gebhart/patrepeval huggingface dataset:
Dual-contrast MR imaging of liver cancer in rats (1988)

MR contrast agents increase hepatic tumor conspicuity, as measured in terms of contrast-to-noise (C/N) ratios. With an animal model of hepatic metastases from breast cancer, IV administration of Gd-DTPA (0.2 mmol/kg) shows a biphasic time response, transiently increasing the signal intensity of liver relative to tumor, with C/N ratio magnitudes increasing from -5.7 to -16.3 (SE 250/20); after a delay, the signal intensity of tumor increases relative to liver with a reversal of the C/N sign from negative to positive and an increase in the C/N magnitude to +25.0. IV administration of ferrite particles (0.05 mmol Fe/kg) shows a monophasic time response, increasing signal intensity of tumor relative to liver from +1.5 to +49.5 (SE 500/30). When both contrast agents were administered together (dual-contrast technique), the tumor-liver C/N magnitude reached a maximum of +67.8 (SE 500/30) 12 min after drug infusion. Analysis of individual contrast and noise factors contributing to this technique revealed a strong correlation between the signal intensity of liver and the signal intensity of ghost artifacts, which increase after administration of Gd-DTPA (r = .89) and decrease after administration of ferrite (r = 1.0). Dual-contrast imaging shows a synergistic addition of contrast and suppression of noise from ghost artifacts, maximizing the C/N and increasing the conspicuity of focal liver lesions.
A semi-automatic approach to home video editing (2000)

Hitchcock is a system that allows users to easily create custom videos from raw video shot with a standard video camera. In contrast to other video editing systems, Hitchcock uses automatic analysis to determine the suitability of portions of the raw video. Unsuitable video typically has fast or erratic camera motion. Hitchcock first analyzes video to identify the type and amount of camera motion: fast pan, slow zoom, etc. Based on this analysis, a numerical "unsuitability" score is computed for each frame of the video. Combined with standard editing rules, this score is used to identify clips for inclusion in the final video and to select their start and end points. To create a custom video, the user drags keyframes corresponding to the desired clips into a storyboard. Users can lengthen or shorten the clip without specifying the start and end frames explicitly. Clip lengths are balanced automatically using a spring-based algorithm.
Immune responses to varicella-zoster in the aged (1982)

Absence of hemosiderin from the bone marrow is sometimes encountered in patients who are not iron deficient. Two cases of autoimmune hemolytic anemia are described in which there was little or no hemosiderin in the marrow but large amounts in the spleen, which had been the major site of accelerated RBC destruction. (<i>Arch Intern Med</i>1982;142:287-288)
Bayesian analysis of empirical software engineering cost models (1999)

Many parametric software estimation models have evolved in the last two decades (L.H. Putnam and W. Myers, 1992; C. Jones, 1997; R.M. Park et al., 1992). Almost all of these parametric models have been empirically calibrated to actual data from completed software projects. The most commonly used technique for empirical calibration has been the popular classical multiple regression approach. As discussed in the paper, the multiple regression approach imposes a few assumptions frequently violated by software engineering datasets. The paper illustrates the problems faced by the multiple regression approach during the calibration of one of the popular software engineering cost models, COCOMO II. It describes the use of a pragmatic 10 percent weighted average approach that was used for the first publicly available calibrated version (S. Chulani et al., 1998). It then moves on to show how a more sophisticated Bayesian approach can be used to alleviate some of the problems faced by multiple regression. It compares and contrasts the two empirical approaches, and concludes that the Bayesian approach was better and more robust than the multiple regression approach.
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 (2010)

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
Solid-Phase Synthesis (2000)

The solid support strategy in solid-phase synthesis amino acids -alpha-amino protecting groups side-chain protecting groups solid supports for the synthesis of peptides and small molecules coupling methods - solid-phase formation of amide and ester bonds homodetic cyclic peptides disulfide formation in synthetic peptides and proteins -the state of the art solid-phase convergent approaches to the synthesis of native peptides and proteins preparation of glyco-, phospho-, and sulfopeptides oligonucleotide synthesis synthesis of oligonucleotide-peptide conjugates and nucleopeptides the chemistry of peptide nucleic acids solid-phase synthesis of pseudopeptides and oligomeric peptide backbone mimetics instrumentation the purification of synthetic peptides analysis of synthetic peptides the chromatographic analysis of combinational arrays - parallel HPLC and HPLC-MS.
Introduction to simulation (2009)

