Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermus thermophilus L11 Methyltransferase, PrmA, Is Dispensable for Growth and Preferentially Modifies Free Ribosomal Protein L11 Prior to Ribosome Assembly

ABSTRACT The ribosomal protein L11 in bacteria is posttranslationally trimethylated at multiple amino acid positions by the L11 methyltransferase PrmA, the product of the prmA gene. The role of L11 methylation in ribosome function or assembly has yet to be determined, although the deletion of Escherichia coli prmA has no apparent phenotype. We have constructed a mutant of the extreme thermophile Thermus thermophilus in which the prmA gene has been disrupted with the htk gene encoding a heat-stable kanamycin adenyltransferase. This mutant shows no growth defects, indicating that T. thermophilus PrmA, like its E. coli homolog, is dispensable. Ribosomes prepared from this mutant contain unmethylated L11, as determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and are effective substrates for in vitro methylation by cloned and purified T. thermophilus PrmA. MALDI-TOF MS also revealed that T. thermophilus L11 contains a total of 12 methyl groups, in contrast to the 9 methyl groups found in E. coli L11. Finally, we found that, as with the E. coli methyltransferase, the ribosomal protein L11 dissociated from ribosomes is a more efficient substrate for in vitro methylation by PrmA than intact 70S ribosomes, suggesting that methylation in vivo occurs on free L11 prior to its incorporation into ribosomes.
Synthetic Surfactants: The Search Goes on

When Avery and Mead1 first described surfactant deficiency as being responsible for hyaline-membrane disease, it seemed as if the therapeutic implications would be simple: Because we knew that pulmonary surfactant was made up primarily of phosphatidyl choline, perhaps administering a solution or aerosol of this readily available lipid to the surfactant-deficient lung should solve the problem. Unfortunately, this simplistic approach did not work regardless of whether surfactant was delivered to humans2 or animals.3 Improving the spreading characteristics by adding alcohols or altering the physical preparation improved the function somewhat,4,5 but the first dramatic effect on pulmonary function and survival was shown only with modified natural surfactants that had been extracted from lung minces6,7 and airway washes of animal lungs.8 Various head-to-head trials of natural versus synthetic surfactants have consistently favored the natural preparations.9 Accordingly, although 2 synthetic surfactant preparations (Exosurf and Pumactant) were approved for commercial distribution in the United States and Britain, respectively, Exosurf is no longer readily available in the United States, and Pumactant was recently removed from the market in Britain. The search for a synthetic preparation that is equivalent or superior to the animal-derived surfactants has continued, because there has always been concern about the potential antigenic and infectious complications that might be associated with animal-derived … Address correspondence to John Kattwinkel, MD, Department of Pediatrics, University of Virginia, Charlottesville, VA 22908. E-mail: jk3f{at}virginia.edu
Sensory substitution using 3-degree-of-freedom tangential and normal skin deformation feedback

During manual interactions, we experience both kinesthetic forces and tactile sensations. Friction and normal force between the fingerpads and the tool/interaction surfaces cause shear and normal deformation of the skin. Capitalizing on this observation, we designed a 3-degree-of-freedom (DoF) tactile device that is grasped by a user and can render both tangential skin stretch and normal deformation on the skin of the user's fingerpads. Tactile feedback from the device is delivered in a manner consistent with natural tactile cues from manual interaction. An experiment assessed the accuracy with which users can locate the center of a contoured hole on a virtual surface. The task was completed under four conditions: the cases of skin deformation and force feedback, with both 3- and 1-DoF feedback in each case. With 3-DoF feedback, users located the hole faster and more accurately than with 1-DoF feedback, for both force and skin deformation feedback. These results indicated that users were able to interpret the additional DoF cues provided by our 3-DoF tactile device to improve task performance.
Achieving Magnet Redesignation: A Framework for Cultural Change

