gebhart/patrepeval huggingface dataset:
Lower Bounds on the Capacity of Gaussian Relay Channel (2004)

It has been shown recently that the overall throughput of dense wireless networks can increase significantly when wireless nodes collaborate in transmission of different packets.In this paper, we focus on a simple network known as the relay channel, where there is a single relaying node in the system assisting a sender-receiver pair.We present a new achievable rate for the case of Gaussian relay channels, which outperforms the best known schemes in many cases of interest.The proposed scheme is a variation of the amplify and forward method, and is labeled as a scale and forward scheme, signifying that the relay does not use all its power amplifying the received signal.By controlling the scaling and time-correlation of the relay signal, we show that the proposed scheme can outperform all known schemes for several channel gains, especially those where the best known methods provide no improvement over direct transmission.Numerical results are presented to quantify in which regimes the proposed scheme is the best known coding scheme for the Gaussian relay channel.
Discovery and Directed Evolution of a Glyphosate Tolerance Gene (2004)

The herbicide glyphosate is effectively detoxified by N-acetylation. We screened a collection of microbial isolates and discovered enzymes exhibiting glyphosate N-acetyltransferase (GAT) activity. Kinetic properties of the discovered enzymes were insufficient to confer glyphosate tolerance to transgenic organisms. Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orders of magnitude from 0.87 mM-1 min-1 to 8320 mM-1 min-1. From the fifth iteration and beyond, GAT enzymes conferred increasing glyphosate tolerance to Escherichia coli, Arabidopsis, tobacco, and maize. Glyphosate acetylation provides an alternative strategy for supporting glyphosate use on crops.
Expression of Id helix-loop-helix proteins in colorectal adenocarcinoma correlates with p53 expression and mitotic index. (2001)

Id helix-loop-helix (HLH) proteins function as regulators of cell growth and differentiation and when overexpressed can induce malignant transformation. In a series of 34 cases of primary human colorectal adenocarcinoma, immunoreactivity for Id1, Id2, and Id3 was found to be significantly elevated in tumor compared with normal mucosa (P = 0.001 for Id1 and Id2; P = 0.002 for Id3). No elevation of Id expression was observed in 17 cases of adenoma. Expression of Id1 and to a lesser extent of Id2 was correlated with mitotic index (P = 0.005 for Id1; P = 0.042 for Id2) in human adenocarcinomas, and expression of all three Id proteins was correlated with p53 immunoreactivity (a marker of mutational 'inactivation' of p53 function; P = 0.002 for Id1; P = 0.006 for Id2; P = 0.016 for Id3). In normal intestinal mucosa of p53-null mice and in spontaneous tumors arising in Min+/- mice, expression of all three Id proteins was also found to be up-regulated. Antisense oligonucleotide blockade of Id protein expression inhibited the proliferation of human adenocarcinoma cells. Enforced, ectopic expression of the E47 basic HLH (bHLH) protein in human adenocarcinoma cell lines efficiently sequestered endogenous Id proteins as Id-bHLH heterodimers, as shown by coimmunoprecipitation and subcellular colocalization studies. This led to growth arrest of the cells. Enforced overexpression of a mutant E47 protein, deficient in transactivation and DNA binding function, also partially inhibited cell growth. Taken together, these data imply that deregulated expression of Id proteins in colorectal adenocarcinoma arises at least in part as a consequence of loss of p53 function and contributes to the uncontrolled proliferation of tumor cells in colorectal cancer.
Rapid and Simple Quantification of Bacterial Cells by Using a Microfluidic Device (2005)

This study investigated a microfluidic chip-based system (on-chip flow cytometry) for quantification of bacteria both in culture and in environmental samples. Bacterial numbers determined by this technique were similar to those obtained by direct microscopic count. The time required for this on-chip flow cytometry was only 30 min per 6 samples.
NMR identification of epitopes of lyme disease antigen OspA to monoclonal antibodies (1998)

