gebhart/patrepeval huggingface dataset:
Extracellular Matrix Remodeling: The Common Denominator in Connective Tissue Diseases <i>Possibilities for Evaluation and Current Understanding of the Matrix as More Than a Passive Architecture, but a Key Player in Tissue Failure</i> (2012)

Increased attention is paid to the structural components of tissues. These components are mostly collagens and various proteoglycans. Emerging evidence suggests that altered components and noncoded modifications of the matrix may be both initiators and drivers of disease, exemplified by excessive tissue remodeling leading to tissue stiffness, as well as by changes in the signaling potential of both intact matrix and fragments thereof. Although tissue structure until recently was viewed as a simple architecture anchoring cells and proteins, this complex grid may contain essential information enabling the maintenance of the structure and normal functioning of tissue. The aims of this review are to (1) discuss the structural components of the matrix and the relevance of their mutations to the pathology of diseases such as fibrosis and cancer, (2) introduce the possibility that post-translational modifications (PTMs), such as protease cleavage, citrullination, cross-linking, nitrosylation, glycosylation, and isomerization, generated during pathology, may be unique, disease-specific biochemical markers, (3) list and review the range of simple enzyme-linked immunosorbent assays (ELISAs) that have been developed for assessing the extracellular matrix (ECM) and detecting abnormal ECM remodeling, and (4) discuss whether some PTMs are the cause or consequence of disease. New evidence clearly suggests that the ECM at some point in the pathogenesis becomes a driver of disease. These pathological modified ECM proteins may allow insights into complicated pathologies in which the end stage is excessive tissue remodeling, and provide unique and more pathology-specific biochemical markers.
Guillaume Triébert制作的10键双簧管（续） (2006)

在我的Triebert双簧管上是靠右手小指控制的小字一组c和小字一组降e音（同时也控制小字二组降e音）。这两个键是在18世纪开始应用的。这样的按键在19世纪以前只被普遍用在双簧管上。低音b用左手小指控制，向下扩充了一个半音。在博德（Brod）所绘的指法表里，把这个b音误指成c音，显然这是个错误。另外一个键很可能是为^#c设计的，虽然这个键显然并不常用，但博德用的是传统的指法（用c键）来得到这个上方音。
From the Lab to the Clinic (1999)

Even as tissue engineers work to produce whole organs such as bladders and livers (see main text), lab-grown versions of more than a dozen different tissues, ranging from skin and cartilage to heart valves and corneas, are either in the clinic or under development. Here's a sample:
Optical flip-flop based on two-coupled mode-locked ring lasers (2004)

We report an all-optical flip-flop that is based on two coupled actively mode-locked fiber ring lasers. The lasers are coupled so that when one of the lasers lases, it quenches lasing in the other laser. The state of the flip-flop is determined by the wavelength of the laser that is currently lasing. The concept of the flip-flop is explained and experimental results are presented that indicate a flip-flop operation over 25-dB contrast ratio and less than 0.3-mW switching power.
Translation and rotation of multi-point contacted virtual objects (2003)

Simulation of multi-finger grasps and contact in a haptic device presents a number of problems over the use of single finger interactions. These problems include how to model friction and how to resolve the contribution of forces from multiple finger contact points as well as dealing with more general object physics. Friction is a vital aspect of modelling in multi-point haptic interactions. A friction model is needed to allow a grasp using two or more fingers without the fingers slipping from the virtual object. Friction is also needed when lifting an object from a surface to stabilise the object in the grasp before it is lifted away. Once clear of the surface it is appropriate to provide a simulation of the mass and inertia of the object to allow the object to be moved, rotated and placed upon another surface. This paper presents methods for modelling haptic contact friction in situations where an object is being both translated and rotated based upon the use of god-objects [1] and friction cones [6] as well as residual force/torque methods for the subsequent translation and rotation of the grasped object.
A limiting amplifier with LOS indication for gigabit ethernet (2008)