Magnet recognition is the highest award that the ANCC bestows on an institution and exemplifies a hospital's accomplishments in providing commitment, support, and resources for nursing excellence throughout the organization. Magnet hospitals attain their status based on structure and outcome criteria known as the 14 Forces of Magnetism. The authors discuss one hospital's journey and the outstanding models integrated in their organization that paved the way for their first award, followed by their journey toward redesignation.
Measurement and Computer-Aided Modeling of Microstrip Discontinuities by an Improved Resonator Method

The broad-band characterization of microstrip discontinuities by an improved resonator technique is describecl. This technique involves hitherto unknown expressions accounting for nonsymmetrical gap coupling and employs an efficient error function for the computer-aided modeling of microstrip n-ports. It is applied to derive new analytical results for microstrip corners and chamfered right-angle bends.
Small Molecule Disruption of Gβγ Signaling Inhibits the Progression of Heart FailureNovelty and Significance

Rationale: Excess signaling through cardiac Gβγ subunits is an important component of heart failure (HF) pathophysiology. They recruit elevated levels of cytosolic G protein–coupled receptor kinase (GRK)2 to agonist-stimulated β-adrenergic receptors (β-ARs) in HF, leading to chronic β-AR desensitization and downregulation; these events are all hallmarks of HF. Previous data suggested that inhibiting Gβγ signaling and its interaction with GRK2 could be of therapeutic value in HF. Objective: We sought to investigate small molecule Gβγ inhibition in HF. Methods and Results: We recently described novel small molecule Gβγ inhibitors that selectively block Gβγ-binding interactions, including M119 and its highly related analog, gallein. These compounds blocked interaction of Gβγ and GRK2 in vitro and in HL60 cells. Here, we show they reduced β-AR–mediated membrane recruitment of GRK2 in isolated adult mouse cardiomyocytes. Furthermore, M119 enhanced both adenylyl cyclase activity and cardiomyocyte contractility in response to β-AR agonist. To evaluate their cardiac-specific effects in vivo, we initially used an acute pharmacological HF model (30 mg/kg per day isoproterenol, 7 days). Concurrent daily injections prevented HF and partially normalized cardiac morphology and GRK2 expression in this acute HF model. To investigate possible efficacy in halting progression of preexisting HF, calsequestrin cardiac transgenic mice (CSQ) with extant HF received daily injections for 28 days. The compound alone halted HF progression and partially normalized heart size, morphology, and cardiac expression of HF marker genes (GRK2, atrial natriuretic factor, and β-myosin heavy chain). Conclusions: These data suggest a promising therapeutic role for small molecule inhibition of pathological Gβγ signaling in the treatment of HF.
EMR usability: bridging the gap between nurse and computer.

H ealth information technology (HIT) and electronic medical record (EMR) adoption within hospitals, physician practices, long-term-care facilities, and home health agencies has been growing as care providers seek to improve workflow efficiencies and the quality of patient care. This growth is expected to increase as the healthcare industry receives over $20 billion in research and incentive funding from the American Recovery and Reinvestment Act of 2009 to stimulate automation and the meaningful use of EMRs. With over 2.5 million RNs making up over a third of the healthcare workers in the United States today, the increase in HIT and EMR adoption places nurses in a key end-user role.1,2 Ensuring usability of EMRs is essential for all nurses on the front lines of healthcare delivery because it will lead to increased enduser satisfaction and productivity and reduced training hours, costs, and HIT unintended consequence errors. Usability bridges the gap between people and machines, promising the completion of tasks with minimum effort, maximum end-user satisfaction, and reduced errors and increased patient safety through enabling and ensuring the correct use of systems.3 Usability also allows nurses to focus on their patients rather than the technology.4 As adoption of EMRs increases, the nursing profession must understand basic usability principles; look for these principles when selecting EMR systems; demand usability by engaging system analysts, developers, and vendors when articulating workflow requirements; and follow and support the industry’s usability activities.
A Comparative Proteomic Strategy for Subcellular Proteome Research

