gebhart/patrepeval huggingface dataset:
Automation of IC Layout with Analog Constraints (2009)

<P>A methodology for the automatic synthesis of fullcustom IC layout with analog constraints is presented. The methodology guarantees that all performance constraints are met when feasible, or otherwise, infeasibility is detected as soon as possible, thus providing a robust and efficient design environment In the proposed approach, performance specifications are translated into lower-level bounds on parasitics or geometric parameters, using sensitivity analysis. Bounds can be used by a set of specialized layout tools performing stack generation, placement, routing, and compaction. For each tool, a detailed description is provided of its functionality, of the way constraints are mapped and enforced, and of its impact on the design flow. Examples drawn from industrial applications are reported to illustrate the effectiveness of the approach.</P>
Resequencing control and analysis in computer networks (1988)

This dissertation is concerned with the design and analysis of efficient scheduling policies to minimize resequencing problems occurring in computer communication networks, distributed systems, and manufacturing systems.
In packet switched networks, messages are often transmitted from source nodes to designation nodes over paths called virtual circuits. For efficiency and reliability reasons, logical channels connecting adjacent nodes of a virtual circuit may consist of multiple physical links. Due to different link speeds and variable packet size, packets may arrive at the destination node in an order different from that in which they were originally generated at the source node. Given that First-In-First-Out delivery is required, out of sequence packets must wait at the destination node to be placed back into proper sequence. Consequently, out of sequence packets experience delay called resequencing delay, in addition to queueing delay. This dissertation examines the impact of threshold type policies on the resequencing delay. Various methods for analyzing resequencing problems are developed and exact expressions for the resequencing delay distributions are obtained. These techniques are applicable in many other contexts where the resequencing problem arises.
The analytical results reveal that the resequencing delay is affected by the way customers are dispatched to the servers. A general class of dispatching policies called Fixed Position Policies is presented. This dissertation investigates the problem of the judicious selection of the system parameters so as to achieve certain performance requirements.
This dissertation also addresses the resequence buffer design issue. The appropriate buffer size is determined by the distribution of the number of packets in the resequence buffer. This distribution in turn depends on the scheduling policy being employed. This relation is explored and the policies which keep the system performance within specified design limits are obtained.
The resequencing problem is also studied in a system of two parallel queues with multiple classes. The system controller dispatches arriving messages to the queues randomly. This dissertation examines the load balancing problem when resequencing delay is taken into account. The optimal routing probabilities that minimize the average system response time are derived.
PulmonDB: a curated lung disease gene expression database (2019)

ABSTRACT Chronic Obstructive Pulmonary Disease (COPD) and Idiopathic Pulmonary Fibrosis (IPF) have contrasting clinical and pathological characteristics, and interesting whole-genome transcriptomic profiles. However, data from public repositories are difficult to reprocess and reanalyze. Here we present PulmonDB, a web-based database ( http://pulmondb.liigh.unam.mx/ ) and R library that facilitates exploration of gene expression profiles for these diseases by integrating transcriptomic data and curated annotation from different sources. We demonstrated the value of this resource by presenting the expression of already well-known genes of COPD and IPF across multiple experiments and the results of two differential expression analyses in which we successfully identified differences and similarities. With this first version of PulmonDB, we create a new hypothesis and compare the two diseases from a transcriptomics perspective.
Supplementary Table 7 from Cancer-Associated Fibroblasts Promote Aggressive Gastric Cancer Phenotypes via Heat Shock Factor 1–Mediated Secretion of Extracellular Vesicles (2023)

&lt;p&gt;Gene set enrichment analysis (GSEA) using MSigDB (Hallmark gene sets) on the full stromal patient RNA-seq data&lt;/p&gt;
A Tunable Electrostatic MEMS Pressure Switch (2019)