Outer surface protein A (OspA) from the Lyme disease spirochete Borrelia burgdorferi has been a focus of vaccine development. We have identified epitopes of OspA to two monoclonal antibodies (mAbs) by comparing NMR chemical shifts of free OspA and those in Fab complexes. Deuteration of non-labile protons in OspA extended the size limit of this technique so that it was applicable to the 78 kDa complexes of OspA and the Fab fragment. The epitope identified by NMR to an mAb, 184.1, agrees well with that previously defined by the crystal structure of the same complex, indicating the ability of the NMR method to accurately map an epitope in a large protein complex. The technique mapped the epitope to mAb 336, a mAb of clinical interest, to a region centered at the C-terminal alpha-helix. The results provides a basis for rational design of OspA-based Lyme disease vaccines.
OX40L blockade is therapeutic in arthritis, despite promoting osteoclastogenesis (2014)

An immune response is essential for protection against infection, but, in many individuals, aberrant responses against self tissues cause autoimmune diseases such as rheumatoid arthritis (RA). How to diminish the autoimmune response while not augmenting infectious risk is a challenge. Modern targeted therapies such as anti-TNF or anti-CD20 antibodies ameliorate disease, but at the cost of some increase in infectious risk. Approaches that might specifically reduce autoimmunity and tissue damage without infectious risk would be important. Here we describe that TNF superfamily member OX40 ligand (OX40L; CD252), which is expressed predominantly on antigen-presenting cells, and its receptor OX40 (on activated T cells), are restricted to the inflamed joint in arthritis in mice with collagen-induced arthritis and humans with RA. Blockade of this pathway in arthritic mice reduced inflammation and restored tissue integrity predominantly by inhibiting inflammatory cytokine production by OX40L-expressing macrophages. Furthermore, we identify a previously unknown role for OX40L in steady-state bone homeostasis. This work shows that more targeted approaches may augment the "therapeutic window" and increase the benefit/risk in RA, and possibly other autoimmune diseases, and are thus worth testing in humans.
Randomized, Double-Blind, Placebo-Controlled Study Evaluating the Lidocaine/Tetracaine Patch for Induction of Local Anesthesia prior to Minor Dermatologic Procedures in Geriatric Patients (2006)

The lidocaine/tetracaine patch is a safe and effective method for noninvasive induction of local anesthesia for minor dermatologic procedures in patients over the age of 65 years.
APRI: An Easy and Validated Predictor of Hepatic Fibrosis in Chronic Hepatitis C (2006)

The APRI is a good estimator of hepatic fibrosis and was more accurate in a prospective group than a retrospective one. It potentially could be used to decrease the number of liver biopsies.
The Telomerase Reverse Transcriptase (hTERT) Gene Is a Direct Target of the Histone Methyltransferase SMYD3 (2007)

Recent evidence has accumulated that the dynamic histone methylation mediated by histone methyltransferases and demethylases plays key roles in regulation of chromatin structure and transcription. In the present study, we show that SET and MYND domain-containing protein 3 (SMYD3), a histone methyltransferase implicated in oncogenesis, directly trans-activates the telomerase reverse transcriptase (hTERT) gene that is essential for cellular immortalization and transformation. SMYD3 occupies its binding motifs on the hTERT promoter and is required for maintenance of histone H3-K4 trimethylation, thereby contributing to inducible and constitutive hTERT expression in normal and malignant human cells. Knocking down SMYD3 in tumor cells abolished trimethylation of H3-K4, attenuated the occupancy by the trans-activators c-MYC and Sp1, and led to diminished histone H3 acetylation in the hTERT promoter region, which was coupled with down-regulation of hTERT mRNA and telomerase activity. These results suggest that SMYD3-mediated trimethylation of H3-K4 functions as a licensing element for subsequent transcription factor binding to the hTERT promoter. The present findings provide significant insights into regulatory mechanisms of hTERT/telomerase expression; moreover, identification of the hTERT gene as a direct target of SMYD3 contributes to a better understanding of SMYD3-mediated cellular transformation.
Lecithin organogel: A unique micellar system for the delivery of bioactive agents in the treatment of skin aging (2012)

