gebhart/patrepeval huggingface dataset:
A model for leakage control by MOS transistlor stacking (1997)

Prevailing CMOS design practice has been very conservative with regard to choice of transistor threshold voltage, so as to avoid the difficult problems of threshold variations and high leakage currclnts. It is becoming necessary to scale threshold voltages more aggress~vely in order to obtain further power reduction, performance improven~ent, and integration density. Substantial leakage reduction can be achi~ved in single Vt designs by stacking low \.'t transistors. We have derived a simplified theoretical model which predicts the quiescent leakage current and the worst case time required to settle to quiescent levels in a single stack of transistors. This model can be used in a design environment to make quick estimation of leakage with respect to design changes. Model results are compared to circuit sirnulation. Leakage current predictions were found to rnatch simulation results very closely for a wide random selection of design parameter values and temperatures. Transistor stacks with mt~ltiple transistors turned off were found to have anywhere from 2 to 30 times lower leakage current than stack with only one transistor turned off. The time requirecl for a transistor stack to settle to quiescent current levels varied from a few microseconds up to tens of milliseconds.
Field Studies of Protection from Infection by Experimental Trachoma Virus Vaccine in Preschool-Aged Children on Taiwan. (1963)

Field trials of experimental egg-grown trachoma virus vaccine have been carried out in preschool-aged children in 2 rural areas on Taiwan. Four hundred and five children randomly divided between a placebo and trachoma vaccine groups have been followed for 2 1/2 years during which 4 injections of vaccine have been given. Eighteen per cent of the placebo group have converted to trachoma compared to 8% of those receiving vaccine. An average of 2.98 months of trachoma have been observed in the placebo group compared to 1.22 months in the vaccine group. Both these measures suggested that the vaccine was approximately 60% effective in reducing trachoma. A third study in an urban area with 89 children showed similar vaccine effectiveness.
Preparation of Ultrafine Chalcopyrite Nanoparticles via the Photochemical Decomposition of Molecular Single-Source Precursors (2006)

The synthesis and characterization of ultrafine CuInS2 nanoparticles are described. Ultraviolet irradiation was used to decompose a molecular single source precursor, yielding organic soluble approximately 2 nm sized nanoparticles with a narrow size distribution. UV-vis absorption, 1H and 31P{1H} NMR, and fluorescence spectroscopies and mass spectrometry were used to characterize decomposition of the precursors and nanoparticle formation. The nanoparticles were characterized by high-resolution transmission electron microscopy (HRTEM), scanning electron microscopy energy dispersive X-ray spectroscopy, powder X-ray diffraction (XRD), electron diffraction, inductively coupled plasma analysis, UV-vis absorption spectroscopy, and fluorescence spectroscopy. They have a wurzite-type crystal structure with a copper-rich composition. The hypsochromic shift in their emission band due to quantum confinement effects is consistent with the size of the nanocrystals indicated in the HRTEM and XRD analyses.
Protease-activated receptors and inflammatory hyperalgesia (2005)

Recent advances in basic science pointed to a role for proteinases, through the activation of proteinase-activated receptors (PARs) in nociceptive mechanisms. Activation of PAR1, PAR2 and PAR4 either by proteinases or by selective agonists causes inflammation inducing most of the cardinal signs of inflammation: swelling, redness, and pain. Sub-inflammatory doses of PAR2 agonist still induced hyperalgesia and allodynia while PAR2 has been shown to be implicated in the generation of hyperalgesia in different inflammatory models. In contrast, sub-inflammatory doses of PAR1 increases nociceptive threshold, inhibiting inflammatory hyperalgesia, thereby acting as an analgesic agent. PARs are present and functional on sensory neurons, where they participate either directly or indirectly to the transmission and/or inhibition of nociceptive messages. Taken together, the results discussed in this review highlight proteinases as signaling molecules to sensory nerves. We need to consider proteinases and the receptors that are activated by proteinases as important potential targets for the development of analgesic drugs in the treatment of inflammatory pain.
[Frequency of molecular alterations in heterozygous beta-thalassemia in southern Spain and their relation to the hematologic phenotype]. (1994)

