gebhart/patrepeval huggingface dataset:
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences (2007)

OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase its expression level. Three methods of optimization are available: the 'one amino acid-one codon' method, a guided random method based on a Monte Carlo algorithm, and a new method designed to maximize the optimization with the fewest changes in the query sequence. One of the main features of OPTIMIZER is that it makes it possible to optimize a DNA sequence using pre-computed codon usage tables from a predicted group of highly expressed genes from more than 150 prokaryotic species under strong translational selection. These groups of highly expressed genes have been predicted using a new iterative algorithm. In addition, users can use, as a reference set, a pre-computed table containing the mean codon usage of ribosomal protein genes and, as a novelty, the tRNA gene-copy numbers. OPTIMIZER is accessible free of charge at http://genomes.urv.es/OPTIMIZER.
DHTTP: An Efficient and Cache-Friendly Transfer Protocol for the Web (2004)

Today's HTTP carries Web interactions over client-initiated TCP connections. An important implication of using this transport method is that interception caches in the network violate the end-to-end principle of the Internet, which severely limits deployment options of these caches. Furthermore, while an increasing number of Web interactions are short, and in fact frequently carry only control information and no data, TCP is often inefficient for short interactions We propose a new transfer protocol for the Web, called Dual-Transport HTTP (DHTTP), which splits the traffic between UDP and TCP channels. When choosing the TCP channel, it is the server who opens the connection back to the client. Through server-initiated connections, DHTTP upholds the Internet end-to-end principle in the presence of interception caches, thereby allowing unrestricted caching within backbones. Moreover, the comparative performance study of DHTTP and HTTP using trace-driven simulation as well as testing real HTTP and DHTTP servers showed a significant performance advantage of DHTTP when the bottleneck is at the server and comparable performance when the bottleneck is in the network.
Interactive image segmentation for radiation treatment planning (1992)

COVIRA (COmputer VIsion in RAdiology) is a project in the European Community's Advanced Informatics in Medicine program. The goal is to improve the diagnosis and planning of treatment (radiotherapy) for patients with brain tumors and other diseases. The aim of radiotherapy is to provide a high dose of radiation to a tumor while sparing as much as possible of the surrounding healthy tissue. A necessary first step is defining the target volume and organs at risk by manually outlining the required contours on magnetic resonance or computed tomography scans. For a full three-dimensional plan this is time-consuming, as 40 or more scans are used. Computer image segmentation speeds up the process, and a method that combines information from edge and region detectors is described. Since this method is not able to completely meet the clinical requirements, an interactive image segmentation algorithm has been developed that enables the operator to employ clinical judgment. Probabilities are assigned to edges and regions and presented to the user as a hierarchy of segmentations. The approach is being subjected to extensive clinical evaluation, using pilot applications running on IBM RISC System/6000 workstations.
Characterization of monocyte maturation in adherent and suspension cultures and its application to study monocyte differentiation in Hodgkin's disease. (1983)

Monocytes purified with cell scatter monitored counterflow centrifugation were cultured in plastic (adherent) and in teflon culture bags (suspension). Sequential changes were monitored during 15 days by measuring intracellular activity of three enzymes of intermediary metabolism: glucose-6-phosphate dehydrogenase (G-6-PDH), phosphohexose isomerase (PHI) and isocitrate dehydrogenase (ICDH), and the two acid hydrolases: acid phosphatase (ACP) and N-acetyl-beta-glucosaminidase (NAG). In teflon grown macrophages a significantly lower G-6-PDH activity was seen after 15 days in comparison to plastic adherent macrophages (P less than 0.0002). For the other enzymes similar values for both culture modalities were found. The significantly, cycloheximide insensitive, higher values for G-6-PDH, PHI and ICDH in 2 h plastic adherent monocytes in comparison with plastic non-adherent monocytes, suggest a relationship between adherent capacity and the level of intermediary metabolism. The overall yield of plastic adherent macrophages after 15 days was 35% in contrast with 89% for the in suspension cultured macrophages. This corroborates the existence of adherent and non-adherent monocytes, both capable of differentiation in vitro. In 14 patients with advanced Hodgkin's disease (HD) and 14 normal controls, monocyte differentiation was studied applying both culture modalities. The enzyme levels, reflecting growth and intermediary metabolism, were similar for both groups. The adherent capacity and yield, both in teflon and in plastic, after 15 days was comparable for both groups. It was concluded that in vitro monocyte differentiation in the presence of autologous serum was qualitatively and quantitatively normal in advanced HD; this is in favour of an intrinsically normal function of monocytes in HD.
Prospects for quantum coherent computation using superconducting electronics (1997)

