gebhart/patrepeval huggingface dataset:
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features (2013)

featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
Social Distributed Hash Table (2007)

This paper presents an architecture called social distributed hash table (SDHT) that combines strengths of distributed hash table (DHT) algorithms and social networks making mobile search fast and context oriented. The paper presents possible implementations of the proposed architecture in the IP multimedia subsystem (IMS) and as a standalone SIP based system. The architecture forms a cost efficient platform for providing innovative mobile services that take advantage of social context of human communication. The architecture can be used to deploy a global virtual mobile network by placing SDHT nodes in different geographical regions. The paper also presents a content sharing inside community service.
A packaging technique for silicon MEMS strain sensors on steel (2008)

A packaging technique suited to applying MEMS strain sensors realized on a silicon chip to a steel flat surface is described. The method is based on adhesive bonding of the silicon chip rear surface on steel using two types of glue normally used for standard piezoresistive strain sensors (M-bond200/600), using direct wire bonding of the chip to a Printed Circuit Board, also fixed on steel. In order to protect the sensor from the external environment, and to improve the MEMS performance, the silicon chip is encapsulated with a metal cap hermetically sealed-off under vacuum condition with a vacuum adhesive in which the bonding wires are also protected from possible damage. In order to evaluate the mechanical coupling of the silicon chip with the bar and the stress transfer extent to the silicon surface, commercial strain sensors have been applied on the chip glued on a steel bar in a laboratory setup able to generate strain by inflection, yielding a stress transfer around 70% from steel to silicon.
Sequence at the Site of Attachment of an Affinity‐Label Derivative of Puromycin on 23‐S Ribosomal RNA of Escherichia coli Ribosomes (1978)

The puromycin analogue, 5′ O ‐( N ‐bromoacetyl‐ p ‐aminophenylphosphoryl)‐3′‐ N ‐L‐phenylalanyl puromycin aminonucleoside, acts as an affinity label in covalently binding to 23‐S RNA in the active centre of peptidyl transferase of Escherichia coli ribosomes [Greenwell, P., Harris, R. J. &amp; Symons, R. H. (1974) Eur. J. Biochem. 49 , 539–554]. The sequence of a pentanucleotide fragment of 23‐S RNA to which the affinity label is attached has now been determined. In an attempt to determine the nucleotide residue to which the affinity label was attached, a 32 P‐labelled affinity label was reacted with ribosomal RNA, poly(A), poly(C), poly(G) and poly(U) under the conditions used for affinity labelling of ribosomes. However, no specific reaction occurred, confirming our earlier observation that this required the functional integrity of the ribosome. An alternative approach of affinity labelling ribosomes labelled by incubating E. coli in the presence of [ 3 H]adenosine, [ 3 H]cytidine, [ 3 H]guanosine or [ 3 H]uridine, showed that the affinity label was attached to a CMP residue. Affinity‐labelled oligonucleotide fragments were purified for sequence analysis as follows. The free α‐amino group of the affinity‐label molecule attached to 23‐S ribosomal [ 32 P]RNA was coupled to biotin by reaction with the N ‐hydroxysuccinimide ester of biotin. After digestion of the RNA with either ribonuclease A or T 1 , the basic protein avidin was added to form the avidin · biotin – affinity‐label‐oligonucleotide fragment. Stepwise chromatography on phosphocellulose, followed (after dissociation of the avidin) by electrophoresis on DEAE‐cellulose at pH 1.9 gave substantial purification of the biotin–affinity‐label‐oligonucleotide. From the nucleotide composition of the purified ribonuclease A and T 1 fragments, the pentanucleotide sequence of G‐U‐C*‐C‐Gp was obtained, where C* represents C modified by the affinity label.
Leave-in-Time (1995)