The paper presents a high-gain and large-bandwidth limiting amplifier with a maximum data rate of 1.25 Gb/s for Gigabit Ethernet. Composed of a multi-stage amplifier, an output driver, an offset cancellation circuit and a signal-detection circuit, the limiting amplifier provides constant positive-referenced emitter-coupled logic (PECL) output voltage and features a programmable loss-of-signal (LOS) indication and a squelch function that mutes the data output signal when the input voltage falls below the programmable threshold. It is implemented in TSMC 0.35-mum BiCMOS technology, with an active area of 1.3times1.1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Using a single 3.3-V supply voltage, measured results demonstrate that the input dynamic range is larger than 52 dB and the power consumption is only 60 mW.
Framework and Implementation of A Web-based Multi-objective Decision Support System: WMODSS (2003)

This paper presents a web-based general decision support system for solving multi-objective decision problems.This is referred to WMODSS.The system provides three decision-making methods in its method base.They deal with a wide range of linear multiobjective decision-making problems and different user requirements for the solution process.In particular, the WMODSS provides an intelligent guide to help users select a most suitable method from the method base by evaluating the relevant problems and user requirements.A satisfactory solution can thus be obtained in an interactive and flexible manner.
Nonredundant Roles for B Cell-Derived IL-10 in Immune Counter-Regulation (2009)

IL-10 plays a central role in restraining the vigor of inflammatory responses, but the critical cellular sources of this counter-regulatory cytokine remain speculative in many disease models. Using a novel IL-10 transcriptional reporter mouse, we found an unexpected predominance of B cells (including plasma cells) among IL-10-expressing cells in peripheral lymphoid tissues at baseline and during diverse models of in vivo immunological challenge. Use of a novel B cell-specific IL-10 knockout mouse revealed that B cell-derived IL-10 nonredundantly decreases virus-specific CD8(+) T cell responses and plasma cell expansion during murine cytomegalovirus infection and modestly restrains immune activation after challenge with foreign Abs to IgD. In contrast, no role for B cell-derived IL-10 was evident during endotoxemia; however, although B cells dominated lymphoid tissue IL-10 production in this model, myeloid cells were dominant in blood and liver. These data suggest that B cells are an underappreciated source of counter-regulatory IL-10 production in lymphoid tissues, provide a clear rationale for testing the biological role of B cell-derived IL-10 in infectious and inflammatory disease, and underscore the utility of cell type-specific knockouts for mechanistic limning of immune counter-regulation.
Using Verbosity: Common Sense Data from Games with a Purpose (2010)

Verbosity, a ``game with a purpose'', uses the collective activity of people playing an Internet word game as a body of common sense knowledge. One purpose of Verbosity has always been to provide large quantities of input for a common sense knowledge base, and we have now achieved this purpose by connecting it to the Open Mind Common Sense (OMCS) project. Verbosity now serves as a way to contribute to OMCS in addition to being an entertaining game in its own right. Here, we explain the process of filtering and adapting Verbosity's data for use in OMCS, showing that the results are of a quality comparable to OMCS's existing data, and discuss how this informs the future development of games for common sense.
Granulocytopoiesis. I. Senescence and Random Loss of Neutrophilic Granulocytes in Human Beings (1964)

Abstract Tritiated thymidine labeling of DNA with a subsequent autoradiographic and cytologic study of the peripheral blood and oral lavages reveal: 1. Direct cytologic evidence for a random loss of granulocytes from the blood into the oral cavity is given. Presumably there are larger random losses in the gastrointestinal tract. This observation supports the conclusions based upon disappearance of radioactivity from the blood after autotransfusion of DFP32 labeled granulocytes. 2. The delayed appearance of label in the pyknotic granulocytes (Ab-bauformen) is strong evidence that those cells are older degenerating granulocytes and that it takes about 24-30 hours for labeled granulocytes to age to the point of becoming pyknotic senescent granulocytes. 3. The process of senescence truncates the exponential curves of random disappearance of granulocytes from the blood. 4. A model showing the relationship between random loss and senesence is constructed and discussed. 5. A mathematical description of this model is presented. The equations developed are highly sensitive to variations in input data thus limiting their practical usefulness for computations unless precise measurements are possible and are made on each subject studied for each variant in the equation.
Adaptive selection of access path and join method (2003)