We discuss the prospects and challenges for implementing a quantum computer using superconducting electronics. It appears that Josephson junction devices operating at milli-Kelvin temperatures can achieve a quantum dephasing time of milliseconds, allowing quantum coherent computations of 10/sup 10/ or more steps. This figure of merit is comparable to that of atomic systems currently being studied for quantum computation.
Urinary chiro-Inositol Excretion is an Index Marker of Insulin Sensitivity in Japanese Type II Diabetes (1994)

The urinary excretion of chiro-inositol was much lower in the diabetic patients (32.3 +/- 16.0 mumol/day, means +/- SD) than in the NGT subjects (96.0 +/- 17.6; P < 0.0001) and IGT subjects (58.9 +/- 11.6; P < 0.0001). SI was much lower in the diabetic patients (3.81 +/- 1.49) than in the NGT subjects 6.30 +/- 1.59, P < 0.0005). SG was much lower in the diabetic patients (2.14 +/- 0.56) than in the NGT subjects (3.07 +/- 0.38, P < 0.0001). There was a significant correlation between urinary chiro-inositol excretion and SI (r = 0.766), as well as a significant correlation between urinary chiro-inositol excretion and SG (r = 0.747).
Heartphones: Sensor Earphones and Mobile Application for Non-obtrusive Health Monitoring (2009)

This paper describes the development and evaluation of wearable sensor earphones coupled with a mobile platform for comfortable assessment of cardiovascular function. Photoplethysmographic sensors were integrated into regular earphones to provide discreet and non-stigmatizing heart rate measurements. Preliminary results indicate that the proposed system has a high degree of accuracy at rest with an average error of 0.63%.
New Forces in German Life (1927)

Journal Article New Forces in German Life Get access E. C. Lindeman E. C. Lindeman Search for other works by this author on: Oxford Academic Google Scholar Social Forces, Volume 5, Issue 3, March 1927, Pages 456–458, https://doi.org/10.1093/sf/5.3.456 Published: 01 March 1927
Mapping of Sugar and Amino Acid Availability in Soil around Roots with Bacterial Sensors of Sucrose and Tryptophan (1999)

We developed a technique to map the availability of sugars and amino acids along live roots in an intact soil-root matrix with native microbial soil flora and fauna present. It will allow us to study interactions between root exudates and soil microorganisms at the fine spatial scale necessary to evaluate mechanisms of nitrogen cycling in the rhizosphere. Erwinia herbicola 299R harboring a promoterless ice nucleation reporter gene, driven by either of two nutrient-responsive promoters, was used as a biosensor. Strain 299RTice exhibits tryptophan-dependent ice nucleation activity, while strain 299R(p61RYice) expresses ice nucleation activity proportional to sucrose concentration in its environment. Both biosensors exhibited up to 100-fold differences in ice nucleation activity in response to varying substrate abundance in culture. The biosensors were introduced into the rhizosphere of the annual grass Avena barbata and, as a control, into bulk soil. Neither strain exhibited significant ice nucleation activity in the bulk soil. Both tryptophan and sucrose were detected in the rhizosphere, but they showed different spatial patterns. Tryptophan was apparently most abundant in soil around roots 12 to 16 cm from the tip, while sucrose was most abundant in soil near the root tip. The largest numbers of bacteria (determined by acridine orange staining and direct microscopy) occurred near root sections with the highest apparent sucrose or tryptophan exudation. High sucrose availability at the root tip is consistent with leakage of photosynthate from immature, rapidly growing root tissues, while tryptophan loss from older root sections may result from lateral root perforation of the root epidermis.
brt, a mouse gene encoding a novel receptor-type protein-tyrosine kinase, is preferentially expressed in the brain. (1994)