Leave-in-Time is a new rate-based service discipline for packet-switching nodes in a connection-oriented data network. Leave-in-Time provides sessions with upper bounds on end-to-end delay, delay jitter, buffer space requirements, and an upper bound on the probability distribution of end-to-end delays. A Leave-in-Time session's guarantees are completely determined by the dynamic traffic behavior of that session, without influence from other sessions. This results in the desirable property that these guarantees are expressed as functions derivable simply from a single fixed-rate server (with rate equal to the session's reserved rate) serving only that session. Leave-in-Time has a non-work-conserving mode of operation for sessions desiring low end-to-end delay jitter. Finally, Leave-in-Time supports the notion of delay shifting, whereby the delay bounds of some sessions may be decreased at the expense of increasing those of other sessions. We present a set of admission control algorithms which support the ability to do delay shifting in a systematic way.
Analogues of the antibiotic puromycin as potential prodrugs of 3′‐amino‐3′‐deoxythymidine (1992)

Abstract Condensation of L‐ and D‐3′‐amino‐2′,3′‐dideoxynucleosides 2–5 with N ‐BOC‐protected aminoacids 6 and 13 using dicyclohexylcarbodiimide and N ‐hydroxysuccinimide in DMF is reported to give the N ‐BOC‐protected acylamino aminonucleosides 7– 9 and 14 in 51–81% yield. After deprotection using trifluoroacetic acid the corresponding unprotected new analogues of puromucin 10–12 and 15 were obtained in 43–56% yield. These compounds did not show any significant antiviral activity using HIV (stain HTLV‐III B)‐infected MT‐4 cells as target system.
Comprehensive human genome amplification using multiple displacement amplification (2002)

Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4-6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20-30 microg product from as few as 1-10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.
Time scale for cold-air pool breakup by turbulent erosion (2003)

Turbulent erosion has been proposed as a major mechanism for removing wintertime cold-air pools (CAPs) from basins and valleys. The time scales involved in this erosion process, which are of great interest for winter weather forecasting, have not been studied systematically in the past. In this short contribution, a semi-analytical model is developed to estimate the time required for the dissipation of cold air pools from above by downward micro-scale turbulent erosion for different wind speeds aloft, different static stabilities inside the cold pool, and for different basin cross sections. The calculations show that micro-scale turbulent erosion is a rather slow process and that the erosion rate decreases rapidly with time as static stability increases in the capping inversion at the top of the cold pool. The rate of erosion is determined mainly by wind speed above the CAP and the temperature inversion strength inside the CAP; it is less sensitive to the shape of the topography. Shallow CAPs of a few tens of meters in depth with a weak inversion may be removed in a matter of hours if winds aloft are sufficiently strong to initiate and maintain turbulent mixing. It is unlikely, however, that deeper CAPs with a moderate to strong inversion can be destroyed by micro-scale turbulent erosion unless combined with other regional and synoptic-scale processes that produce larger-scale turbulent mixing. Erosion durch Turbulenz ist schon lange als wesentlicher Prozess bei der Zerstörung von winterlichen Kaltluftseen in Becken und TÄlern betrachtet worden. Der Zeitraum dieses Erosionsprozesses, der besonders wichtig für Vorhersagen im Winter ist, ist bis jetzt jedoch noch nicht systematisch untersucht worden. In diesem Beitrag wird ein semi-analytisches Modell beschrieben, das die benötigte Zeit für die Auflösung eines Kaltluftsees durch mikroskalige turbulente Erosion von oben abschÄtzt. Dieses Modell berücksichtigt die Windgeschwindigkeit oberhalb und die StabilitÄt innerhalb des Kaltluftsees sowie den Querschnitt des Beckens bzw. Tales. Die Berechnungen zeigen, dass mikroskalige turbulente Erosion ein langsamer Prozess ist und dass sich die Erosionsrate im Laufe der Zeit stark verlangsamt, wenn die statische StabilitÄt in der abgrenzenden Inversion oberhalb des Kaltluftsees zunimmt. Die Erosionsrate wird vor allem von der Windgeschwindigkeit oberhalb des Kaltluftsees und vom Temperaturgradienten innerhalb des Sees bestimmt. Der Querschnitt des Beckens bzw. Tales spielt dabei eine weniger wichtige Rolle. Ein flacher Kaltluftsee von einigen Metern (< 50 m) mit einem schwachen Temperaturgradienten kann durch mikroskalige turbulente Erosion in einigen Stunden zerstört werden, wenn die Windgeschwindigkeit oberhalb des Sees ausreichend ist, um turbulente Durchmischung zu initiieren bzw. aufrechtzuhalten. Es ist unwahrscheinlich, dass ein tiefer Kaltluftsee mit einem mÄßigen bis starken Temperaturgradienten allein durch mikroskalige turbulente Erosion zerstört werden kann, außer dass regionale oder synoptische Prozesse vorhanden sind, die größere Wirbel verursachen.
RRB1 and RRB2 Encode Maize Retinoblastoma-Related Proteins That Interact with a Plant D-Type Cyclin and Geminivirus Replication Protein (1997)