From the practical point of view, this study indicates that we were able to detect more than 90% of heterozygous beta-tal. with 5 out of 6 ASO probes used in this work. Thus, our data also provides a further implication in prenatal diagnosis.
Protein-misfolding in neurodegenerative disease (2009)

Many of the neurodegenerative diseases share common features and molecular patterns that suggest their pathology may be directly comparable. Diseases such as Parkinson’s disease, Alzheimer’s disease and Prion diseases are all characterised by abnormal accumulations of proteins and selective neuronal degeneration. This article reviews the known pathology and aetiology of these diseases in order to explore the links between them including defective free radical accumulation, mitochondrial dysfunction and impairment of protein degradation pathways.
[Expression of cathepsin-B and -D in rat's brain after traumatic brain injury]. (2006)

Cathepsin-B and -D could be the diagnostic markers of TBI and can estimating time course of lateral TBI. They blocked caspase-3 activation at the beginning period after TBI and started to promote cell death with caspase-3 6 h after TBI.
What brings pericytes to tumor vessels? (2003)

Toll-like receptors (TLRs) recognize microbial molecular signatures and can initiate innate immune responses against invading pathogens. A new study (see the related article beginning on page 1234) reports how TLR2 expression by endothelia is locally upregulated by the action of activated polymorphonuclear neutrophils via an unprecedented mechanism involving cell-cell interaction and NAD(P)H oxidase. The report reveals yet another way in which the primordial innate immune system is remarkably complex.
Heterostructures of Single-Walled Carbon Nanotubes and Carbide Nanorods (1999)

A method based on a controlled solid-solid reaction was used to fabricate heterostructures between single-walled carbon nanotubes (SWCNTs) and nanorods or particles of silicon carbide and transition metal carbides. Characterization by high-resolution transmission electron microscopy and electron diffraction indicates that the heterostructures have well-defined crystalline interfaces. The SWCNT/carbide interface, with a nanometer-scale area defined by the cross section of a SWCNT bundle or of a single nanotube, represents the smallest heterojunction that can be achieved using carbon nanotubes, and it can be expected to play an important role in the future fabrication of hybrid nanodevices.
Ste5 RING-H2 Domain: Role in Ste4-Promoted Oligomerization for Yeast Pheromone Signaling (1997)

Ste5 is a scaffold for the mitogen-activated protein kinase (MAPK) cascade components in a yeast pheromone response pathway. Ste5 also associates with Ste4, the β subunit of a heterotrimeric guanine nucleotide–binding protein, potentially linking receptor activation to stimulation of the MAPK cascade. A RING-H2 motif at the Ste5 amino terminus is apparently essential for function because Ste5(C177S) and Ste5(C177A C180A) mutants did not rescue the mating defect of a ste5Δ cell. In vitro Ste5(C177A C180A) bound each component of the MAPK cascade, but not Ste4. Unlike wild-type Ste5, the mutant did not appear to oligomerize; however, when fused to a heterologous dimerization domain (glutathione S-transferase), the chimeric protein restored mating in an ste5Δ cell and an ste4Δ ste5Δ double mutant. Thus, the RING-H2 domain mediates Ste4-Ste5 interaction, which is a prerequisite for Ste5-Ste5 self-association and signaling.
IL-15 but not IL-2 rapidly induces lethal xenogeneic graft-versus-host disease (2005)