Using polymerase chain reaction (PCR)-mediated cloning procedure, we have isolated a novel gene encoding protein-tyrosine kinase from fetal mouse brain. This gene, named brt (from brain tyrosine kinase), had an open reading frame that encoded 856 amino acids. The deduced amino acid sequence revealed that the gene product had all the hallmarks of a receptor-type protein-tyrosine kinase. The brt protein showed significant homology to the axl/ufo protein that has an oncogenic potential. Northern blot analysis showed that brt was expressed preferentially in the brain of both embryo and adult. Thus, brt is a new member of the subfamily of receptor-type protein-tyrosine kinases and is suggested to play important roles in development and functions in the central nervous system.
Quasimaximum Likelihood Estimators for Two-parameter Gamma Distributions (1973)

The Gamma probability distribution is defined by the density function [β <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">α</sup> γ(α)] <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> exp (−x/β). This paper presents new estimators for the parameters α <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> and β. Required calculations are simple, primarily involving the inner product of certain elementary statistics and their logarithms. Both of the new estimators are shown to be unbiased. The variance formulas for each and their covariance formula are derived—counterparts of these for the method of moments (MM) and the method of maximum likelihood (ML) not being known except in the asymptotic form. Curve-fitting results from samples of size 50 are provided. They support the proposition that the new quasimaximum likelihood estimators (QML) are at least as effective as MM and ML estimators. Illustrative estimation based on samples of size 5 also is presented for comparison; the results highlight relative smaller variances for the ML estimators. The same Monte Carlo results signal a possibility that significant negative bias occurs with both the MM and ML techniques if small samples are used.
Cell detachment activates the Hippo pathway via cytoskeleton reorganization to induce anoikis (2012)

Cell attachment to the extracellular matrix (ECM) is crucial to cell physiology such as polarity, motility, and proliferation. In normal cells, loss of attachment to the ECM induces a specific type of apoptosis, termed anoikis. Resistance to anoikis in cancer cells promotes their survival in circulation and dispersion to distant anatomic sites, leading to tumor metastasis. The Yes-associated protein (YAP) transcription coactivator is a human oncogene and a key regulator of organ size. The Hippo tumor suppressor pathway phosphorylates and inhibits YAP. However, little is known about the signals that regulate the Hippo pathway. Here we report that through cytoskeleton reorganization, cell detachment activates the Hippo pathway kinases Lats1/2 and leads to YAP phosphorylation and inhibition. The detachment-induced YAP inactivation is required for anoikis in nontransformed cells, whereas in cancer cells with deregulation of the Hippo pathway, knockdown of YAP and TAZ restores anoikis. Furthermore, we provided evidence that Lats1/2 expression level is indeed significantly down-regulated in metastatic prostate cancer. Our findings provide a novel connection between cell attachment and anoikis through the Hippo pathway and have important implications in cancer therapeutics.
Molecular Virology of Hepatitis B Virus (2004)

Hepatitis B virus (HBV) has evolved a unique life cycle that results in the production of enormous viral loads during active replication without actually killing the infected cell directly. Because HBV uses reverse transcription to copy its DNA genome, mutant viral genomes emerge frequently. Particular selection pressures, both endogenous (host immune clearance) and exogenous (vaccines and antiviral drugs), readily select out these escape mutants. Which particular viral mutations or combination of mutations directly affect the clinical outcome of infection are not known. Further studies are clearly needed to identify the pathogenic basis and clinical sequelae arising from the selection of these mutants.
Attenuation of Astroglial Reactivity by Interleukin-10 (1996)