In this article, we demonstrate a tunable air pressure switch. The switch detects when the ambient pressure drops below a threshold value and automatically triggers without the need for any computational overhead to read the pressure or trigger the switch. The switch exploits the significant fluid interaction of a microelectro-mechanical systems beam undergoing a large oscillation from electrostatic levitation to detect changes in ambient pressure. If the oscillation amplitude near the resonant frequency is above a threshold level, dynamic pull-in is triggered and the switch is closed. The pressure at which the switch closes can be tuned by adjusting the voltage applied to the switch. The use of electrostatic levitation allows the device to be released from their pulled-in position and reused many times without mechanical failure. A theoretical model is derived and validated with experimental data. It is experimentally demonstrated that the pressure switching mechanism is feasible.
Nanosecond Pulse Amplification in a Higher-Order Mode Erbium-Doped Fiber Amplifier (2010)

The nonlinear properties of a nanosecond pulse in a higher-order-mode, Er-doped-fiber amplifier with 2440µm2 effective area are compared to a conventional 880 µm2 area fiber. Both 1480nm pump and 1554nm signal propagate in the LP09 mode.
Regulation of protein tyrosine phosphatases by reversible oxidation (2011)

Oxidation of the catalytic cysteine of protein-tyrosine phosphatases (PTP), which leads to their reversible inactivation, has emerged as an important regulatory mechanism linking cellular tyrosine phosphorylation and signalling by reactive-oxygen or -nitrogen species (ROS, RNS). This review focuses on recent findings about the involved pathways, enzymes and biochemical mechanisms. Both the general cellular redox state and extracellular ligand-stimulated ROS production can cause PTP oxidation. Members of the PTP family differ in their intrinsic susceptibility to oxidation, and different types of oxidative modification of the PTP catalytic cysteine can occur. The role of PTP oxidation for physiological signalling processes as well as in different pathologies is described on the basis of well-investigated examples. Criteria to establish the causal involvement of PTP oxidation in a given process are proposed. A better understanding of mechanisms leading to selective PTP oxidation in a cellular context, and finding ways to pharmacologically modulate these pathways are important topics for future research.
A 90 nm CMOS MS/RF based foundry SOC technology comprising superb 185 GHz f/sub T/ RFMOS and versatile, high-Q passive components for cost/performance optimization (2004)

A versatile mixed-signal and RF (MS/RF) technology based on a foundry 90 nm CMOS process was demonstrated with excellent MOS transistor f/sub T/ at 160-185 GHz. Passive elements of various process schemes were fabricated for cost/performance evaluation. To realize low-cost system-on-chip (SOC), passive elements like 0.9 /spl mu/m Cu inductors and metal-stacked capacitors (MOM) were implemented using a standard logic back-end process. For high performance MS/RF solutions, inductors with 3 /spl mu/m Cu and ultra thick 6 /spl mu/m Cu top metal were fabricated to achieve high quality factors, Q>15 at 1 GHz and peak Q>20. Precision metal-sandwiched capacitors (MIM) with unit capacitances of 1.0, 1.5 and 2.0 fF//spl mu/m/sup 2/ were characterized and compared. Comparable or better matching was observed for MIM with higher unit capacitance, implying the possibility for chip size reduction. Specifically, the advantage of better MIM matching was demonstrated for the first time on the data resolution improvement of an A-to-D converter.
Bench to Bedside: The Role of Mitochondrial Medicine in the Pathogenesis and Treatment of Cellular Injury (2003)

Interest in the study of mitochondria has undergone a revival. The term mitochondrial medicine developed around evidence pointing to the mitochondria as a logical target for therapy. This article reviews the normal functions of mitochondria and integration of mitochondrial processes in cells. Changes in mitochondria that occur in ischemia and reperfusion, production of reactive oxygen species by mitochondria, stimulation of apoptosis, and roles of mitochondria in sepsis also are reviewed. The authors also review therapies that are based on targeting drugs to mitochondria, regulating calcium availability, substrate preferences, and activation of poly (ADP-ribose) polymerase and apoptosis. The purpose of this article is to provide a framework for emergency medicine academicians to understand the roles of mitochondria in pathology and to facilitate the transition of this information into therapeutic strategies based on mitochondrial medicine. For individuals interested in the biochemistry of mitochondria, knowledge of this fundamental organelle is expanding at a rapid rate.
The Composition of Crude Corn Oil Recovered after Fermentation via Centrifugation from a Commercial Dry Grind Ethanol Process (2010)