Subcellular proteomics, as an important step to functional proteomics, has been a focus in proteomic research. However, the co-purification of “contaminating” proteins has been the major problem in all the subcellular proteomic research including all kinds of mitochondrial proteome research. It is often difficult to conclude whether these “contaminants” represent true endogenous partners or artificial associations induced by cell disruption or incomplete purification. To solve such a problem, we applied a high-throughput comparative proteome experimental strategy, ICAT approach performed with two-dimensional LC-MS/MS analysis, coupled with combinational usage of different bioinformatics tools, to study the proteome of rat liver mitochondria prepared with traditional centrifugation (CM) or further purified with a Nycodenz gradient (PM). A total of 169 proteins were identified and quantified convincingly in the ICAT analysis, in which 90 proteins have an ICAT ratio of PM:CM >1.0, while another 79 proteins have an ICAT ratio of PM:CM <1.0. Almost all the proteins annotated as mitochondrial according to Swiss-Prot annotation, bioinformatics prediction, and literature reports have a ratio of PM:CM >1.0, while proteins annotated as extracellular or secreted, cytoplasmic, endoplasmic reticulum, ribosomal, and so on have a ratio of PM:CM <1.0. Catalase and AP endonuclease 1, which have been known as peroxisomal and nuclear, respectively, have shown a ratio of PM:CM >1.0, confirming the reports about their mitochondrial location. Moreover, the 125 proteins with subcellular location annotation have been used as a testing dataset to evaluate the efficiency for ascertaining mitochondrial proteins by ICAT analysis and the bioinformatics tools such as PSORT, TargetP, SubLoc, MitoProt, and Predotar. The results indicated that ICAT analysis coupled with combinational usage of different bioinformatics tools could effectively ascertain mitochondrial proteins and distinguish contaminant proteins and even multilocation proteins. Using such a strategy, many novel proteins, known proteins without subcellular location annotation, and even known proteins that have been annotated as other locations have been strongly indicated for their mitochondrial location.
Biochemical properties of purified human terminal deoxynucleotidyltransferase.

The kinetic mechanism and limited substrate specificity of purified terminal deoxynucleotidyltransferase from human leukemic cells is described. The reaction which utilizes two substrates, dATP as monomer, and p(dA), as initiator (where n is the chain length from 4 through 50), proceeds by a rapid equilibrium random mechanism. The polymerization reaction occurs only in the presence of a divalent metal cation, with an order of specificity: M 8 + > Zn2+ > Co2+ > Mn2+. The K,,, and V,,, values for oligodeoxyadenylates in the range n = 6 through 50 indicate that affinity of the enzyme for the growing chain and the corresponding rate of polymerization are directly proportional. The apparent deviation in substrate utilization by the human enzyme as compared with the calf enzyme occurs at the tetranucleotide level, in which the binding constant differs by more than 2 orders of magnitude over the K,,, for initiators which have more than 5 nucleotide residues. Model kinetic systems utilizing p(dA)m and dATP-Mg provide no evidence that the binding of one substrate facilitates or hinders the addition of the second substrate for this random mechanism, and dissociation constants are identical to the limiting Michaelis constants (&ATP = 110 p~ and K p ( d A ) s = 0.4 PM). A metal site (possibly zinc) on the enzyme, which is distinct from the divalent cation requirement for deoxynucleoside 5’-triphosphates, is implicated from studies with the metal chelators, o-phenanthroline, a,a’-bipyridyl, and EDTA. The putative metal site on the enzyme appears to be in the vicinity of the initiator binding site rather than at the nucleotide binding site. An energy of activation for the human terminal transferase reaction was determined to be 18.6 kcal, and the temperature at which all enzymatic reactions are conducted in these studies (35°C) falls within the linear region of an Arrhenius plot.
A STUDY ON THE PHOTO RESPONSE NON-UNIFORMITY NOISE PATTERN BASED IMAGE FORENSICS IN REAL-WORLD APPLICATIONS

In this paper, we study Photo Response Non-Uniformity (PRNU) based image tampering detection methods and their applicability in real-world image tampering detection applications. Experiments using current PRNU based image forensic methods were conducted to evaluate the performance of existing methods in the realistic applications. The PRNU based forensic approach was tested on the images taken by cameras including current and popular DSLR/sub-DSLR models which have rarely been tested and reported. In our experiments, over 800 PRNU noise patterns are generated from 80 authentic photos and the biometric-like experiments have been conducted to study the similarities between intra-class and inter-class PRNU noise patterns. The analysis for the performance of current methods and the suggestions for the further research and development towards PRNU based image forensic approach are presented.
Ingeniería de Software e Ingeniería del Conocimiento: Reporte de las JIISIC-CEIS’2015

