gebhart/patrepeval huggingface dataset:
The representation of the auditory and somatosensory systems in the external nucleus of the cat inferior colliculus (1981)

Parallel single unit and retrograde tracing experiments were carried out in the anesthetized cat to elucidate the representation of the auditory and somatosensory systems in the external nucleus of the inferior colliculus (ICX). Units responding to tonal stimuli were more commonly encountered in ICX and the adjacent intercollicular area (ICA) than were units with identified tactile receptive fields. Concomitantly, a larger number of retrogradely labeled cells were identified in midbrain auditory structures, following injections of horseradish peroxidase (HRP) into CRX, than were found in the combined dorsal column nuclei. Microelectrode recording revealed that the entire accessible body surface was represented in ICX, and receptive fields of individual units were usually large and mostly located on the contralateral side. HRP-labeled cells were scattered throughout the contralateral cuneate, gracile, and spinal trigeminal nuclei. tations of tone pips. Responses to complex sound were commonly observed. Binaural stimuli influenced the firing of the majority of auditory units. Labeled auditory neurons following ICX injections were found mainly in the inferior colliculus of both sides. Spread of tracer into the central and pericentral nuclei was associated with labeling of many neurons in hind brain auditory structures. Only vague suggestions of somatotopy or tonotopy were observed in the electrophysiological experiments; similarly, no topographical relationship between HRP injection site and locus of retrograde label in a given projecting nucleus could be discerned. Speculations were made, in the light of the dual convergent sensory representation in ICX, about the role of this structure in acoustico-motor mechanisms.
Error detecting multiple block (d,k) codes (1989)

The authors present a construction for two families of error detecting multiple block (d,k) codes. The first family has the ability to detect when encoded blocks have become offset in time by a single bit cell, while the second family has the ability to detect when a one in an encoded block is misdetected and appears in an adjacent bit cell. The authors present sub-block constructions for the two families of error detecting (d,k) codes and maximize the code rate over the set of all legitimate (d,k) codes formed from single and multiple sub-blocks. It is noted that, for both families of error detection codes, the construction is able to retain over half of the (d,k) sequences of a given length usable in a non-error-detecting block code. Therefore, using this construction, a non-error-detecting (d,k) block code which encodes m binary bits to an average of n channel bits can be converted to an error detecting (d,k) block with a rate loss of at most 1/n.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Histone deacetylase inhibitor but not arsenic trioxide differentiates acute promyelocytic leukaemia cells with t(11;17) in combination with all‐trans retinoic acid (2000)

Acute promyelocytic leukaemia (APL) with t(11;17)/PLZF-RARalpha responds poorly to all-trans retinoic acid (ATRA) and arsenic trioxide (As2O3), in contrast to APL with t(15;17)/PML-RARalpha. Molecular studies have shown that histone deacetylase (HDAC) recruited by PLZF-RARalpha is associated with the ATRA resistance. Here, we analysed in vitro the differentiation of APL cells with t(11;17) using ATRA, As203, granulocyte colony-stimulating factor (G-CSF), HDAC inhibitor trichostatin A (TSA), or combinations of these. Although 1 microM ATRA, which stimulated the differentiation of APL cells with t(15;17), was insufficient to induce differentiation, 3 microM ATRA induced terminal differentiation into granulocytes. As203 alone or in combination with ATRA induced neither differentiation nor apoptosis. However, the combination of TSA and 1 microM ATRA had a potent differentiating effect, although TSA alone had little effect. The combination of 1 microM ATRA and G-CSF did not induce differentiation. These results indicate that APL cells with t(11;17) need a higher concentration of ATRA than those with t(15;17) to differentiate and suggest that HDAC inhibitor is a promising differentiation enhancer in APL with t(11;17).
DNA Damage and Cytotoxicity Induced by Minor Groove Binding Methyl Sulfonate Esters (2003)

Minor groove specific DNA equilibrium binding peptides (lex) based on N-methylpyrrole-carboxamide and/or N-methylimidazolecarboxamide subunits have been modified with an O-methyl sulfonate ester functionality to target DNA methylation in the minor groove at Ade/Thy- and/or Gua/Cyt-rich sequences. HPLC and sequencing gel analyses show that the Me-lex compounds all selectively react with DNA to afford N3-alkyladenine as a major adduct. The formation of the N3-alkyladenine lesions is sequence-dependent based on the equilibrium binding preferences of the different lex peptides. In addition to the reaction at adenine, the molecules designed to target Gua/Cyt sequences also generate lesions at guanine; however, the methylation is not sequence dependent and takes places in the major groove at the N7-position. To determine if and how the level of the different DNA adducts and the sequence selectivity for their formation affects cytotoxicity, the Me-lex analogues were tested in wild type Escherichia coli and in mutant strains defective in base excision repair (tag and/or alkA or apn). The results demonstrate the importance of 3-methyladenine, and in some cases 3-methylguanine, lesions in cellular toxicity, and the dominant protective role of the DNA glycosylases. There is no evidence that the sequence specificity is related to toxicity.
Genetic studies of avermectin biosynthesis in Streptomyces avermitilis (1987)