Interleukin-2 (IL-2) and IL-15 are structurally related cytokines that share receptor components but display markedly different effects in multiple in vivo model systems. Here we demonstrate that IL-15 but not IL-2 exacerbates xenogeneic graft-versus-host disease (X-GVHD) in severe combined immunodeficient murine recipients of human peripheral-blood lymphocytes (hu-PBL-SCID). Treatment of hu-PBL-SCID mice with IL-15 resulted in rapid fatality, lymphocytic infiltrations in the liver, lung, and spleen consistent with X-GVHD, and a marked expansion of human CD4+ and CD8+ T cells compared with controls. Depletion of human T cells in vivo abrogated the lethality of IL-15 treatment. To our knowledge, these data are the first to demonstrate in vivo activation and expansion of human T lymphocytes in response to IL-15 with concomitant exacerbation of human T-cell-mediated X-GVHD.
BET bromodomain inhibition suppresses transcriptional responses to cytokine‐Jak‐STAT signaling in a gene‐specific manner in human monocytes (2014)

Disruption of the interaction of bromo and extraterminal (BET) proteins with acetylated histones using small molecule inhibitors suppresses Myc-driven cancers and TLR-induced inflammation in mouse models. The predominant mechanism of BET inhibitor action is to suppress BET-mediated recruitment of positive transcription elongation factor b and, thus, transcription elongation. We investigated the effects of BET inhibitor I-BET151 on transcriptional responses to TLR4 and TNF in primary human monocytes and also on responses to cytokines IFN-β, IFN-γ, IL-4, and IL-10, which activate the JAK-STAT signaling pathway and are important for monocyte polarization and inflammatory diseases. I-BET151 suppressed TLR4- and TNF-induced IFN responses by diminishing both autocrine IFN-β expression and transcriptional responses to IFN-β. I-BET151 inhibited cytokine-induced transcription of STAT targets in a gene-specific manner without affecting STAT activation or recruitment. This inhibition was independent of Myc or other upstream activators. IFN-stimulated gene transcription is regulated primarily at the level of transcription initiation. Accordingly, we found that I-BET151 suppressed the recruitment of transcriptional machinery to the CXCL10 promoter and an upstream enhancer. Our findings suggest that BET inhibition reduces inflammation partially through suppressing cytokine activity and expands the understanding of the inhibitory and potentially selective immunosuppressive effects of inhibiting BET proteins.
Hepatic Stellate Cells and Liver Fibrosis (2007)

Substantial evidence now exists to recognize hepatic stellate cells (HSCs) as the main matrix-producing cells in the process of liver fibrosis. Liver injury of any etiology will ultimately lead to activation of HSCs, which undergo transdifferentiation to fibrogenic myofibroblast-like cells. Quantitative analysis of HSC activation by immunohistochemistry has been shown to be useful in predicting the rate of progression of liver fibrosis in some clinical situations. In the activation process, transforming growth factor beta is thought to be the main mediator of fibrogenesis and platelet-derived growth factor is the major inducer of HSC proliferation. Different platelet-derived growth factor and transforming growth factor beta inhibitors have been shown to effectively prevent liver fibrosis in animal models and represent promising therapeutic agents for humans.
Toward better understanding of artifacts in variant calling from high-coverage samples (2014)

Supplementary data are available at Bioinformatics online.
Dangerous Curves (1997)