Unlike mammalian and yeast cells, little is known about how plants regulate G1 progression and entry into the S phase of the cell cycle. In mammalian cells, a key regulator of this process is the retinoblastoma tumor suppressor protein (RB). In contrast, G1 control in Saccharomyces cerevisiae does not utilize an RB-like protein. We report here the cloning of cDNAs from two Zea mays genes, RRB1 and RRB2, that encode RB-related proteins. Further, RRB2 transcripts are alternatively spliced to yield two proteins with different C termini. At least one RRB gene is expressed in all the tissues examined, with the highest levels seen in the shoot apex. RRB1 is a 96-kDa nuclear protein that can physically interact with two mammalian DNA tumor virus oncoproteins, simian virus 40 large-T antigen and adenovirus E1A, and with a plant D-type cyclin. These associations are abolished by mutation of a conserved cysteine residue in RRB1 that is also essential for RB function. RRB1 binding potential is also sensitive to deletions in the conserved A and B domains, although differences exist in these effects compared to those of human RB. RRB1 can also bind to the AL1 protein from tomato golden mosaic virus (TGMV), a protein which is essential for TGMV DNA replication. These results suggest that G1 regulation in plant cells is controlled by a mechanism which is much more similar to that found in mammalian cells than that in yeast.
Quantitative Identification of Mutant Alleles Derived from Lung Cancer in Plasma Cell-Free DNA via Anomaly Detection Using Deep Sequencing Data (2013)

The detection of rare mutants using next generation sequencing has considerable potential for diagnostic applications. Detecting circulating tumor DNA is the foremost application of this approach. The major obstacle to its use is the high read error rate of next-generation sequencers. Rather than increasing the accuracy of final sequences, we detected rare mutations using a semiconductor sequencer and a set of anomaly detection criteria based on a statistical model of the read error rate at each error position. Statistical models were deduced from sequence data from normal samples. We detected epidermal growth factor receptor (EGFR) mutations in the plasma DNA of lung cancer patients. Single-pass deep sequencing (>100,000 reads) was able to detect one activating mutant allele in 10,000 normal alleles. We confirmed the method using 22 prospective and 155 retrospective samples, mostly consisting of DNA purified from plasma. A temporal analysis suggested potential applications for disease management and for therapeutic decision making to select epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI).
Calcitonin gene‐related peptide (CGRP) antagonists: blockers of neuronal transmission in migraine (2004)

The neuropeptide calcitonin gene-related peptide (CGRP) is a potent vasodilator that is contained in and released from sensory nerves. CGRP has been implicated in migraine, and the nonpeptide CGRP antagonist BIBN4096BS has been shown to be effective in clinical trials in migraine. To date, it has been largely assumed that the CGRP antagonist is effective due to its ability to block vasodilator activity. Goadsby and co-workers present data that now suggest that CGRP antagonists may also block neuronal transmission in migraine.
On statistical multiplexing, traffic mixes, and VP management (2002)