A genetic recombination study of an industrial strain of Streptomyces avermitilis which produces avermectin is described. A genetic map has been constructed by analysis of haploid recombinants and linkage relationships of 16 marker loci. Fifteen avermectin-nonproducing mutants, produced by mutagenesis, were classified into two phenotypically different groups, of which one produced avermectin aglycon and the other was able to convert avermectin aglycon to avermectins. Two different mutants were found to map closely to each other.
RoleMiner (2006)

Role engineering, the task of defining roles and associating permissions to them, is essential to realize the full benefits of the role-based access control paradigm. Essentially, there are two basic approaches to accomplish this: the top-down and the bottom-up. The top-down approach relies on a careful analysis of the business processes to define job functions and then specify appropriate roles from them. While this approach can aid in defining roles more accurately, it is tedious and time consuming since it requires that the semantics of the business processes be well understood. Moreover, it ignores existing permissions within an organization and does not utilize them. On the other hand, the bottom-up approach starts with existing permissions and attempts to derive roles from them, thus helping to automate role definition. In this paper, we present an unsupervised approach called RoleMiner that mines roles from existing user-permission assignments. Since a role is nothing but a set of permissions, when no semantics are available, the task of role mining is essentially that of clustering users that have same (or similar) permissions. However, unlike the traditional applications of data mining that ideally require identification of non-overlapping clusters, roles will have overlapping permission needs and thus permission sets that define roles should be allowed to overlap. It is this distinction from traditional clustering that makes the problem of role mining non-trivial. Our experiments with real and simulated data sets indicate that our role mining process is quite accurate and efficient.
Lumbar disc degeneration: correlation with age, sex, and spine level in 600 autopsy specimens. (1988)

Using data from 16 published reports, the authors correlated macroscopic disc degeneration grades with age, sex, and spine level in 600 lumbar intervertebral discs from 273 cadavers (ages: 0-96 years). Male discs were more degenerated than female discs at most ages; significantly so in the second, fifth, sixth, and seventh decades. On average, L4-L5 and L3-L4 level discs showed more degeneration than discs at other lumbar levels. These macroscopic findings corroborate radiographic data from epidemiologic studies. The calculations suggest that higher mechanical stress, perhaps combined with longer nutritional pathways, may be responsible for the earlier degeneration of male discs.
Spatial Division Multiple Access (SDMA) in Wireless Communications (1995)

This paper describes the utilization of antenna arrays at the base stations of wireless communication systems. Multiple antennas can provide a processing gain to increase the base station range and improve coverage. Also, by exploiting the angular selectivity of an antenna array at the base stations of a wireless system, users may be spatially multiplexed to increase system capacity. We address several aspects of the reception and transmission problems that arise when the spatial dimension is considered. Both the forward and reverse channels are discussed and an overview of related research conducted at the signal processing group, KTH is presented. 1 Introduction The dramatic expansion of wireless communications over the last years has emphasized the importance of efficient use of frequency bandwidth. There is an increasing demand for capacity in wireless systems which traditionally directly translates into a demand for more bandwidth which is quite limited. Also, the infrastructural...
<title>Raman imaging of bone mineral and matrix: composition and function</title> (1999)

We discuss the use of Raman microprobe spectroscopy and Raman imaging to study the chemical composition of fresh, unmounted bone at a microscopic level. A specimen of human cortical bone was analyzed and evidence for the presence of amorphous-type calcium phosphate, a theoretical precursor in the bone formation process, was found. In general the amorphous4ype calcium phosphate appears away from osteons, in the interstitial tissue. This finding calls into question the role of amorphous-type calcium phosphate as a precursor to apatitic phosphate, since it was not found in the recently remodeled bone near the osteon center, but rather in older bone tissue. Some reasons for the presence of amorphous calcium phosphate are proposed. Possible relations ofthe amorphous mineral to bone damage and bone remodeling are discussed.
An Empirical Evaluation of Generic Convolutional and Recurrent Networks for Sequence Modeling (2018)

For most deep learning practitioners, sequence modeling is synonymous with recurrent networks. Yet recent results indicate that convolutional architectures can outperform recurrent networks on tasks such as audio synthesis and machine translation. Given a new sequence modeling task or dataset, which architecture should one use? We conduct a systematic evaluation of generic convolutional and recurrent architectures for sequence modeling. The models are evaluated across a broad range of standard tasks that are commonly used to benchmark recurrent networks. Our results indicate that a simple convolutional architecture outperforms canonical recurrent networks such as LSTMs across a diverse range of tasks and datasets, while demonstrating longer effective memory. We conclude that the common association between sequence modeling and recurrent networks should be reconsidered, and convolutional networks should be regarded as a natural starting point for sequence modeling tasks. To assist related work, we have made code available at http://github.com/locuslab/TCN .
Nuclear localization and hepatic zonation of rat "spot 14" protein: immunohistochemical investigation employing anti-fusion protein antibodies. (1992)