Skin aging is an unavoidable aspect of human life. Premature skin aging can result from poor care, environmental pollutants, and ultraviolet radiation exposure. Wrinkles, lines, spots, uneven skin tone, and pigmentation are often indicators of skin aging. One cannot avoid aging but cosmetics and pharmaceutical approaches can minimize and delay the damage. Topical applications of biocompatible and biodegradable vehicles have been explored for delivering anti-aging compounds. Lecithin organogel (LO) is an effective vehicle for topical delivery of many bioactive agents used in aging treatment. Lecithin is cell component isolated from soya beans or eggs and purified to show excellent gelation in non-polar solvents when combined with water. LO can form a heat-stable, resistant to microbial growth, visco-elastic, optically transparent, and non-birefringent micellar system. It serves as an organic medium to enhance dermal permeation of poorly permeable drugs by effectively partitioning into the skin. Its ability to dissolve in hydrophilic as well as in lipophilic drugs makes it a dynamic vehicle, which can be explored as a carrier for anti-aging agents.
Pilot analysis of global ecosystems: Agroecosystems (2000)

A joint study by International Food Policy Research Institute and World Resources Institute with Analytical Contributions from Niels H. Batjes, ISRIC; Andrew Farrow, CIAT; Jean Marc Faurès, FAO; Günther Fischer, IIASA; Gerhard Heilig, IIASA; Julio Henao, IFDC; Robert Hijmans, CIP; Freddy Nachtergaele, FAO; Peter Oram, IFPRI; and Manuel Winograd, CIAT
How support staff can be helped to challenge unacceptable practice (2010)

Healthcare assistants (HCAs) play an increasingly important role in the provision of patient care and are well-placed to witness and challenge poor practice, yet often lack the confidence to do so. This article assesses the success of a two-day training course to empower HCAs to question their colleagues about practice, and the implications of this course for senior nurses.
Isolation of telomeric DNA from the filamentous fungusPodospora anserinaand construction of a self-replicating linear plasmid showing high transformation frequency (1993)

It has been previously shown that linear plasmids bearing Tetrahymena telomeric sequences are able to replicate autonomously in the filamentous fungus Podospora anserina (1). However, autonomous replication occurs in only 50-70% of the transformants, suggesting a defect in the recognition of the Tetrahymena telomeric template by the putative P. anserina telomerase so that only a fraction of entering DNA is stabilized into linear extrachromosomal molecules. We have cloned DNA sequences added to the Tetrahymena (T2G4)n ends of the linear plasmid. Nucleotide sequencing showed that these sequences are exclusively composed of T2AG3 repeat units. Hybridization experiments of Bal31 treated DNA showed that T2AG3 repeats are confined within 200 bp in chromosomal P. anserina telomeres. A new plasmid has been constructed so that after linearization, the terminal sequences contain T2AG3 repeats. This linear molecule transforms P. anserina with a high frequency (up to 1.75 x 10(4) transformants/micrograms), autonomous replication occurs in 100% of the transformants and the plasmid copy number is about 2-3 per nucleus. These results underscore the importance of the telomeric repeat nucleotide sequence for efficient recognition as functional telomeric DNA in vivo and provide the first step toward the development of an artificial chromosome cloning system for filamentous fungi.
Evaluation of neural plasticity in adult stem cells (2007)

The role of stem cells has long been known in reproductive organs and various tissues including the haematopoietic system and skin. During the last decade, stem cells have also been identified in other organs, including the nervous system, both during development and in post-natal life. More recently, evidence has been presented that stem cells thought to be responsible for the generation of mature differentiated cells of one organ, such as haematopoietic stem cells, may have the ability to also differentiate across lineages and contribute to tissues other than haematopoietic cells, including neuronal tissue, suggesting that easily accessible stem cells sources may one day be useful in the therapy of ischaemic (stroke) and also degenerative diseases of the nervous system. Here, we will evaluate the validity of such claims based on a number of criteria we believe need to be fulfilled to definitively conclude that certain stem cells can give rise to functional neural cells that might be suitable for therapy of neural disorders.
Identification and characterization of batk, a predominantly brain‐specific non‐receptor protein tyrosine kinase related to Csk (1994)