Abstract A study was conducted to examine the chemical composition of corn oil obtained after fermentation of corn to make fuel ethanol via centrifugation and compare its composition to that of corn germ oil (commercial corn oil) and experimental corn oils. The levels of free fatty acids in the post fermentation corn oil were high (11–16%), as previously reported. The levels of free phytosterols and hydroxycinnamate steryl esters (similar to oryzanol in rice bran oil) were higher than those of corn germ oil and were comparable to those of ethanol‐extracted corn kernel oil. The levels of tocopherols were lower in post‐fermentation oil than in either corn germ oil or ethanol extracted corn kernel oil. The levels of lutein and zeaxanthin in post‐fermentation were much higher than those in corn germ oil and were comparable to those in ethanol‐extracted corn kernel oil. Overall, exposure to all upstream processes of a fuel ethanol plant, including high‐temperature liquefaction, saccharification and fermentation appeared to have the most notable effect on tocopherols, but it had little effect on the levels of free phytosterols, hydroxycinnamate steryl esters, lutein and zeaxanthin. It may be desirable to recover these valuable functional lipids prior to using the post‐fermentation corn oil for industrial applications such as making biodiesel if a cost‐effective recovery process can be developed.
Focus on maximal miniaturisation of transradial coronary access materials and techniques by the Slender Club Japan and Europe: an overview and classification (2015)

Slender TRI is a new challenge to maximise patient value by improving outcome and reducing costs during TRI. Materials and techniques are continuously being refined and miniaturised to the highest standards. Whether outcome improves while reducing costs remains to be validated.
VidMAP: video monitoring of activity with prolog (2006)

This paper describes the architecture of a visual surveillance system that combines real time computer vision algorithms with logic programming to represent and recognize activities involving interactions amongst people, packages and the environments through which they move. The low level computer vision algorithms log primitive events of interest as observed facts, while the higher level Prolog based reasoning engine uses these facts in conjunction with predefined rules to recognize various activities in the input video streams. The system is illustrated in action on a multi-camera surveillance scenario that includes both security and safety violations.
Current sensorless speed servo system of a PM motor based on the current estimation method (2002)

Abstract This paper proposes a new speed servo system for a PM motor without a current sensor, which is constructed by the current simulator of a PM motor. The proposed speed servo system is simple and economical. The sensor of the proposed system is only a position sensor used as an encoder. Hence, the proposed speed servo system has little influence on the switching noise of a PWM inverter. Moreover, the resolution of the proposed current simulator can be higher than that of the conventional actual feedback system. In this paper, the experimental results point out that the proposed current sensorless speed servo system has the desired current and speed response. The current waveform of the proposed system is smooth and clean. Moreover, this paper proposes a new identification algorithm for motor resistance R a and main flux Φ fa by using only a position sensor. © 2002 Wiley Periodicals, Inc. Electr Eng Jpn, 142(3): 64–73, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.10084
Correction: Efficient planar n-i-p type heterojunction flexible perovskite solar cells with sputtered TiO2 electron transporting layers (2017)

Correction for ‘Efficient planar n-i-p type heterojunction flexible perovskite solar cells with sputtered TiO 2 electron transporting layers’ by Sawanta S. Mali et al. , Nanoscale , 2017, DOI: 10.1039/c6nr09032j.
Bone morphogenetic protein receptor 2 inhibition destabilizes microtubules promoting the activation of lysosomes and cell death of lung cancer cells (2021)

These studies reveal that the inhibition of BMPR2 destabilizes the microtubules promoting cell death of cancer cells that involves the activation of the lysosomes. Resistance to small molecules targeting BMPR2 may occur if the BMPR2 is localized predominantly to the cytoplasm and/or fails to localize to the lysosome for degradation. Video Abstract.
Increased apoptosis and accelerated epithelial migration following inhibition of hedgehog signaling in adaptive small bowel postresection (2006)