S14 protein and mRNA levels are rapidly regulated by hormones and diet. We have purified a 45-Kd fusion protein from lysates of transformed E. coli that includes the entire S14 polypeptide. Affinity-purified rabbit anti-fusion protein antibodies were used in immunohistochemistry to determine the distribution of S14 protein across the hepatic lobule, and to reassess its intracellular location. In hyperthyroid liver, S14 protein clustered near the central venous zone, and was not detectable in the periportal area of the acinus. The signal in perivenous hepatocytes was primarily nuclear in location, in stark contrast to previous subcellular fractionation studies. Visualization of identical hepatic distribution and subcellular localization employing anti-synthetic peptide antiserum provided evidence for the specificity of the immunostaining, as did attenuation of the signal by preincubation of the antibody with its antigen. No staining was observed in sections of heart or hypothyroid liver, as expected from the low levels of S14 protein in those tissues. The data indicate that induction of S14 protein expression by T3 occurs through enhanced expression by perivenous hepatocytes, rather than by recruitment of cells in more peripheral zones of the lobule. Nuclear localization of the S14 protein by immunohistochemistry suggests that it is lost from nuclei during standard fractionation procedures, and prompts consideration of a role for S14 in regulation of nuclear structure and/or function.
Differential induction of genes related to solvent formation during the shift from acidogenesis to solventogenesis in continuous culture of Clostridium acetobutylicum (1995)

The expression of all sequenced acetone and butanol formation genes was followed using mRNA analysis during the shift from acidogenesis to solventogenesis in continuous culture of Clostridium acetobutylicum. Differential induction or derepression of the bdhA, bdhB, and adc genes as well as the sol operon was observed during the pH-induced shift. The order of induction of the three different butanol dehydrogenase genes was found to be bdhA-sol operon-bdhB, offering an explanation for the physiological role of the respective enzymes. Peak mRNA synthesis of an autolysin and a heat shock gene at the onset of solventogenesis was detected in addition to the above-mentioned genes. None of the hitherto sequenced genes of butanologenic enzymes was found to be involved in butanol production during the Methyl viologen-induced shift, indicating the presence of yet unknown genes encoding alcohol and aldehyde dehydrogenases.
Optimized light trapping in thin film silicon solar cells by metal nanoparticle (2010)

Detailed design for nanoparticle plasmons-enhanced solar cells is presented in this article. Optimal structure for the max enhancement from the nanoparticle arrays is investigated by varying the size, shape and period of the nanoparticle, and thickness of Si absorber. Tolerance of the nanoparticle arrays provides guidance for fabrication in practice. Contribution of front and back structure as well as the nanoparticle arrays to the photocurrent is analyzed respectively. After optimization short circuit current density attains 20mA/cm<sup>2</sup> with a 185% enhancement compared to that of the 700nm thick Si.
A survey of fast mode decision algorithms for inter-prediction and their applications to high efficiency video coding (2012)

The emerging High Efficiency Video Coding (HEVC) standard attempts to improve the coding efficiency by a factor of two over H.264/AVC using new compression tools with high computational complexity. The increased computational complexity makes the real-time execution with reasonable computing power become one of the critical concerns for the commercialization of HEVC. A large number of prediction modes are the main causes of the increased complexity of HEVC. Thus, a fast decision of a prediction mode needs to be effectively used to reduce the computational complexity. To take advantage of large amounts of previous works and to find a guide for application to HEVC, this paper presents a survey of these efforts for the previous standards, especially for H.264/AVC, and examines the possibility of the previous algorithms to be applicable for HEVC. To this end, previous algorithms are categorized and then the effectiveness of each category for HEVC is evaluated. For this evaluation, a previous algorithm is modified for HEVC when it is not applicable to HEVC directly. Simulation results show that most previous algorithms with slight modification, in general, improve the encoding speed with a relatively small degradation of the compression efficiency. Among them, hierarchical mode decision is especially effective whereas mode pre-decision using motion or spatial homogeneity often results in inaccurate results.
Prostate cancer: 9. Treatment of advanced disease. (1999)

