gebhart/patrepeval huggingface dataset:
Genome analysis of the smallest free-living eukaryote <i>Ostreococcus tauri</i> unveils many unique features (2006)

The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C(4) photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.
Exoelectrogenic biofilm as a template for sustainable formation of a catalytic mesoporous structure (2014)

Mesoporous structures can increase catalytic activity by maximizing the ratio of surface area to volume, but current synthesis techniques utilize expensive polymers and toxic chemicals. A Geobacter sulfurreducens biofilm was used as a sustainable template to form mesoporous Pd structures while eliminating the need for synthetic chemicals. The bulk of the biofilm material was removed by thermal treatments after nanoparticle formation, producing a catalytic Pd mesoporous (pore size 9.7 ± 0.1 nm) structure attached to the graphite electrode with a 1.5-2 µm thick backbone composed of nanoparticles (∼200 nm). A control electrode electrochemically plated with Pd in the absence of a biofilm exhibited a variable planar Pd base (∼0.5-3 µm thick) with sporadic Pd extrusions (∼2 µm across, 1-5 µm tall) from the surface. The biotemplated mesoporous structure produced 15-20% higher stable current densities during H2 oxidation tests than the electrochemically plated control electrode, even though 30% less Pd was present in the biotemplated catalyst. These results indicate that electroactive biofilms can be used as a sustainable base material to produce nanoporous structures without the need for synthetic polymers. Biotechnol. Bioeng. 2014;111: 2349-2354. © 2014 Wiley Periodicals, Inc.
Amphiphilic Tobramycin Analogues as Antibacterial and Antifungal Agents (2015)

In this study, we investigated the in vitro antifungal activities, cytotoxicities, and membrane-disruptive actions of amphiphilic tobramycin (TOB) analogues. The antifungal activities were established by determination of MIC values and in time-kill studies. Cytotoxicity was evaluated in mammalian cell lines. The fungal membrane-disruptive action of these analogues was studied by using the membrane-impermeable dye propidium iodide. TOB analogues bearing a linear alkyl chain at their 6″-position in a thioether linkage exhibited chain length-dependent antifungal activities. Analogues with C12 and C14 chains showed promising antifungal activities against tested fungal strains, with MIC values ranging from 1.95 to 62.5 mg/liter and 1.95 to 7.8 mg/liter, respectively. However, C4, C6, and C8 TOB analogues and TOB itself exhibited little to no antifungal activity. Fifty percent inhibitory concentrations (IC50s) for the most potent TOB analogues (C12 and C14) against A549 and Beas 2B cells were 4- to 64-fold and 32- to 64-fold higher, respectively, than their antifungal MIC values against various fungi. Unlike conventional aminoglycoside antibiotics, TOB analogues with alkyl chain lengths of C12 and C14 appear to inhibit fungi by inducing apoptosis and disrupting the fungal membrane as a novel mechanism of action. Amphiphilic TOB analogues showed broad-spectrum antifungal activities with minimal mammalian cell cytotoxicity. This study provides novel lead compounds for the development of antifungal drugs.
Seeing the Patient and Family Through: Nurses and Physicians Experiences With Withdrawal of Life-Sustaining Therapy in the ICU (2018)

Withdrawal of life-sustaining therapy at the end of life is a complex phenomenon. Intensive care nurses and physicians are faced with caring for patients and supporting families, as these difficult decisions are made. The purpose of this study was to explore and describe the experience of critical care nurses and physicians participating in the process of withdrawal of life-sustaining therapy. A hermeneutic phenomenological approach was used to guide this qualitative investigation. Interviews were conducted with critical care nurses and physicians from 2 medical centers. An inductive approach to data analysis was used to understand similarities between the nurses and the physicians' experiences. Methodological rigor was established, and data saturation was achieved. The main categories that were inductively derived from the data analysis included from novice to expert, ensuring ethical care, uncertainty to certainty, facilitating the process, and preparing and supporting families. The categories aided in understanding the experiences of nurses and physicians, as they worked individually and together to see patients and families through the entire illness experience, withdrawal of life-sustaining therapy decision-making process and dying process. Understanding the perspectives of health-care providers involved in the withdrawal of life-sustaining therapy process will help other health-care providers who are striving to provide quality care to the dying and to their families.
Augmented Reality 6th Sense (2014)