The intestinal epithelium undergoes a marked adaptive response following loss of functional small bowel surface area characterized by increased crypt cell proliferation and increased enterocyte migration from crypt to villus tip, resulting in villus hyperplasia and enhanced nutrient absorption. Hedgehog (Hh) signaling plays a critical role in regulating epithelial-mesenchymal interactions during morphogenesis of the embryonic intestine. Our previous studies showed that blocking Hh signaling in neonatal mice results in increased small intestinal epithelial crypt cell proliferation and altered enterocyte fat absorption and morphology. Hh family members are also expressed in the adult intestine, but their role in the mature small bowel is unclear. With the use of a model of intestinal adaptation following partial small bowel resection, the role of Hh signaling in the adult gut was examined by determining the effects of blocking Hh signaling on the regenerative response following loss of functional surface area. Hh-inactivating monoclonal antibodies or control antibodies were administered to mice that sustained a 50% intestinal resection. mRNA analyses of the preoperative ileum by quantitative real-time PCR revealed that Indian hedgehog was the most abundant Hh family member. The Hh receptor Patched was more abundant than Patched 2. Analyses of downstream targets of Hh signaling demonstrated that Gli3 was twofold more abundant than Gli1 and Gli2 and that bone morphogenetic protein (BMP)2 was most highly expressed compared with BMP1, -4, and -7. Following intestinal resection, the expression of Hh, Patched, Gli, and most BMP genes was markedly downregulated in the remnant ileum, and, in anti-Hh antibody-treated mice, expression of Patched 2 and Gli 1 was further suppressed. In Hh antibody-treated mice following resection, the enterocyte migration rate from crypt to villus tip was increased, and by 2 wk postoperation, apoptosis was increased in the adaptive gut. However, crypt cell proliferation, villus height, and crypt depth were not augmented. These data indicate that Hh signaling plays a role in adult gut epithelial homeostasis by regulating epithelial cell migration from crypt to villus tip and by enhancing apoptosis.
Vagus nerve stimulation using an endovascular electrode array (2023)

<i>Objective</i>. Vagus nerve stimulation (VNS), which involves a surgical procedure to place electrodes directly on the vagus nerve (VN), is approved clinically for the treatment of epilepsy, depression, and to facilitate rehabilitation in stroke. VNS at surgically implanted electrodes is often limited by activation of motor nerve fibers near and within the VN that cause neck muscle contraction. In this study we investigated endovascular VNS that may allow activation of the VN at locations where the motor nerve fibers are not localized.<i>Approach</i>. We used endovascular electrodes within the nearby internal jugular vein (IJV) to electrically stimulate the VN while recording VN compound action potentials (CAPs) and neck muscle motor evoked potentials (MEPs) in an acute intraoperative swine experiment.<i>Main Results</i>. We show that the stimulation electrode position within the IJV is critical for efficient activation of the VN. We also demonstrate use of fluoroscopy (cone beam CT mode) and ultrasound to determine the position of the endovascular stimulation electrode with respect to the VN and IJV. At the most effective endovascular stimulation locations tested, thresholds for VN activation were several times higher than direct stimulation of the nerve using a cuff electrode; however, this work demonstrates the feasibility of VNS with endovascular electrodes and provides tools to optimize endovascular electrode positions for VNS.<i>Significance</i>. This work lays the foundation to develop endovascular VNS strategies to stimulate at VN locations that would be otherwise too invasive and at VN locations where structures such as motor nerve fibers do not exist.
New Aspects in Thrombosis Research: Possible Role of Mast Cells as Profibrinolytic and Antithrombotic Cells (2002)

Venous thromboembolism represents a significant cause of morbidity worldwide. The factors that underly thrombophilia are manifold. The concept of Virchow defines the well known triad of stasis, humoral factors, and pathologies of the vascular wall. In the current article, an additional factor, the "accumulation of repair cells" is discussed. This novel concept highlights the mast cell that accumulates around thrombosed vessels and provides a number of important repair molecules including heparin, profibrinolytic tPA, and fibrinogenolytic beta-tryptase. Thus, mast cell recruitment and activation may result in local thrombolysis and prevention of coagulation. In line with this concept, mast cell-deficient mice are more susceptible to lethal thrombogenic stimuli compared to normal mice. The factors (cytokines) that trigger mast cell accumulation and release of repair molecules have also been identified - the most important one appears to be stem cell factor (SCF). All in all. our novel concept suggests that the patho-physiology of thrombosis may involve a "physiologic" cell that provides the same repair molecules that are used for treatment of thrombotic disorders by the physician. Whether an altered availability of components of this cellular repair system can predispose for thrombophilia remains to be determined.
Two Mammalian Genes Transcribed from Opposite Strands of the Same DNA Locus (1987)