ATM-based integrated services networks are likely to rely on the virtual path (VP) concept as an intermediate resource management layer wherein key decisions concerning resource allocation, sharing, and flow aggregation are made. In this paper we consider the impact that statistically multiplexing heterogeneous services on VP connections will have on network design and management. Based on simple models we consider several questions including the following: given two traffic types with different quality of service requirements, should one segregate such flows on their own VPs, or is it to the network's advantage to multiplex the flows on a single VP guaranteeing the most stringent QoS requirement? Assuming two VPs have been set up between a given origin-destination pair and heterogeneous flows are to be carried, how should one route the connections to achieve good performance?.
Some experience in interactive system development and application (1975)

Minicomputers pgoggammed in a high-level interactive language form a very attractive basis fog the development of systems involving close man-computer collaboration. This paper is based on a wide range of experience of interactive minicomputer systems in commercial, medical, industrial, and scientific applications. It is first argued that the development of systems fog effective man-computer collaboration requires not only interactive system use but also interactive system depelopment. The designer needs to be able to tailor the system to user requirements at least partially as an experimental dialogue at a terminal with a user. There follows a critique of certain features of central computer utilities that limit their effectiveness in interactive apllications, leading to a proposal fog the use of minicomputer-based systems programmed, and used, interactively. We then give a number of case histories of our own experience in developing and using such systems in commercial, medical, and scientific appllications. From this experience, we have extracted a number of rules for programming interaction between the user and computer system which are outed. Finally, the main features of the software technology underlying these systems are briefly described.
Rollout strategies for sequential fault diagnosis (2003)

Test sequencing is a binary identification problem wherein one needs to develop a minimal expected cost testing procedure to determine which one of a finite number of possible failure sources, if any, is present. The problem can be solved optimally using dynamic programming or AND/OR graph search methods (AO*, CF and HS). However, for large systems, the associated computation with dynamic programming or AND/OR graph search methods is substantial, due to the rapidly increasing number of OR nodes (denoting ambiguity states) and AND nodes (denoting tests) in the search graph. In order to overcome the computational explosion, the one-step or multi-step lookahead heuristic algorithms have been developed to solve the test sequencing problem. In this paper, we propose to apply rollout strategies, which can be combined with the one-step or multi-step lookahead heuristic algorithms to obtain near-optimal solutions in a computationally efficient manner than the optimal strategies. The rollout strategies are illustrated and tested using a range of real-world systems. We show computational results, which suggest that the information-heuristic based rollout policies are significantly better than other rollout policies based on Huffman coding and entropy.
Modelling lipid metabolism in the rumen. (2000)

Nutritional manipulation through fat supplementation of diets is of interest because of the large energy requirements of high-producing ruminants, and because of human health concerns about saturated long-chain fatty acids (LCFA) in ruminant products. High dietary fat levels may adversely affect microbial activity and nutrient degradation in the rumen. Mathematical models of the rumen fermentation process have been developed and applied to quantify the profile of nutrients available for absorption. However, the representation of lipid dynamics is limited in these rumen models. Therefore, an extant rumen model was modified to represent the effects of LCFA on microbial metabolism and nutrient digestion. The primary objective of the model currently being developed is to integrate LCFA metabolism with microbial metabolism of other substrates in the rumen, and to predict the effect of amount and composition of dietary fat upon the profile of nutrients available for absorption. In the modified model, there are three rumen lipid pools: unhydrolysed lipid (Li), saturated free LCFA (Fs) and unsaturated free LCFA (Fu). Inputs to these pools are from the feed and outputs are flows to the duodenum. The rate of biohydrogenation is dependent on the amount of fibre and of unsaturated LCFA in the rumen. The unsaturated LCFA are considered to inhibit fibrolytic bacterial metabolism, but not amylolytic bacterial metabolism, whilst saturated LCFA are assumed not to affect bacterial metabolism. Protozoal metabolism is assumed to be inhibited by both saturated and unsaturated LCFA. The rates of biohydrogenation and inhibition of bacterial metabolism are represented by sigmoidal Michaelis-Menten equations, with parameters derived from in vitro and in vivo data. Preliminary results of sensitivity analyses suggest that the model responds appropriately to perturbations in dietary inputs. The degradation of fibre in the rumen was reduced when the amount of unsaturated LCFA in the diet was raised, but the reduction in fibre degradation was far more pronounced with a low forage diet in comparison to a high forage diet. In all cases, the efficiency of microbial growth was increased upon an increase in dietary LCFA content because of a reduction in protozoal numbers and consequently in microbial recycling within the rumen. Decreasing the forage proportion of the diet decreases the degree of saturation of LCFA flowing to the duodenum. A decrease in acetate to propionate ratio in rumen fluid was only apparent when a diet high in unsaturated LCFA was fed. Such responses are related to the effects of unsaturated LCFA and saturated LCFA on metabolism of amylolytic and fibrolytic bacteria and of protozoa, and consequently on nutrient degradation in the rumen.
Reversal of hypercalcemia with the vitamin D analogue EB1089 in a human model of squamous cancer. (1999)