Augmented Reality is considered an extension of Virtual Reality. Augmented reality is a technology in which we combine the real world entities with virtually created objects. Augmented reality is huge technique and we are adopting a part of this technique. In our paper, we are controlling the windows media player using augmented reality. Here, we are going to perform the operations of windows media player (viz pause/play, forward and backward) using a virtual touch surface which will be monitored using a web camera. The paper suggests two stages: Integration of digital and real world in which we create a virtual touch surface and Integration of touch surface with application like Windows Media Player.
SOFTWARE RELEASE PLANNING (2005)

One of the most critical activities in software product development is the decisional process that assigns features to subsequent releases under technical, resource, risk, and budget constraints.This decision-centric process is referred to as software release planning (SRP).This briefing will expose a state of the art on SRP.A survey of the most relevant approaches will be presented.Emphasis will be made on their applicability (concerning e.g.type of development process -being more predictive versus more adaptive, type of system -commercial, open source product or mobile app), tool support and degree of validation in industry.One of these approaches, EVOLVE, will be analysed in detail. CCS Concepts• Software and its engineering➝Software creation and management➝Software post-development issues➝Software evolution.
O-acetylation of G<scp>d</scp>3 (2002)

Glycosphingolipids (GSLs) are amphipathic molecules with a polar glycan chain as a head group and a hydrophobic sphingosine-containing ceramide tail, which is typically embedded in the outer leaflet of the plasma membrane ([1][1]). GSLs are no longer thought to be mere physical components of the
PAC DSP Core and Application Processors (2006)

This paper provides an overview of the parallel architecture core (PAC) project led by SoC Technology Center of Industrial Technology Research Institute (STC/ITRI) in Taiwan. The background of PAC project, a brief introduction to PAC core technologies, PAC SoC development suite, PAC benchmarks, and applications are presented. The main objective of the PAC development plan is to enhance industrial development competitiveness in the core technology related to key components, especially for portable multimedia applications
Enzymatic Synthesis of 1-Sinapoylglucose from Free Sinapic Acid and UDP-Glucose by a Cell-Free System from Raphanus sativus Seedlings (1980)

Abstract Protein extracts from seedlings of Raphanus sativus catalyze the transfer of the glucosyl moiety of UDP-glucose to the carboxyl group of phenolic acids. Enzymatic activity was determined spectrophotometrically by measuring the increase in absorbance at 360 nm and/or by the aid of high performance liquid chromatography (HPLC). From 12 phenolic acids tested as acceptors, sinapic acid was by far the best substrate. The glucosyltransfer to sinapic acid has a pH optimum near 7 and requires as SH group for activity, p-Chloromercuribenzoate (PCMB) inhibits activity, which can be restored by the addition of dithiothreitol (DTT). The formation of 1-sinapoylglucose was found to be a reversible reaction, since the addition of UDP results in a breakdown of the ester.
Hypocretin (Orexin) Levels in Cerebrospinal Fluid of Patients with Narcolepsy: Relationship to Cataplexy and HLA DQB1*0602 Status (2002)