A novel cDNA, brain-associated tyrosine kinase (Batk), was isolated from a rat hippocampal library and appears to encode a new member of the Csk subfamily of non-receptor protein tyrosine kinases, with 52% overall amino acid identity to rat Csk. Batk resembles kinases of the Src family in that it contains a Src homology 2 (SH2) domain and an SH3 domain, followed by a tyrosine kinase domain. Analysis of incompletely spliced Batk cDNAs suggests that the genomic structure of Batk is similar to that of Csk with identical exon/intron boundaries. Batk also shows significant homology (86% overall amino acid identity) to the recently described human megakaryocyte-specific Matk. Although Batk is 41 amino acids shorter than Matk, Southern blot analysis suggests that Batk might be a rat homolog of Matk. Batk is predominantly expressed in the brain, with lower expression in the spleen and undetectable expression in other tissues. In situ hybridization and Northern blot analysis show that Batk is widely distributed throughout the adult brain, being primarily expressed in neurons, including those of the hippocampus and cortex. In contrast, embryos appear to have markedly decreased expression levels. Analysis of postnatal day 1 brain suggests that Batk may be upregulated at birth throughout the brain except in the cerebellum. In view of its homology to Csk, a negative regulator of Src family tyrosine kinases, and its generalized expression in the adult brain, we suggest that Batk may function as a brain-specific regulator of kinases involved in the development and maintenance of the nervous system.
FlexCache: A Framework for Flexible Compiler Generated Data Caching (2000)

This paper describes our work in progress on FlexCache, a framework for exible, compiler generated data caching. FlexCache substitutes the tag-memory and cache controller hardware with a compiler managed tag-like data structure, address translation, and tag-check. This allows the division of the data-array into separately controlled partitions, allows the selection of cache line sizes, the support of highly associative mappings, and the selection of various replacement policies on a per program basis. FlexCache leverages compile-time static information to selectively virtualize memory, to eliminate cache-tag accesses, and to guide the replacement of con- icting cache lines. For the applications studied the FlexCache compiler techniques eliminate in average more than 90% of the cache-tag lookups, enabling the support of highly associative caching schemes. Even without any hardware support, FlexCache can outperform xed hardware caches by improving caching eectiveness, eliminating mapping conicts, and eliminating the cache pollution caused by register spills. The beauty of FlexCache is that its core techniques could be augmented with additional software techniques and/or hardware support (i.e., special instructions) to look into optimizing data caching in areas such as low-power, real-time systems, and high-performance microprocessors. 1
Reliable Video Communication over Lossy Packet Networks using Multiple State Encoding and Path Diversity (2001)

Video communication over lossy packet networks suchastheInternet is hampered by limited bandwidth and packet loss. This paper presents a system for providing reliable video communication over these networks, where the system is composed of two subsystems: (1) multiple state video encoder/decoder and (2) a path diversity transmission system. Multiple state video coding combats the problem of error propagation at the decoder by coding the video into multiple independently decodable streams, each with its own prediction process and state. If one stream is lost the other streams can still be decoded to produce usable video, and furthermore, the correctly received streams provide bidirectional (previous and future) information that enables improved state recovery for the corrupted stream. This video coder is a form of multiple description coding (MDC), and its novelty lies in its use of information from the multiple streams to perform state recovery at the decoder. The path diversity transmission system explicitly sends different subsets of packets over different paths, as opposed to the default scenarios where the packets proceed along a single path, thereby enabling the end-to-end video application to effectively see an average path behavior. We refer to this as path diversity. Generally, seeing this average path behavior provides better performance than seeing the behavior of any individual random path. For example, the probability that all of the multiple paths are simultaneously congested is much less than the probability that a single path is congested. The resulting path diversityprovides the multiple state video decoder with an appropriate virtual channel to assist in recovering from lost packets, and can also simplify system design, e.g. FEC design. Weproposetwoarch...
Effects of pH, Temperature, and Water Quality on Chloride Removal with Ultra‐High Lime with Aluminum Process (2006)

The ultra high-lime with aluminum process (UHLA) has the ability to remove sulfate and chloride in addition to other scale-forming materials from recycled cooling water. Laboratory experiments have demonstrated that the UHLA process can achieve high chloride removal from recycled cooling water, and an equilibrium model was developed to describe chemical behavior during chloride removal. This paper describes the influence of pH, temperature, and initial chloride concentration on chloride removal by UHLA and identifies the precipitated solids formed during treatment. The optimum pH for maximum chloride removal efficiency was found to be 12 +/- 0.2. Chloride removal efficiency was higher at a high initial chloride concentration than at a low initial chloride concentration with the chemical doses used. Solids formed during UHLA treatment were identified by x-ray diffraction as calcium chloroaluminate, tricalcium hydroxyaluminate, and tetracalcium hydroxyaluminate. This supports the assumption of the equilibrium model that these compounds are present and form a solid solution.
Frontal lobe dementia and motor neuron disease. (1990)