Prominent responses that follow brain trauma include the activation of microglia, recruitment of blood-derived macrophages, and astroglial reactivity. Based on evidence that cytokines produced by macrophages/microglia may cause astrocytes to become reactive, the aim of this study was to determine whether astroglial reactivity could be attenuated by interleukin (IL)-10, a potent inhibitor of cytokine synthesis by macrophages/microglia. Four days after the local application of IL-10 to the site of corticectomy in adult mice, the number of reactive astrocytes and their state of hypertrophy was reduced (by 60%) when compared with vehicle controls. In the majority of IL-10-treated mice, but not in any vehicle controls, the tissue in the immediate vicinity of IL-10 application contained viable but non reactive astrocytes. The mechanism by which IL-10 attenuates astroglial reactivity is likely via the reduction of cytokine production by macrophages/microglia because, based on Mac-1 immunohistochemistry, the macrophages/microglia of IL-10 brains had a decreased activation state compared with vehicle-controls. Another macrophage/microglia deactivating agent, macrophage inhibitory factor, also reduced astroglial activity in vivo. Furthermore, IL-10 had no direct effect on purified astrocytes in culture, indicating that its in vivo action on astroglial reactivity is likely via indirect mechanisms. Finally, injury resulted in the substantial rise of tumor necrosis factor-alpha mRNA levels, and this elevation was significantly inhibited by IL-10. The ability to manipulate the extent of astrogliosis should provide a means of addressing the neurotrophic or inhibitory role of reactive astrocytes in neurological recovery.
The metamorphic algorithm: a speaker mapping approach to data augmentation (1994)

Large vocabulary speaker-dependent speech recognition systems adjust to the acoustic peculiarities of each new speaker based on some enrolment data provided by this speaker. As the amount of data required increases with the sophistication of the underlying acoustic models, the enrolment may get lengthy. To streamline it, it is therefore desirable to make use of previously acquired speech data. The authors describe a data augmentation strategy based on a piecewise linear mapping between the feature space of a new speaker and that of a reference speaker. This speaker-normalizing mapping is used to transform the previously acquired data of the reference speaker onto the space of the new speaker. The performance of the resulting procedure, dubbed the metamorphic algorithm, is illustrated on an isolated utterance speech recognition task with a vocabulary of 20000 words. Results show that the metamorphic algorithm can substantially reduce the word error rate when only a limited amount of enrolment data is available. Alternatively, it leads to a level of performance comparable to that obtained when a much greater amount of enrolment data is required from the new speaker. In addition, it can also be used for tracking spectral evolution over time, thus providing a possible means for robust speaker self-adaptation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
CD4-Induced Conformational Changes in the Human Immunodeficiency Virus Type 1 gp120 Glycoprotein: Consequences for Virus Entry and Neutralization (1998)

Human immunodeficiency virus type 1 (HIV-1) entry into target cells involves sequential binding of the gp120 exterior envelope glycoprotein to CD4 and to specific chemokine receptors. Soluble CD4 (sCD4) is thought to mimic membrane-anchored CD4, and its binding alters the conformation of the HIV-1 envelope glycoproteins. Two cross-competing monoclonal antibodies, 17b and CG10, that recognize CD4-inducible gp120 epitopes and that block gp120-chemokine receptor binding were used to investigate the nature and functional significance of gp120 conformational changes initiated by CD4 binding. Envelope glycoproteins derived from both T-cell line-adapted and primary HIV-1 isolates exhibited increased binding of the 17b antibody in the presence of sCD4. CD4-induced exposure of the 17b epitope on the oligomeric envelope glycoprotein complex occurred over a wide range of temperatures and involved movement of the gp120 V1/V2 variable loops. Amino acid changes that reduced the efficiency of 17b epitope exposure following CD4 binding invariably compromised the ability of the HIV-1 envelope glycoproteins to form syncytia or to support virus entry. Comparison of the CD4 dependence and neutralization efficiencies of the 17b and CG10 antibodies suggested that the epitopes for these antibodies are minimally accessible following attachment of gp120 to cell surface CD4. These results underscore the functional importance of these CD4-induced changes in gp120 conformation and illustrate viral strategies for sequestering chemokine receptor-binding regions from the humoral immune response.
Rapid learning curve assessment in an ex vivo training system for microincisional glaucoma surgery (2017)