Hypocretin (orexin) deficiency (< 40 pg/ml) is highly associated with narcolepsy with cataplexy (89.5%) and more specifically with patients with cataplexy who are HLA DQB1*0602 positive (95.7%). The relationship between hypocretin-1 levels and narcolepsy without cataplexy or the DQB1*0602 allele is less clear. This study compared cerebrospinal (CSF) hypocretin-1 in 13 patients with HLA DQB1*0602 allele and cataplexy to 4 HLA negative patients with cataplexy, 3 HLA positive patients without cataplexy, and 6 HLA negative patients without cataplexy, plus 15 neurologic controls. Data were collected at a sleep disorders center. Twenty-six patients with narcolepsy, with and without HLA DQB1*0602 and with and without cataplexy, as well as 15 neurologic controls. N/A Using analysis of variance techniques, statistically significant differences were found between the CSF hypocretin-1 levels in HLA positive patients and all other groups (P<0.01). Although the sample size was small, subjects with the DQB1*0602 allele without cataplexy had lower hypocretin-1 levels than did other groups (other than the HLA and cataplexy positive group). Hypocretin-1 levels were not associated with age at diagnosis, age at lumbar puncture, body mass index at time of diagnosis, or body mass index at time of lumbar puncture. This data confirms the previous finding that undetectable hypocretin-1 levels are highly specific for HLA positive narcolepsy with cataplexy. The data suggests that the pathophysiology and, by extension, etiology of this disorder are distinctly different from the other conditions studied. The relationship of the DQB1*0602 allele and reduced hypocretin-1 levels needs further study.
High On/Off Current Ratio p-InGaN/AlGaN/GaN HEMTs (2012)

An excellent on/off current ratio of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> and a nearly ideal subthreshold slope of 65 mV/dec was confirmed in a p-InGaN/AlGaN/GaN high-electron-mobility transistor. Favorable <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> - <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> characteristics were achieved with the p-InGaN cap layer under the gate electrode. A dry etching technique with a low-damage p-InGaN cap layer resulted in a significantly low leakage current of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-11</sup> A/mm.
Chromatin Mediation of a Transcriptional Memory Effect in Yeast (2015)

Previous studies have described a transcriptional "memory effect," whereby transcript levels of many Abf1-regulated genes in the budding yeast Saccharomyces cerevisiae are undiminished even after Abf1 has dissociated from its regulatory sites. Here we provide additional support for this effect and investigate its molecular basis. We show that the effect is observed in a distinct abf1 ts mutant from that used in earlier studies, demonstrating that it is robust, and use chromatin immunoprecipitation to show that Abf1 association is decreased similarly from memory effect and transcriptionally responsive genes at the restrictive temperature. We also demonstrate that the association of TATA-binding protein and Pol II decreases after the loss of Abf1 binding for transcriptionally responsive genes but not for memory effect genes. Examination of genome-wide nucleosome occupancy data reveals that although transcriptionally responsive genes exhibit increased nucleosome occupancy in abf1 ts yeast, the promoter regions of memory effect targets show no change in abf1 ts mutants, maintaining an open chromatin conformation even after Abf1 eviction. This contrasting behavior reflects different inherent propensity for nucleosome formation between the two classes, driven by the presence of A/T-rich sequences upstream of the Abf1 site in memory effect gene promoters. These sequence-based differences show conservation in closely related fungi and also correlate with different gene expression noise, suggesting a physiological basis for greater access to "memory effect" promoter regions. Thus, our results establish a conserved mechanism underlying a transcriptional memory effect whereby sequences surrounding Abf1 binding sequences affect local nucleosome occupancy following loss of Abf1 binding. Furthermore, these findings demonstrate that sequence-based differences in the propensity for nucleosome occupancy can influence the transcriptional response of genes to an altered regulatory signal.
CCN forwarding engine based on Bloom filters (2012)

The lack of scalable routing algorithms is one of the main obstacles that slow down a large deployment of Content Centric Networking on an Internet-scale. From one side, content based networking promises to solve the current problems of the Internet. On the other hand, instead, it requires routers to account for a very huge amount of content names. Bloom Filters are widely recognized as a possible solution to this limitation. At the same time, their adoption requires careful tuning rules and novel design methodologies. In this perspective, the present contribution proposes a Bloom Filter-based routing scheme for Content Centric Networking (CCN) and shows several preliminary observations about Bloom Filters size and signaling overhead.
Selection of working fluids for organic rankine cycle (ORC) in waste heat power generation system (2013)