A number of general observations can be made from these recent studies. Lactate is a ubiquitous substance that is produced and removed from the body at all times, even at rest, both with and without the availability of oxygen. It is now recognized that lactate accumulates in the blood for several reasons, not just the fact that oxygen supply to the muscle is inadequate. Lactate production and removal is a continuous process; it is a change in the rate of one or the other that determines the blood lactate level. Rather than a specific threshold, there is most likely a period of time during which lactate production begins to exceed the body's capacity to remove it (through buffering or oxidation in other fibers). It may be appropriate to replace the term "anaerobic threshold" to a more functional description, since the muscles are never entirely anaerobic nor is there always a distinct threshold ("oxygen independent glycolysis" among others has been suggested) Lactate plays a major role as a metabolic substrate during exercise, is the preferred fuel for slow-twitch muscle fibers, and is a precursor for liver gluconeogenesis. The point at which lactate begins to accumulate in the blood, causing an increase in ventilation, is important to document clinically. Irrespective of the underlying mechanism or specific model that describes the process, the physiologic changes associated with lactate accumulation have significant import for cardiopulmonary performance. These include metabolic acidosis, impaired muscle contraction, hyperventilation, and altered oxygen kinetics, all of which contribute to an impaired capacity to perform work. Thus, any delay in the accumulation of blood lactate which can be attributed to an intervention (drug, exercise training, surgical, etc) may add important information concerning the efficacy of the intervention. A substantial body of evidence is available demonstrating that lactate accumulation occurs later (shifting to a higher percentage of Vo2max) after a period of endurance training. In athletes, the level of work that can be sustained prior to lactate accumulation, visually determined, is an accurate predictor of endurance performance. Presumably, these concepts have implications related to vocation/disability among patients with cardiovascular and pulmonary disease, but few such applied studies have been performed outside the laboratory. Blood lactate during exercise and its associated ventilatory changes maintain useful and interesting applications in both the clinical exercise laboratory and the sport sciences. However, the mechanism, interpretation, and application of these changes continue to rely more on tradition and convenience than science.
Yeast Pyruvate Decarboxylase Tetramers Can Dissociate into Dimers along Two Interfaces. Hybrids of Low-Activity D28A (or D28N) and E477Q Variants, with Substitution of Adjacent Active Center Acidic Groups from Different Subunits, Display Restored Activity (2002)

The tetrameric enzyme yeast pyruvate decarboxylase (YPDC) has been known to dissociate into dimers at elevated pH values. However, the interface along which the dissociation occurs, as well as the fundamental kinetic properties of the resulting dimers, remains unknown. The active sites of YPDC are comprised of amino acid residues from two subunits, a property which we utilize to address the issue as to which dimer interface is cleaved under different conditions of dissociation. Hydroxide-induced dissociation of the active site D28A (or D28N) and E477Q variants, each at least 100 times less reactive than wild-type YPDC, followed by reassociation of D28A (or D28N) and E477Q variants led to a remarkable 35-50-fold increase in activity. This result is possible only if the hydroxide-induced dissociation results in a cleavage along the interface between two subunits so that residues D28 and E477 are now separated. Upon reassociation, one of the two active sites of the hybrid dimer will have both residues substituted, whereas the second one will be of the wild-type phenotype. In contrast to the hydroxide-induced dimers, the urea-induced dissociation recently proposed results in dissociation along dimer-dimer interfaces, without separating the active sites, and therefore, on reassociation, these dimers do not regain activity. The significance of the results is discussed in light of a recently proposed alternating sites mechanism for YPDC. A preparative ion-exchange method is reported for the separation and purification of hybrid enzymes.
Synthesiser review for pan-European digital cellular radio (1990)

A pan-European cellular radio system is being devised by the Groupe Special Mobile (GSM), a committee originally set up by the CEPT and now transferred into ETSI. The system will employ a digital radio link with GMSK at a data rate of approximately 270 kb/s. Modulation requirements and frequency hopping pose many problems in the design of the synthesiser/modulator for handheld terminal equipment. The paper reviews solutions to implement the synthesiser/modulator functions, considering both fundamental problems and circuit cost, size and power requirements. The direct synthesis of GMSK by DSP and digital to analog conversion can meet modulation accuracy requirements, but is limited by speed and cost. However, direct modulation for the GSM radio system is not possible with many standard forms of synthesiser. These problems are discussed, and the use of two point modulation which overcomes the fundamental limitations is introduced.
Targeted chromosomal deletions in human cells using zinc finger nucleases (2009)