Simulation is experimentation with a model. The behavior of the model imitates some salient aspect of the behavior of the system under study and the user experiments with the model to infer this behavior. This general framework has proven a powerful adjunct to learning, problem solving, and design. In this tutorial, we focus principally on discrete-event simulation-its underlying concepts, structure, and application.
Enhanced Power Plane with Photonic Band Gap Structures for Wide Band Suppression of Parallel Plate Resonances (2005)

In high speed digital circuits, with high clock frequency and resulting fast rising and falling time, simultaneous switching noise (SSN) has become a major concern for EMI/EMC engineers. The use of power planes containing low period photonic band gap (PBG) structures has been proposed for SSN suppression (Tzong-Lin Wu et al., IEEE Microwave and Wireless Components Letters, vol.14, p.337-9, 2004). Though this structure shows wide bandwidth, it cannot suppress SSN in the frequency range below a few GHz. We propose an enhanced power plane employing PBG with meander line. The advantage of proposed power plane is an efficient suppression of resonances in a broader bandwidth than conventional methods. Therefore, the proposed structure is useful in high frequency digital circuits and systems. Compared with a reference board, the proposed power plane has a band gap from 0.4 GHz to 3.8 GHz and highly efficient suppression with minimum -30 dB, and maximum -100 dB. The bandwidth of the proposed structure is broader.
Silicon Nanowires Wrapped with Au Film (2002)

In an attempt to provide ohmic contacts to silicon nanowires (SiNWs), SiNWs wrapped with Au film have been fabricated. Au particles were deposited on the as-grown SiNWs and followed by electron beam annealing under transmission electron microscopy (TEM). The high-resolution TEM (HRTEM) study showed the transformation of the Au particles into crystalline Au film. The uniformity of Au film was dependent upon the size and the separation of the Au particles.
Virtual-memory-mapped network interfaces (1995)

In today's multicomputers, software overhead dominates the message-passing latency cost. We designed two multicomputer network interfaces that significantly reduce this overhead. Both support virtual-memory-mapped communication, allowing user processes to communicate without expensive buffer management and without making system calls across the protection boundary separating user processes from the operating system kernel. Here we compare the two interfaces and discuss the performance trade-offs between them.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Adenovirus-pulsed dendritic cells stimulate human virus-specific T-cell responses in vitro (1996)

Adenovirus infections cause significant morbidity and mortality in immunocompromised patients, yet little is known about the immune response to adenovirus infections. We established a system for the generation of a cytotoxic immune response to adenovirus in vitro. Cytotoxic T cells (CTLs) were derived from normal donors by using peripheral blood dendritic cells as antigen-presenting cells. The CTLs were found to contain a mixture of effector cells that recognized virus peptides in the context of both class I and class II antigens. Endogenous viral gene expression was not required to sensitize cells to lysis by adenovirus-specific CTLs. CTLs raised against subgroup C adenovirus type 5 can lyse cells infected with subgroup B adenovirus type 11, indicating that viruses of different subgroups have epitopes in common. This system holds promise for defining the human immune response to adenovirus, including characterization of the viral protein(s) against which the response is generated, and the identity of the effector cells. Such studies are in progress.
A Programmer's View of Computer Architecture: With Assembly Language Examples from the MIPS RISC Architecture (1993)

