium channels. We then used the model to predict the effects of these drugs on normal human ventricular cellular and tissue electrical activity in the setting of a common arrhythmia trigger, spontaneous ventricular ectopy. The model forecasts the clinically relevant concentrations at which flecainide and lidocaine exacerbate, rather than ameliorate, arrhythmia. Experiments in rabbit hearts and simulations in human ventricles based on magnetic resonance images validated the model predictions. This computational framework initiates the first steps toward development of a virtual drug-screening system that models drug-channel interactions and predicts the effects of drugs on emergent electrical activity in the heart.
Improved Algorithm Simulation of Adaptive Blade Pitch Control for Electrically Controlled Rotor (2012)

Based on the former adaptive blade pitch control method of the Electrically Controlled Rotor in time domain, two improved control algorithms are proposed. One method is through adding a weight-constrained function for active control filter, which can prevent the divergent of control system caused by interference signal of error channel. The other method is through adding a desired signal of scaling factor to replace the identification process of the forward path. The algorithm can enhance the real time characteristics and the response characteristics of control system. In addition, the comparison between two improved methods and the former method is conducted, and the simulation analysis is made based on the matlab/simulink. The simulation results show that the two proposed methods have better system robustness, and the control characteristics are obviously superior to the former system.
Photocrosslinkable Gelatin Hydrogel for Epidermal Tissue Engineering (2015)

Natural hydrogels are promising scaffolds to engineer epidermis. Currently, natural hydrogels used to support epidermal regeneration are mainly collagen- or gelatin-based, which mimic the natural dermal extracellular matrix but often suffer from insufficient and uncontrollable mechanical and degradation properties. In this study, a photocrosslinkable gelatin (i.e., gelatin methacrylamide (GelMA)) with tunable mechanical, degradation, and biological properties is used to engineer the epidermis for skin tissue engineering applications. The results reveal that the mechanical and degradation properties of the developed hydrogels can be readily modified by varying the hydrogel concentration, with elastic and compressive moduli tuned from a few kPa to a few hundred kPa, and the degradation times varied from a few days to several months. Additionally, hydrogels of all concentrations displayed excellent cell viability (>90%) with increasing cell adhesion and proliferation corresponding to increases in hydrogel concentrations. Furthermore, the hydrogels are found to support keratinocyte growth, differentiation, and stratification into a reconstructed multilayered epidermis with adequate barrier functions. The robust and tunable properties of GelMA hydrogels suggest that the keratinocyte laden hydrogels can be used as epidermal substitutes, wound dressings, or substrates to construct various in vitro skin models.
Application-level isolation and recovery with solitude (2008)

When computer systems are compromised by an attack, it is difficult to determine the precise extent of the damage caused by the attack because the state changes made by an attacker and those made by regular users can be closely intertwined. This problem occurs due to implicit sharing in operating systems, and it can be especially severe for persistent state. In particular, the file system provides a single namespace that when compromised can have cascading effects on the entire system, making intrusion analysis and recovery a time-consuming and error-prone process.
Chronic Pseudomonas aeruginosa lung infection is more severe in Th2 responding BALB/c mice compared to Th1 responding C3H/HeN mice (1997)

The chronic Pseudomonas aeruginosa lung infection in cystic fibrosis (CF) is characterized by a pronounced antibody response and microcolonies surrounded by numerous polymorphonuclear neutrophils (PMN). Poor prognosis is correlated with a high antibody response to P. aeruginosa antigens. An animal model of this infection was established in two strains of mice: C3H/HeN and BALB/c, generally known as Th1 and Th2 responders, respectively, which were challenged with alginate-embedded P. aeruginosa. Mortality was significantly lower in C3H/HeN compared to BALB/c mice (p < 0.025). P. aeruginosa was cleared more efficiently in C3H/HeN mice and significantly more C3H/HeN mice showed normal lung histopathology (p < 0.02), and we found significantly fewer microabscesses in C3H/HeN mice than in BALB/c mice (p < 0.005). In supernatants from P. aeruginosa antigen and concanavalin A-stimulated spleen cells from the two strains of mice, the interferon-(IFN-) gamma levels were higher, whereas IL-4 levels were lower in C3H/HeN mice than in BALB/c mice. The implications of these findings for CF patients with chronic P. aeruginosa lung infection are discussed.