Four patients are described, in whom a profound and rapidly progressive dementia occurred in association with clinical features of motor neuron disease. The pattern of dementia indicated impaired frontal lobe function, confirmed by reduced tracer uptake in the frontal lobes on single photon emission computed tomography (SPECT). Pathological examination of the brains of two patients revealed frontal-lobe atrophy, with mild gliosis and spongiform change. The spinal cord changes were consistent with motor neuron disease. The clinical picture and pathological findings resembled those of dementia of frontal-lobe type and were distinct from those of Alzheimer's disease. The findings have implications for the understanding of the spectrum of non-Alzheimer forms of primary degenerative dementia.
Long-term increases in neurotransmitter release from neuronal cells expressing a constitutively active adenylate cyclase from a herpes simplex virus type 1 vector. (1993)

Signal-transduction pathways mediate a wide range of short-term changes in the physiology of neuronal systems from invertebrates to mammals. However, examples of long-term changes in neuronal physiology mediated by these pathways have been limited to invertebrate systems. In this report, long-term changes in the physiology of mammalian neurons were studied by using genetic intervention to cause a long-lasting activation of the cAMP pathway. The catalytic domain of yeast adenylate cyclase (cyr), encoding a constitutive enzyme activity, was expressed in neuronal cells infected with a defective herpes simplex virus vector (pHSVcyr). In PC-12 cells infected with pHSVcyr, increases were seen in cAMP levels, protein kinase A activity, protein phosphorylation, phosphorylation of the tyrosine hydroxylase protein kinase A site (Ser40), and catecholamine release. Infection of sympathetic neurons with pHSVcyr increased cAMP levels, protein phosphorylation, and catecholamine release. Yeast adenylate cyclase immunoreactivity and elevated cAMP levels were localized to the cell bodies of sympathetic neurons. The increase in neurotransmitter release was both Ca(2+)- and activity-dependent and persisted for at least 1 week after infection of the sympathetic neurons, suggesting that sustained physiological activation of the cAMP pathway may mediate long-term changes in the neuronal physiology of mammalian systems.
Immunofluorescence studies on the occurrence and localization of the CEA-related biliary glycoprotein I (BGP I) in normal human gastrointestinal tissues. (1979)

Biliary glycoprotein, I(BGP I) is a carcinoembryonic antigen (CEA) cross-reactive glycoprotein of normal human bile. Its occurrence and localization was studied in normal human gastrointestinal tissues by means of direct immunofluorescence using immunadsorbent purified BGP I antibodies with high selectivity for BGP I, as compared to CEA and 'non-specific cross-reacting antigen' (NCA). As controls fluorescein-labelled CEA and NCA were used. Specific BGP I fluorescence was only found in the biliary tract, i.e. in bile canaliculi, in the lumen of large bile ducts and on the surface of the gall bladder mucosa. No fluorescence was found in the hepatocytes or in the cells lining larger bile ducts or the gall bladder. Fluorescence probably due to cross-reaction with NCA was obtained in the cytoplasm of macrophages in different organs and on the surface of bowel epithelium.
A comparison of several approximate algorithms for finding multiple (N-best) sentence hypotheses (1991)

The authors introduce a new, more efficient algorithm, the word-dependent N-best algorithm, for finding multiple sentence hypotheses. The proposed algorithm is based on the assumption that the beginning time of a word depends only on the preceding word. The authors compare this algorithm with two other algorithms for finding the N-best hypotheses: the exact sentence-dependent method and a computationally efficient lattice N-best method. Although the word-dependent algorithm is computationally much less expensive than the exact algorithm, it appears to result in the same accuracy. The lattice method, which is still more efficient, has a significantly higher error rate. It is demonstrated that algorithms that use Viterbi scoring have significantly higher error rates than those that use total likelihood scoring.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>