1. Abstractions and Computers 1.1 Levels of Abstraction 1.2 The Tower of Computer Abstractions 1.3 A Programming Language as an Abstraction 1.4 Computer Architecture 1.5 Computer Execution Basics 2. SAL: A Simple Abstract Language 2.1 On Assembly and Compilation 2.2 Variable Declaration 2.3 Arithmetic Operations 2.4 Control Structures 2.5 Communication with the User 2.6 A SAL Program 2.7 Procedures 2.8 A Modular SAL Program 3. Number Systems 3.1 Numbers and Their Representation 3.2 Weighted Positional Notation 3.3 Transformations Between Radices 3.4 Representation of Non-Integer Numbers 3.5 Precision and Accuracy 4. Data Representation 4.1 Numbers versus Their Representation 4.2 Representation of Integers 4.3 Characters 4.4 Floating Point Representation 5. Arithmetic and Logical Operations 5.1 Boolean Operations 5.2 Shift Operations 5.3 Addition and Subtraction 5.4 Multiplication 5.5 Division 6. Floating Point Arithmetic 6.1 Hardware versus Software Calculations 6.2 Addition and Subtraction 6.3 Multiplication 6.4 Division 6.5 Advanced Topics 6.6 SAL Instructions 7. Data Structures 7.l Memory as an Array 7.2 Arrays 7.3 Stacks 7.4 Queues 8. Registers and MAL 8.1 Instructions as a Data Type 8.2 Specifying Addresses in Instructions 8.3 The MAL Architecture 8.4 Example MAL Code 9. Procedures 9.1 MAL Procedure Call and Return Mechanisms 9.2 Dynamic Storage Allocation 9.3 Activation Records 9.4 Parameter Passing 9.5 Saving Registers 9.6 MIPS RISC Register Usage 9.7 A MAL Program that Uses Procedures 10. The Assembly Process 10.1 What Assemblers Do 10.2 True Assembly Language (TAL) 10.3 Machine Code Format and Generation 10.4 Program Relocation 11. Input and Output 11.1 Typical I/O Devices 11.2 The Processor-I/O Interface 12. Interrupts and Exception Handling 12.1 The Exception Mechanism 12.2 The Role of the Operating System 12.3 The MIPS RISC Exception Mechanism 12.4 A Sample Exception Handler 12.5 Operating System Issues 13. Architectural Performance 13.1 On Minimal Instruction Sets and Choices 13.2 Pipelining 13.3 Branching Techniques 13.4 Memory Hierarchies 14. Alternative Architectures 14.1 What's All This About RISC? 14.2 The Single-Chip Constraint 14.3 The Motorola 68000 Family 14.4 The Intel iAPS 86 Architecture 14.5 The Cray-1 14.6 SPARC Appendix A SAL Appendix B MAL Appendix C TAL
Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth (2011)

Faecalibacterium prausnitzii is one of the most abundant commensal bacteria in the healthy human large intestine, but information on genetic diversity and substrate utilization is limited. Here, we examine the phylogeny, phenotypic characteristics, and influence of gut environmental factors on growth of F. prausnitzii strains isolated from healthy subjects. Phylogenetic analysis based on the 16S rRNA sequences indicated that the cultured strains were representative of F. prausnitzii sequences detected by direct analysis of fecal DNA and separated the available isolates into two phylogroups. Most F. prausnitzii strains tested grew well under anaerobic conditions on apple pectin. Furthermore, F. prausnitzii strains competed successfully in coculture with two other abundant pectin-utilizing species, Bacteroides thetaiotaomicron and Eubacterium eligens, with apple pectin as substrate, suggesting that this species makes a contribution to pectin fermentation in the colon. Many F. prausnitzii isolates were able to utilize uronic acids for growth, an ability previously thought to be confined to Bacteroides spp. among human colonic anaerobes. Most strains grew on N-acetylglucosamine, demonstrating an ability to utilize host-derived substrates. All strains tested were bile sensitive, showing at least 80% growth inhibition in the presence of 0.5 μg/ml bile salts, while inhibition at mildly acidic pH was strain dependent. These attributes help to explain the abundance of F. prausnitzii in the colonic community but also suggest factors in the gut environment that may limit its distribution.
Effect of Metacycloprodigiosin, an Inhibitor of Killer T Cells, on Murine Skin and Heart Transplants. (1996)

Metacycloprodigiosin is an antibiotic that has been shown to suppress T-cell proliferation induced by concanavalin A in vitro. We examined the effect of metacycloprodigiosin on murine allogenic skin and heart transplantation models, and compared graft rejection with donor-specific cytotoxic T-cells and antibody activity. The antibiotic slightly prolonged the survival of C57Bl/6 heart and skin grafts in BALB/c mice, although the effect was less that that of cyclosporin A. The effect was more evident in Bm1 (H-2D mutant) skin grafts on C57B1/6 hosts or in a minor histocompatibility antigen-mismatched model. In contrast, metacycloprodigiosin suppressed anti-graft cytotoxic T-cell activity of BALB/c spleen grafted with C57B1/6 skin as comparable to cyclosporin A, but had only partial effect on antibody production. Thus, metacycloprodigiosin is more effective in reducing splenic cytotoxic T-cell activity than in prolonging murine skin or cardiac allografts.
Differential induction of inflammatory cytokines by dendritic cells treated with novel TLR-agonist and cytokine based cocktails: targeting dendritic cells in autoimmunity (2010)

The identification of novel Th1-promoting cocktails allows screening of anti-inflammatory drug candidates by assessing the ability to suppress the activation and differentiation of imDCs into inflammatory DCs with a specific Th1-promoting phenotype. The model thus provides a screening tool, which can identify potential anti-inflammatory effects on the natural regulator of the immune response, the dendritic cell.
Fast Indexing: Support for Size-Changing Algorithms in Stackable File Systems (2001)