This report describes the characterization of a genomic locus in the rat that encodes overlapping genes occupying both strands of the same piece of DNA. One gene (strand) encodes gonadotropin-releasing hormone (GnRH). A second gene, SH, is transcribed from the other DNA strand to produce RNA of undefined function. The RNAs transcribed from each DNA strand are spliced and polyadenylated, and share significant exon domains. GnRH is expressed in the central nervous system while SH transcripts are present in the heart. Thus, the genome of a mammalian organism encodes two distinct genes by using both strands of the same DNA.
Hyperimmune bovine colostrum for treatment of GI infections (2013)

Hyperimmune bovine colostrum (HBC), produced by vaccination of a cow during gestation, is rich in targeted immunoglobulins, and can be used to treat a variety of diseases. The published history of HBC use for treating gastrointestinal infections in humans has developed over the past several decades and demonstrates the promise of this type of therapeutic for GI infectious disease. HBC, or purified derivative products, have been used successfully for treatment or prevention of cryptosporidiosis, shigellosis, rotavirus, enterotoxigenic E. coli, and C. difficile infection (CDI). Given the positive results of previous studies using HBC for treatment of CDI, we have produced HBC with antibodies against the two most important virulence factors of C. difficile, TcdA and TcdB, using a novel recombinant vaccine. Our preliminary results demonstrate efficacy of the HBC product for treatment of CDI in the gnotobiotic piglet model, and warrant more thorough investigation. HBC may provide an effective treatment alternative to antibiotics, which can spare the normal gut microflora, and reduce rates of recurrence and antibiotic resistance.
H.264/AVC for Wireless Applications (2003)

Video transmission in wireless environments is a challenging task calling for high compression efficiency as well as a network friendly design. These have been major goals of the H.264/AVC standardization effort addressing &amp;quot;conversational&amp;quot; (i.e., video telephony) and &amp;quot;non-conversational&amp;quot; (i.e., storage, broadcast, or streaming) applications. The video compression performance of the H.264/AVC Video Coding Layer typically provides a significant improvement. The network-friendly design goal of H.264/AVC is addressed via the Network Abstraction Layer that has been developed to transport the coded video data over any existing and future networks including wireless systems. The main objective of this paper is to provide an overview over the tools which are likely to be used in wireless environments and discusses the most challenging application, wireless conversational services in greater detail. Appropriate justifications for the application of different tools based on experimental results are presented.
Neoepitope Antibodies Against MMP-Cleaved and Aggrecanase-Cleaved Aggrecan (2009)

Neoepitope antibodies recognize the newly created N or C terminus of protein degradation products but fail to recognize the same sequence of amino acids present in intact or undigested protein. Aggrecan neoepitope antibodies have been pivotal in studies determining the contribution of matrix metalloproteinases (MMPs) and aggrecanases to aggrecanolysis. In particular, an antibody to the A(374)RGSV N terminus was instrumental in the landmark discovery of the aggrecanases, ADAMTS-4 and ADAMTS-5. Antibodies to neoepitopes at the major MMP cleavage site DIPEN(341)/(342)FFGVG helped to distinguish MMP-driven aggrecan loss from aggrecanase-driven aggrecan loss and identified a role for MMPs in late-stage disease. More recently, neoepitope antibodies that recognize cleavage sites in the chondroitin sulphate-rich region of aggrecan have been used to show that aggrecanase cleavage proceeds in a defined manner, beginning at the C terminus and proceeding to the signature cleavage at NITEGE(373)/(374)ARGSV in the interglobular domain. Work with the C-terminal neoepitope antibodies has underscored the need to use a suite of neoepitope antibodies to fully describe aggrecanolysis in vitro. In this chapter, we describe the production of two aggrecan neoepitope antibodies as examples: the monoclonal anti-FFGVG antibody (AF-28) and the polyclonal anti-DIPEN antisera.