An adaptive approach which utilizes the information embedded in indexes to identify the tuples satisfying a given predicate or having a match in a join operation is proposed. An access path (index or table scan) and a join method (index join, nested loop, sort-merge) are chosen to construct the results adaptively. This leads to the optimal evaluation of queries. With an efficient implementation, the adaptive decision process becomes a part of a query evaluation procedure, so that the overhead of the approach is minimized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Job partitioning strategies for multiprocessor scheduling of real-time periodic tasks with restricted migrations (2012)

In this work, we consider the scheduling of real-time periodic tasks on multiprocessors under a restricted-migration constraint (tasks are allowed to migrate whereas jobs are not). We first propose a technique, (offline) job partitioning, which statically assigns jobs to processors before execution. We show that (offline) job partitioning strictly dominates both partitioned and restricted-migration scheduling. We then consider r-RM, a restricted-migration variant of global RM, we design a sufficient schedulability test and we provide a speedup factor for the scheduler.
Genome Sequence of the Marine <i>Janibacter</i> Sp. Strain HTCC2649 (2010)

Janibacter sp. strain HTCC2649 is a novel marine member of the Actinobacteria, family Intrasporangiaceae, and is closely related to Janibacter melonis CM2104(T) and Knoellia sinensis HKI 0119(T). The organism was isolated from a sample collected at Hydrostation S south of Bermuda by using high-throughput culturing techniques. Here we present the genome sequence of Janibacter sp. strain HTCC2649.
Location of tumour necrosis factor alpha by immunohistochemistry in chronic inflammatory bowel disease. (1993)

This study determined the location and tissue density of cells immunoreactive for tumour necrosis factor alpha (TNF alpha) in intestinal specimens from 24 patients with chronic inflammatory bowel disease (15 with Crohn's disease, nine with ulcerative colitis) and 11 controls. There was significantly increased density of TNF alpha immunoreactive cells in the lamina propria of both ulcerative colitis and Crohn's disease specimens, although the distribution of these cells differed in the two conditions. In ulcerative colitis most of the TNF alpha immunoreactivity was seen in the subepithelial macrophages, with comparatively less in the deep lamina propria, while in Crohn's disease immunoreactive cells were distributed evenly throughout the lamina propria. Increased submucosal immunoreactivity was found only in Crohn's disease, in which TNF alpha positive macrophages tended to cluster around arterioles and venules, often infiltrating and disrupting vascular endothelium. It is suggested that this degree of TNF alpha production probably contributes significantly to the pathogenesis of both Crohn's disease and ulcerative colitis, by impairing the integrity of epithelial and endothelial membranes, increasing inflammatory cell recruitment, and by prothrombotic effects on the vascular endothelium.
The Acyl-Coenzyme A: Cholesterol Acyltransferase Inhibitor CI-1011 Reverses Diffuse Brain Amyloid Pathology in Aged Amyloid Precursor Protein Transgenic Mice (2010)

Cerebral accumulation of amyloid-beta (Abeta) is characteristic of Alzheimer disease and of amyloid precursor protein (APP) transgenic mice. Here, we assessed the efficacy of CI-1011, an inhibitor of acyl-coenzyme A:cholesterol acyltransferase, which is suitable for clinical use, in reducing amyloid pathology in both young (6.5 months old) and aged (16 months old) human APP transgenic mice. Treatment of young animals with CI-1011 decreased amyloid plaque load in the cortex and hippocampus and reduced the levels of insoluble Abeta40 and Abeta42 and C-terminal fragments of APP in brain extracts. In aged mice, CI-1011 specifically reduced diffuse amyloid plaques with a minor effect on thioflavin S-positive dense-core plaques. Reduced diffusible amyloid was accompanied by suppression of astrogliosis and enhanced microglial activation. Collectively, these data suggest that CI-1011 treatment reduces amyloid burden in human APP mice by limiting generation and increasing clearance of diffusible Abeta.
Automating the Collection of Ultrathin Serial Sections for Large Volume TEM Reconstructions (2006)