Selection of working fluid is crucial in designing an ORC system. A selection process to get potential pure working fluids for medium-temperature ORC processes has been investigated. Stability, safety and environmental aspects were considered firstly. Then vapor specific volume, latent heat, normal boiling point and critical point of refrigerants and non-refrigerating fluids are analyzed and net power output and cycle efficiency of the ORC system were calculated. Finally, 17 pure fluids were selected for the heat sources of 420 K, 470 K and 520 K respectively. The results indicated that refrigerants such as R245fa, R245ca and R365mfc are good enough for recovering waste heat of temperature ranged from 350 K to 520 K and the optimal turbine inlet pressure was ranged from 1.0 to 1.5 MPa.
Histone Deacetylase Inhibitors Impair the Elimination of HIV-Infected Cells by Cytotoxic T-Lymphocytes (2014)

Resting memory CD4+ T-cells harboring latent HIV proviruses represent a critical barrier to viral eradication. Histone deacetylase inhibitors (HDACis), such as suberanilohydroxamic acid (SAHA), romidepsin, and panobinostat have been shown to induce HIV expression in these resting cells. Recently, it has been demonstrated that the low levels of viral gene expression induced by a candidate HDACi may be insufficient to cause the death of infected cells by viral cytopathic effects, necessitating their elimination by immune effectors, such as cytotoxic T-lymphocytes (CTL). Here, we study the impact of three HDACis in clinical development on T-cell effector functions. We report two modes of HDACi-induced functional impairment: i) the rapid suppression of cytokine production from viable T-cells induced by all three HDACis ii) the selective death of activated T-cells occurring at later time-points following transient exposures to romidepsin or, to a lesser extent, panobinostat. As a net result of these factors, HDACis impaired CTL-mediated IFN-c production, as well as the elimination of HIV-infected or peptide-pulsed target cells, both in liquid culture and in collagen matrices. Romidepsin exerted greater inhibition of antiviral function than SAHA or panobinostat over the dose ranges tested. These data suggest that treatment
CONTINUOUS PULSE OXIMETRY AND THE DIAGNOSIS OF PULMONARY EMBOLISM IN CRITICALLY ILL TRAUMA PATIENTS (1992)

The diagnosis of pulmonary embolism (PE) may be difficult to establish in trauma patients, particularly those who are unresponsive or mechanically ventilated. Based on a prior retrospective study, we hypothesized that patients monitored by continuous pulse oximetry who experienced a 10% or greater sudden sustained drop in arterial oxygen saturation (SaO2) without a change in static lung compliance (Cst) were most likely to have had a PE. We followed SaO2 in 972 patients admitted to our trauma ICU during the 18-month period ending in December 1990. Forty-eight patients (5%) with SaO2 changes, but no Cst changes, were evaluated for suspected PE using pulmonary arteriography (PA). Of these, 21 (44%) had a positive PA study. All patients with a positive PA had either clear chest roentgenograms or no change in underlying pulmonary pathologic processes. Of the remainder, 26 had evidence of a new pathologic entity on chest roentgenograms and only one patient had a SaO2 decrease, no change in Cst, and a negative PA. All mechanically ventilated trauma patients should have SaO2 monitored continuously. Patients with a > 10% drop in Sao2 with no change in Cst and no new roentgenographic chest findings should undergo PA. Based on our experience, this approach would yield a sensitivity, specificity, and predictive value of 100%, 99.9%, and 95%, respectively, for the diagnosis of clinically significant PE.
Semantic-Aware Generative Adversarial Nets for Unsupervised Domain Adaptation in Chest X-ray Segmentation (2018)