Stackable file systems can provide extensible file system functionality with minimal performance overhead and development cost. However, previous approaches provide only limited functionality. In particular, they do not support size-changing algorithms (SCAs), which are important and useful for many applications such as compression and encryption. We propose fast indexing, a technique for efficient support of SCAs in stackable file systems. Fast indexing provides a page mapping between file system layers in a way that can be used with any SCA. We use index files to store this mapping. Index files are designed to be recoverable if lost and add less than 0.1% disk space overhead. We have implemented fast indexing using portable stackable templates, and we have used this system to build several example file systems with SCAs. We demonstrate that fast index files have low overhead for typical user workloads such as large compilations, only 2.3% over other stacked file systems and 4.7% over non-stackable file systems. Our system can deliver better performance with SCAs than userlevel applications, as much as five times faster.
The NTT CHiME-3 system: Advances in speech enhancement and recognition for mobile multi-microphone devices (2015)

CHiME-3 is a research community challenge organised in 2015 to evaluate speech recognition systems for mobile multi-microphone devices used in noisy daily environments. This paper describes NTT's CHiME-3 system, which integrates advanced speech enhancement and recognition techniques. Newly developed techniques include the use of spectral masks for acoustic beam-steering vector estimation and acoustic modelling with deep convolutional neural networks based on the "network in network" concept. In addition to these improvements, our system has several key differences from the official baseline system. The differences include multi-microphone training, dereverberation, and cross adaptation of neural networks with different architectures. The impacts that these techniques have on recognition performance are investigated. By combining these advanced techniques, our system achieves a 3.45% development error rate and a 5.83% evaluation error rate. Three simpler systems are also developed to perform evaluations with constrained set-ups.
Review: Activation patterns of microglia and their identification in the human brain (2012)

Microglia in the central nervous system are usually maintained in a quiescent state. When activated, they can perform many diverse functions which may be either beneficial or harmful depending on the situation. Although microglial activation may be accompanied by changes in morphology, morphological changes cannot accurately predict the function being undertaken by a microglial cell. Studies of peripheral macrophages and in vitro and animal studies of microglia have resulted in the definition of specific activation states: M1 (classical activation) and M2 (sometimes subdivided into alternative activation and acquired deactivation). Some authors have suggested that these might be an overlapping continuum of functions rather than discrete categories. In this review, we consider translational aspects of our knowledge of microglia: specifically, we discuss the question as to what extent different activation states of microglia exist in the human central nervous system, which tools can be used to identify them and emerging evidence for such changes in ageing and in Alzheimer's disease.
Midfield Wireless Powering for Implantable Systems (2013)

Efficient wireless power transfer across tissue is highly desirable for removing bulky energy storage components. Most existing power transfer systems are conceptually based on coils linked by slowly varying magnetic fields (less than 10 MHz). These systems have many important capabilities, but are poorly suited for tiny, millimeter-scale implants where extreme asymmetry between the source and the receiver results in weak coupling. This paper first surveys the analysis of near-field power transfer and associated strategies to optimize efficiency. It then reviews analytical models that show that significantly higher efficiencies can be obtained in the electromagnetic midfield. The performance limits of such systems are explored through optimization of the source, and a numerical example of a cardiac implant demonstrates that millimeter-sized devices are feasible.
Electronic properties of metal nanorods probed by surface-enhanced Raman spectroscopy (2000)

Applying the probe molecule strategy, surface-enhanced Raman spectroscopy has been used, for the first time, as a diagnostic tool of the electronic properties of metal nanorods; the vibrational frequency of the probe molecule SCN− at Cu nanorods is shown to critically depend on the nanorod’s diameter in the range from 50 to 15 nm; the up-shifting of the Fermi level with a decrease of the nanorod’s diameter is interpreted based on the change of cohesive energy owing to the high ratio of surface to bulk atoms.
Biochemistry of coenzyme B12-dependent glycerol and diol dehydratases and organization of the encoding genes (1998)

Glycerol and diol dehydratases exhibit a subunit composition of α2β2γ2 and contain coenzyme B12 in the base-on form. The dehydratase reaction proceeds via a radical mechanism. The dehydratases are subject to reaction inactivation by the substrate glycerol which is caused by a cessation of the catalytic cycle because coenzyme B12 is not regenerated, instead 5′-deoxyadenosine and a catalytically inactive cobalamin are formed. The genetic organization of the dehydratase genes is quite similar in all organisms. Downstream of the dehydratase genes an open reading frame encoding a polypeptide of approximately 600 amino acids was identified which is apparently involved in the reactivation of suicide-inactivated enzyme.