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005
Mechanisms of epithelial-mesenchymal transition in proliferative vitreoretinopathy. (2015)

Proliferative vitreoretinopathy (PVR) is a blinding disease characterized by the formation of epiretinal membranes through the wound repair process. Though the mechanisms of PVR development are still not fully understood, retinal pigment epithelial (RPE) cells are indicated to play the primary role in the pathogenesis of PVR. In the setting of PVR, RPE cells undergo a process named epithelial-mesenchymal transition (EMT), by which differentiated epithelial cells go through a phenotypic conversion that gives rise to the matrix-producing fibroblasts and myofibroblasts. Recent studies indicated that EMT in RPE cells is a main contributor of PVR and involves various growth factors/cytokines, transcriptional factors, and microRNAs. Targeting these factors/microRNAs suppresses the progression of EMT and thus may provide novel ideas for the treatment of PVR. This review highlights the current understandings of EMT in the pathogenesis of PVR and the underlying mechanisms of EMT in RPE cells.
Double Side Polishing for VLSI of Silicon Wafer. One Side Mirror Polishing Considered with Etched Wafer Roughness. (1993)

This paper deals with double-sided polishing technology used in Si wafer production lines.
Schottky diode characteristics and deep levels on hydrogenated n-type GaAs (1992)

Schottky diode characteristics and deep levels of Si-doped n-type GaAs after hydrogen plasma exposure have been investigated as a function of substrate temperature during hydrogenation. The barrier height and reverse breakdown voltage of Au Schottky diodes on Si-doped GaAs increased during hydrogen plasma exposure. The ideality factor of the hydrogenated samples was lowered to 1.11 at substrate temperatures between 150 and 250 degrees C, and deep levels in these samples were effectively passivated at these temperatures. These properties of n-GaAs can be related to hydrogen redistribution in an electrically passivated surface layer. Good diode characteristics and the most effective passivation of deep levels in GaAs could be achieved at a substrate temperature of about 200 degrees C and a power density of 0.06 W cm-2.
Efficient algorithm for virtual topology design in multihop lightwave networks (1994)

One of the major challenges in the virtual topology design of a WDM star based system, is to incorporate in the optimization process both realistic objective functions and real system behavior. The authors present an efficient discrete optimization algorithm that meets these goals while incorporating the prevailing traffic conditions. They simulate the real system and then approximate the objective function by a short term simulation. The optimization process is based on an ordinal optimization approach, i.e., is insensitive to the approximation of the objective function obtained by short term simulation. Another crucial issue in virtual topology design is how to evaluate the quality of the solution obtained by the algorithm. They propose a new metric to evaluate the solution quality, the so called suboptimal quality, obtained by deriving the solution's relative position in the state space according to the performance order. The experiments presented in the paper attest to the quality (efficiency and robustness) of the optimization algorithm and its suitability to solve the wavelength assignment problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Homogeneous Fluorescence Assays for RNA Diagnosis by Pyrene-Conjugated 2′-<b><i>O</i></b>-Methyloligoribonucleotides (2007)

We developed a bispyrene-conjugated 2'-O-methyloligoribonucleotide as an RNA-specific RNA-probe. The probe hybridized with the complementary RNA, greatly enhancing fluorescence and discriminating RNA from DNA. The assay was carried out in homogeneous aqueous media without removing the unbound probe from the detection solution. This homogeneous fluorescence assay also discriminated mismatch sequences in the target RNA. These pyrene probes could possess high potential to detect RNA in biological specimens simply.
gamma/delta and other unconventional T lymphocytes: what do they see and what do they do? (1996)