Increasing prevalence and cost of glaucoma have increased the demand for surgeons well trained in newer, microincisional surgery. These procedures occur in a highly confined space, making them difficult to learn by observation or assistance alone as is currently done. We hypothesized that our ex vivo outflow model is sensitive enough to allow computing individual learning curves to quantify progress and refine techniques. Seven trainees performed nine trabectome-mediated ab interno trabeculectomies in pig eyes (n = 63). An expert surgeon rated the procedure using an Operating Room Score (ORS). The extent of outflow beds accessed was measured with canalograms. Data was fitted using mixed effect models. ORS reached a half-maximum on an asymptote after only 2.5 eyes. Surgical time decreased by 1.4 minutes per eye in a linear fashion. The ablation arc followed an asymptotic function with a half-maximum inflection point after 5.3 eyes. Canalograms revealed that this progress did not correlate well with improvement in outflow, suggesting instead that about 30 eyes are needed for true mastery. This inexpensive pig eye model provides a safe and effective microsurgical training model and allows objective quantification of outcomes for the first time.
A Role for Endothelial NO Synthase in LTP Revealed by Adenovirus-Mediated Inhibition and Rescue (1996)

Pharmacological studies support the idea that nitric oxide (NO) serves as a retrograde messenger during long-term potentiation (LTP) in area CA1 of the hippocampus. Mice with a defective form of the gene for neuronal NO synthase (nNOS), however, exhibit normal LTP. The myristoyl protein endothelial NOS (eNOS) is present in the dendrites of CA1 neurons. Recombinant adenovirus vectors containing either a truncated eNOS (a putative dominant negative) or an eNOS fused to a transmembrane protein were used to demonstrate that membrane-targeted eNOS is required for LTP. The membrane localization of eNOS may optimally position the enzyme both to respond to Ca2+ influx and to release NO into the extracellular space during LTP induction.
Recent Data Sets on Object Manipulation: A Survey (2016)

Data sets is crucial not only for model learning and evaluation but also to advance knowledge on human behavior, thus fostering mutual inspiration between neuroscience and robotics. However, choosing the right data set to use or creating a new data set is not an easy task, because of the variety of data that can be found in the related literature. The first step to tackle this issue is to collect and organize those that are available. In this work, we take a significant step forward by reviewing data sets that were published in the past 10 years and that are directly related to object manipulation and grasping. We report on modalities, activities, and annotations for each individual data set and we discuss our view on its use for object manipulation. We also compare the data sets and summarize them. Finally, we conclude the survey by providing suggestions and discussing the best practices for the creation of new data sets.
Characterization of the biosynthetic gene cluster for the oligosaccharide antibiotic, Evernimicin, in Micromonospora carbonacea var. africana ATCC39149 (2001)

Evernimicin (EV) belongs to the orthosomycin class of antibiotics and consists of several modified L- and D-deoxysugars containing unusual orthoester and glycosyl linkages and two orsellinic acid groups, one that is halogenated. The EV biosynthetic gene cluster from Micromonospora carbonacea var. africana ATCC39149 was localized by hybridization to a dTDP-D-glucose 4,6-dehydratase probe and a 120-kb region containing the EV biosynthetic cluster and surrounding regions has been sequenced. BLAST analysis has identified a type I polyketide synthase for orsellinic acid biosynthesis as well as enzymes required for L- and D-deoxyglucose and D-deoxymannose synthesis. In addition, genes involved in glycosyltransfer and resistance were identified. Insertional mutations in several biosynthetic genes blocked EV production, indicating a role for these genes in EV biosynthesis.
The Acoustic Vector-Sensor's Near-Field Array-Manifold (2010)

The acoustic vector-sensor is a practical and versatile sound-measurement system, for applications in-room, open-air, or underwater. Its <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">far</i> -field measurement model has been introduced into signal processing over a decade ago; and many direction-finding algorithms have since been developed for acoustic vector-sensors, but only for <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">far</i> -field sources. Missing in the literature is a <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">near</i> -field measurement model for the acoustic vector-sensor. This correspondence fills this literature gap.