EB1089, an analogue of 1,25 dihydroxyvitamin D with low calcemic activity is a potent inhibitor of parathyroid hormone-related peptide (PTHRP) production in vitro. The purpose of the present study was to determine whether EB1089 could reverse established hypercalcemia in BALB C nude mice implanted s.c. with a human epithelial cancer previously shown to produce high levels of PTHRP in vitro. Total plasma calcium was monitored before and after tumor development and increased steadily when the tumor reached > or =0.5 cm3. When total calcium was 22.85 mmol/liter, animals were treated with a constant infusion of EB1089 or vehicle alone for a period of 2 weeks. A significant and sustained reduction of plasma calcium from 3.2+/-0.1 to 2.7+/-0.08 (P < 0.01) mmol/liter was observed during infusion with EB1089. In contrast, calcium levels in vehicle-treated animals continued to rise during the infusion period. Tumor growth velocity also slowed significantly after the administration of EB1089 as compared with vehicle-treated animals. Plasma PTHRP levels measured at the end of the 2 weeks' infusion period were significantly lower in animals treated with EB1089 as compared with animals treated with vehicle alone (44+/-8 pg/ml versus 194+/-35 pg/ml, P < 0.001). These results, therefore, demonstrate that EB1089 can reverse established hypercalcemia in a human model of squamous cancer.
New molecular mechanisms of GH resistance (2004)

Primary growth hormone (GH) resistance describes growth failure in the presence of normal, or even elevated, GH secretion. In its classic form, the phenotype is identical to that of GH deficiency, and was originally described in association with defects of the GH receptor. With increasing understanding of the GH-insulin-like growth factor (IGF) axis, it has become apparent that GH resistance can result from either primary IGF deficiency (IGFD) or IGF resistance. Primary IGFD may be due to: (i) defects of the GH receptor, (ii) defects of post-GH receptor signaling or (iii) primary defects of IGF-I synthesis. IGF resistance may result from: (i) defects of the IGF receptor, (ii) defects of post-IGF receptor signaling, (iii) defects of IGF binding proteins or (iv) defects of the epiphyseal growth plate or of regulatory proteins involved in epiphyseal growth.
Application of spectral decomposition to detect deepwater gas reservoir (2007)

In this paper, spectral decomposition techniques are applied to deepwater seismic data from Gulf of Mexico to examine the gas associated spectral anomalies. In the first case, thick gas sand with nearly constant P‐impedance is encased in shale with non‐symmetric P‐impedance, and gas reservoir are bright at low‐frequency iso‐frequency sections; Commercial gas sand and low‐gas saturated sand also show apparently different spectral characteristics. In the second case, gas reservoir includes two consecutive up‐fining sand intervals with gradually changed P‐impedance in each sand interval. Spectral anomalies of gas sand occur at high‐frequency iso‐frequency sections. Detailed forward modeling is analyzed to help understand the underlying physical mechanisms. Reservoir thickness and P‐impedance structure are the first order factors to control the spectral decomposition responses of the above two gas reservoirs. Systematic synthetic model based on reservoir properties is needed to select optimal frequency range to directly detect hydrocarbon for specific reservoir.