We present a novel approach for generating targeted deletions of genomic segments in human and other eukaryotic cells using engineered zinc finger nucleases (ZFNs). We found that ZFNs designed to target two different sites in a human chromosome could introduce two concurrent DNA double-strand breaks (DSBs) in the chromosome and give rise to targeted deletions of the genomic segment between the two sites. Using this method in human cells, we were able to delete predetermined genomic DNA segments in the range of several-hundred base pairs (bp) to 15 mega-bp at frequencies of 10(-3) to 10(-1). These high frequencies allowed us to isolate clonal populations of cells, in which the target chromosomal segments were deleted, by limiting dilution. Sequence analysis revealed that many of the deletion junctions contained small insertions or deletions and microhomologies, indicative of DNA repair via nonhomologous end-joining. Unlike other genome engineering tools such as recombinases and meganucleases, ZFNs do not require preinsertion of target sites into the genome and allow precise manipulation of endogenous genomic scripts in animal and plant cells. Thus, ZFN-induced genomic deletions should be broadly useful as a novel method in biomedical research, biotechnology, and gene therapy.
Improved Microchip Design and Application for In Situ Transmission Electron Microscopy of Macromolecules (2013)

Understanding the fundamental properties of macromolecules has enhanced the development of emerging technologies used to improve biomedical research. Currently, there is a critical need for innovative platforms that can illuminate the function of biomedical reagents in a native environment. To address this need, we have developed an in situ approach to visualize the dynamic behavior of biomedically relevant macromolecules at the nanoscale. Newly designed silicon nitride devices containing integrated "microwells" were used to enclose active macromolecular specimens in liquid for transmission electron microscopy imaging purposes.We were able to successfully examine novel magnetic resonance imaging contrast reagents, micelle suspensions, liposome carrier vehicles, and transcribing viral assemblies. With each specimen tested, the integrated microwells adequately maintained macromolecules in discrete local environments while enabling thin liquid layers to be produced.
Neuroprotective Effects of Glial Cell Line-Derived Neurotrophic Factor Mediated by an Adeno-Associated Virus Vector in a Transgenic Animal Model of Amyotrophic Lateral Sclerosis (2002)

Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive lethal disease that involves selective annihilation of motoneurons. Glial cell line-derived neurotrophic factor (GDNF) is proposed to be a promising therapeutic agent for ALS and other motor neuron diseases. Because adeno-associated virus (AAV) has been developed as an attractive gene delivery system with proven safety, we explored the therapeutic efficacy of intramuscular delivery of the GDNF gene mediated by an AAV vector (AAV-GDNF) in the G93A mouse model of ALS. We show here that AAV-GDNF leads to substantial and long-lasting expression of transgenic GDNF in a large number of myofibers with its accumulation at the sites of neuromuscular junctions. Detection of GDNF labeled with FLAG in the anterior horn neurons, but not beta-galactosidase expressed as a control, indicates that most of the transgenic GDNF observed there is retrogradely transported GDNF protein from the transduced muscles. This transgenic GDNF prevents motoneurons from their degeneration, preserves their axons innervating the muscle, and inhibits the treated-muscle atrophy. Furthermore, four-limb injection of AAV-GDNF postpones the disease onset, delays the progression of the motor dysfunction, and prolongs the life span in the treated ALS mice. Our finding thus indicates that AAV-mediated GDNF delivery to the muscle is a promising means of gene therapy for ALS.
Reversed‐phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells (2011)

In this study, we evaluated a concatenated low pH (pH 3) and high pH (pH 10) reversed-phase liquid chromatography strategy as a first dimension for two-dimensional liquid chromatography tandem mass spectrometry ("shotgun") proteomic analysis of trypsin-digested human MCF10A cell sample. Compared with the more traditional strong cation exchange method, the use of concatenated high pH reversed-phase liquid chromatography as a first-dimension fractionation strategy resulted in 1.8- and 1.6-fold increases in the number of peptide and protein identifications (with two or more unique peptides), respectively. In addition to broader identifications, advantages of the concatenated high pH fractionation approach include improved protein sequence coverage, simplified sample processing, and reduced sample losses. The results demonstrate that the concatenated high pH reversed-phased strategy is an attractive alternative to strong cation exchange for two-dimensional shotgun proteomic analysis.