A 70-year-old man is referred to a urologist for recommendations on the management of metastatic prostate cancer. His cancer was diagnosed 5 years ago, and he underwent radical prostatectomy at that time. The tumour was confined to the prostate gland (Gleason score 7), and during surgery the lymph nodes were assessed as being clear of cancer. Before the surgery, the patient's prostate-specific antigen (PSA) level had been 8 ng/mL. After the prostatectomy, PSA was at first undetectable, but recently the PSA level rose to 2 ng/mL and then, at the most recent test, to 16 ng/mL. A bone scan was ordered to investigate back discomfort, which has been persistent but easily controlled with acetaminophen. Unfortunately, the bone scan shows several sites of metastatic disease. The man's medical history includes type 2 diabetes, which has developed during the past 3 years and which is controlled by diet, as well as asymptomatic hypertension, which is managed by means of a thiazide diuretic. The patient asks what treatments are available, what impact they are likely to have on his disease and what risks are associated with the therapies.
Retroviral Gene Therapy for X-linked Chronic Granulomatous Disease: Results From Phase I/II Trial (2011)

X-linked chronic granulomatous disease (CGD) is an inherited immunodeficiency caused by a defect in the gp91(phox) gene. In an effort to treat X-CGD, we investigated the safety and efficacy of gene therapy using a retroviral vector, MT-gp91. Two X-CGD patients received autologous CD34(+) cells transduced with MT-gp91 after a conditioning regimen consisting of fludarabine and busulfan. The level of gene-marked cells was highest at day 21 (8.3 and 11.7% in peripheral blood cells) but decreased to 0.08 and 0.5%, respectively, 3 years after gene transfer. The level of functionally corrected cells, as determined by nicotinamide adenine dinucleotide phosphate (NADPH) oxidase assay, reached a peak at day 17 (6.5% patient 1 (P1) and 14.3% patient 2 (P2) of total granulocytes) and declined to 0.05% (P1) and 0.21% (P2), 3 years later. Some retroviral vectors were found to have integrated within or close to the proto-oncogenes MDS1-EVI1, PRDM16, and CCND2; however, no abnormal cell expansion or related hematological malignancy was observed. Overall, the gene transfer procedure did not produce any serious adverse effects and was able to convert a significant fraction of blood cells to biologically functional cells, albeit for a short period of time.
Network security via private-key certificates (1990)

We present some practical security protocols that use private-key encryption in the public-key style. Our system combines a new notion of private-key certificates , a simple key-translation protocol, and key-distribution. These certificates can be administered and used much as public-key certificates are, so that users can communicate securely while sharing neither an encryption key nor a network connection.
Cloning and functional expression of CC CKR5, a human monocyte CC chemokine receptor selective for MIP-1α, MIP-1β, and RANTES (1996)

We have cloned a human cDNA for a novel CC chemokine receptor (CC CKR) designated CC CKR5 that has 48-75% amino acid identity to other CC CKRs. CC CKR5 mRNA was detected constitutively in primary adherent monocytes but not in primary neutrophils or eosinophils. Macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, and RANTES were all potent agonists for CC CKR5 (EC50 = 3-30 nM) when calcium flux was measured in transfected HEK 293 cells, yet the apparent binding affinities of the corresponding iodinated chemokines to intact cells expressing the receptor were low (IC50 approximately 100 nM). The calcium flux responses were completely blocked by treatment of transfected cells with pertussis toxin. These data suggest that CC CKR5 is a G(i)-coupled receptor that may mediate monocyte responses to MIP-1alpha, MIP-1beta, and RANTES.
Novel Pentameric Thiophene Derivatives for in Vitro and in Vivo Optical Imaging of a Plethora of Protein Aggregates in Cerebral Amyloidoses (2009)

Molecular probes for selective identification of protein aggregates are important to advance our understanding of the molecular pathogenesis underlying cerebral amyloidoses. Here we report the chemical design of pentameric thiophene derivatives, denoted luminescent conjugated oligothiophenes (LCOs), which could be used for real-time visualization of cerebral protein aggregates in transgenic mouse models of neurodegenerative diseases by multiphoton microscopy. One of the LCOs, p-FTAA, could be utilized for ex vivo spectral assignment of distinct prion deposits from two mouse-adapted prion strains. p-FTAA also revealed staining of transient soluble pre-fibrillar non-thioflavinophilic Abeta-assemblies during in vitro fibrillation of Abeta peptides. In brain tissue samples, Abeta deposits and neurofibrillary tangles (NFTs) were readily identified by a strong fluorescence from p-FTAA and the LCO staining showed complete co-localization with conventional antibodies (6E10 and AT8). In addition, a patchy islet-like staining of individual Abeta plaque was unveiled by the anti-oligomer A11 antibody during co-staining with p-FTAA. The major hallmarks of Alzheimer's disease, namely, Abeta aggregates versus NFTs, could also be distinguished because of distinct emission spectra from p-FTAA. Overall, we demonstrate that LCOs can be utilized as powerful practical research tools for studying protein aggregation diseases and facilitate the study of amyloid origin, evolution and maturation, Abeta-tau interactions, and pathogenesis both ex vivo and in vivo.