In spite of the compelling achievements that deep neural networks (DNNs) have made in medical image computing, these deep models often suffer from degraded performance when being applied to new test datasets with domain shift. In this paper, we present a novel unsupervised domain adaptation approach for segmentation tasks by designing semantic-aware generative adversarial networks (GANs). Specifically, we transform the test image into the appearance of source domain, with the semantic structural information being well preserved, which is achieved by imposing a nested adversarial learning in semantic label space. In this way, the segmentation DNN learned from the source domain is able to be directly generalized to the transformed test image, eliminating the need of training a new model for every new target dataset. Our domain adaptation procedure is unsupervised, without using any target domain labels. The adversarial learning of our network is guided by a GAN loss for mapping data distributions, a cycle-consistency loss for retaining pixel-level content, and a semantic-aware loss for enhancing structural information. We validated our method on two different chest X-ray public datasets for left/right lung segmentation. Experimental results show that the segmentation performance of our unsupervised approach is highly competitive with the upper bound of supervised transfer learning.
Tuning the electronic structure of graphene by ion irradiation (2008)

Mechanically exfoliated graphene layers deposited on ${\text{SiO}}_{2}$ substrate were irradiated with ${\text{Ar}}^{+}$ ions in order to experimentally study the effect of atomic scale defects and disorder on the low-energy electronic structure of graphene. The irradiated samples were investigated by scanning tunneling microscopy and spectroscopy measurements, which reveal that defect sites, besides acting as scattering centers for electrons through local modification of the on-site potential, also induce disorder in the hopping amplitudes. The most important consequence of the induced disorder is the substantial reduction in the Fermi velocity, revealed by bias-dependent imaging of electron-density oscillations observed near defect sites.
Ray tracing error correction in ophthalmic optics (1991)

Ray tracing error correction (RTEC), a new method for various refractive calculations, is introduced. It consists of two procedures: (1) ray tracing that determines whether the ray originating from an infinite point focuses on the fovea and (2) error correction that varies the curvature of the different refractive surfaces according to an error correction formula when the ray is not focused at the fovea. These calculations are continued until the ray is focused at the fovea. The refraction of Gullstrand's schematic eye at relaxation and at accommodation, the desired postoperative corneal curvature for postoperative emmetropia after corneal ablation surgery, and the intraocular power of convex-plano, biconvex, and plano-convex intraocular lenses are presented.
Tackling vitamin A deficiency with biofortified sweetpotato in sub-Saharan Africa (2017)

Orange-fleshed sweetpotato (OFSP) is a rich plant-based source of beta-carotene, which the body converts into vitamin A. In sub-Saharan Africa, sweetpotato is known as a food security crop but most varieties grown are high dry matter white-fleshed types, lacking beta-carotene. In 1995, researchers recognized the potential of OFSP varieties to address widespread vitamin A deficiency in SSA using an integrated agriculture-nutrition approach. With their partners, they confronted conventional wisdom concerning food-based approaches and institutional barriers, to build the evidence base and breed 42 OFSP varieties adapted to farmer needs and consumer preferences. Subsequently, a multi-partner, multi-donor initiative, launched in 2009, has already reached 2.8 million households. This review summarizes that effort describing how the changing policy environment influenced the process.
A 5K-gate bipolar masterslice LSI with a 500 ps loaded gate delay (1983)

A fully ECL-compatible 5K-gate bipolar subnanosecond masterslice has been developed for use in computer and communication systems. A new circuit design and a 1.5-/spl mu/m rule oxide isolation process employing three-level metallization have made possible a high performance of 0.32 pJ/gate and a small cell size of 3937.5 /spl mu/m/SUP 2/. An alterable configuration cell (ACC) circuit based on nonthreshold logic (NTL) is adopted as the basic internal cell. The masterslice has been applied to a dual 36-bit ALU consisting of 3486 cells. An unloaded gate delay of 320 ps and a loaded gate delay of 500 ps with a power dissipation of 1 mW/gate were obtained with a 15-stage ring oscillator and a 10-stage path delay in the 36-bit ALU.