T lymphocytes recognize specific ligands by clonally distributed T-cell receptors (TCR). In humans and most animals, the vast majority of T cells express a TCR composed of an alpha chain and a beta chain, whereas a minor T-cell population is characterized by the TCR gamma/delta. Almost all of our knowledge about T cells stems from alpha/beta T cells and only now are we beginning to understand gamma/delta T cells. In contrast to conventional alpha/beta T cells, which are specific for antigenic peptides presented by gene products of the major histocompatibility complex, gamma/delta T cells directly recognize proteins and even nonproteinacious phospholigands. These findings reveal that gamma/delta T cells and alpha/beta T cells recognize antigen in a fundamentally different way and hence mitigate the dogma of exclusive peptide-major histocompatibility complex recognition by T cells. A role for gamma/delta T cells in antimicrobial immunity has been firmly established. Although some gamma/delta T cells perform effector functions, regulation of the professional and the nonprofessional immune system seems to be of at least equal importance. The prominent residence of gamma/delta T cells in epithelial tissues and the rapid mobilization of gamma/delta T cells in response to infection are consistent with such regulatory activities under physiological and pathologic conditions. Thus, although gamma/delta T cells are a minor fraction of all T cells, they are not just uninfluential kin of alpha/beta T cells but have their unique raison d'être.
On faster convergence of cyclic block coordinate descent-type methods for strongly convex minimization (2018)

The cyclic block coordinate descent-type (CBCD-type) methods, which performs iterative updates for a few coordinates (a block) simultaneously throughout the procedure, have shown remarkable computational performance for solving strongly convex minimization problems. Typical applications include many popular statistical machine learning methods such as elastic-net regression, ridge penalized logistic regression, and sparse additive regression. Existing optimization literature has shown that for strongly convex minimization, the CBCD-type methods attain iteration complexity of $\mathcal{O}(p\log(1/\epsilon))$, where $\epsilon$ is a pre-specified accuracy of the objective value, and $p$ is the number of blocks. However, such iteration complexity explicitly depends on $p$, and therefore is at least $p$ times worse than the complexity $\mathcal{O}(\log(1/\epsilon))$ of gradient descent (GD) methods. To bridge this theoretical gap, we propose an improved convergence analysis for the CBCD-type methods. In particular, we first show that for a family of quadratic minimization problems, the iteration complexity $\mathcal{O}(\log^2(p)\cdot\log(1/\epsilon))$ of the CBCD-type methods matches that of the GD methods in term of dependency on $p$, up to a $\log^2 p$ factor. Thus our complexity bounds are sharper than the existing bounds by at least a factor of $p/\log^2(p)$. We also provide a lower bound to confirm that our improved complexity bounds are tight (up to a $\log^2 (p)$ factor), under the assumption that the largest and smallest eigenvalues of the Hessian matrix do not scale with $p$. Finally, we generalize our analysis to other strongly convex minimization problems beyond quadratic ones.
Real-time linear-predictive coding of speech on the SPS-41 triple-microprocessor machine (1975)

The autocorrelation method for linear-predictive coding of speech [1] has been implemented in real time on the SPS-41, a commercially available system composed of three dissimilar microprocessors working in parallel. Using user-written microcode, one processor performs I/O and master control, the second handles loop indexing and counting, and the third does the actual arithmetic on data. Such parallelism allows 2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> I/O operations and 4 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> multiplications/s, but actually realizing this potential requires fresh approaches to some old algorithms. Most important is a new autocorrelation scheme with several valuable properties. Using 16-bit fixed-point single-precision arithmetic to accumulate autocorrelation sums and invert the autocorrelation matrix presents problems which have been solved reasonably well. The present program converts frames of 256 16-bit samples into 14 coefficients and then into 128 points of logarithmic power spectrum at 100 frames/s.
Decreased serum tryptophan in patients with HIV-1 infection correlates with increased serum neopterin and with neurologic/psychiatric symptoms. (1990)

We investigated serum neopterin, tryptophan, and kynurenine concentrations in 23 HIV-1 seropositive patients (Walter Reed Stage 4-6). Ten patients presented with polyneuropathy and three with dementia, one of the patients with dementia also had polyneuropathy and dementia. We found significant associations between lower trytophan concentrations and neurologic/psychiatric symptoms. The negative correlation of tryptophan with kynurenine and neopterin concentrations indicates activity of indoleamine 2,3-dioxygenase (IDO) in patients. IDO can be induced by cytokines such as interferon-gamma and therefore low tryptophan levels may result from chronic immune stimulation in HIV-1 seropositives.