En el presente documento se presenta el reporte de las XI Jornadas Iberoamericanas de Ingenieria de Software e Ingenieria del Conocimiento asi como del Congreso Ecuatoriano en Ingenieria de Software, celebrados en la Escuela Superior Politecnica de Chimborazo (ESPOCH) los dias 4 y 5 de junio de 2015. De un total de 28 trabajos enviados, en esta edicion se han aceptado 16. En este documento se presentan los titulos y resumenes de los trabajos aceptados.
Local Ecological Knowledge (LEK) on Fish Behavior Around Anchored FADs: the Case of Tuna Purse Seine and Ringnet Fishers from Southern Philippines

Abstract The Fishing Industry in the Philippines plays an important role in the food and employment need of Filipino fishers. By using anchored Fish Aggregating Devices (FADs or payao), the Philippine tuna fisheries was transformed into a million-dollar industry. Minimal studies on exploitation rates and fish behaviour around anchored FADs hampered further understanding of this fishery practice. Studies on fish behavior using Local Ecological Knowledge (LEK) are good complement where data is limited. A study using semi-structured interview (n=46) and three focus group discussions (n=39 participants) to record fishers’ knowledge and observations on the behavior of different fish species around anchored FADs was conducted. This particularly focused on attraction, retention, and departure behaviour of fishes in identified FAD sites. Based on the fishers’ knowledge, tuna schools are attracted to anchored FADs at 10 km distance. In anchored FADs, tuna form schools segregated by species and size. There was no relationship between the attraction distance and the reported school size and the various waiting times for fish to aggregate below the FADs. There was no variation between the species present at day or night time although fishers have reported a distinction of species found near the surface (0-10 m) and those found at other depths (11-20 m). Juvenile yellowfin tuna (Thunnus albacares), skipjack (Katsuwonus pelamis) and frigate and bullet tunas (Auxis spp.) are found to stay at 25-50 m from the FAD at a depth of >20 m. Adult oceanic tunas reside in deeper waters (75 m). The fish visual census produced similar results with the semi-structured interviews and FGDs but did not observe oceanic tunas at depths of 15-20 m in the anchored FADs examined.
(cid:1) -Adrenoceptor stimulation of alveolar ﬂuid clearance is increased in rats with heart failure

-Adrenoceptor stimulation of alveolar ﬂuid clearance is increased in rats with heart failure. Am J Physiol Lung Cell Mol Physiol 297: L487–L495, 2009. alveolar epithelium plays a critical role in resolving pulmonary edema. We thus hypothesized that its function might be upregulated in rats with heart failure, a condition that severely challenges the lung’s ability to maintain ﬂuid balance. Heart failure was induced by left coronary artery ligation. Echocardiographic and cardiovascular hemodynamics con-ﬁrmed its development at 16 wk postligation. At that time, alveolar ﬂuid clearance was measured by an increase in protein concentration over 1 h of a 5% albumin solution instilled into the lungs. Baseline alveolar ﬂuid clearance was similar in heart failure and age-matched control rats. Terbutaline was added to the instillate to determine whether heart failure rats responded to (cid:1) -adrenoceptor stimulation. Alveolar ﬂuid clearance in heart failure rats was increased by 194% after terbutaline stimulation compared with a 153% increase by terbutaline in control rats. To determine the mechanisms responsible for this accelerated alveolar ﬂuid clearance, we measured ion transporter expression (ENaC, Na-K-ATPase, CFTR). No signiﬁcant upregulation was observed for these ion transporters in the heart failure rats. Lung morphology showed signiﬁcant alveolar epithelial type II cell hyperplasia in heart failure rats. Thus, alveolar epithelial type II cell hyperplasia is the likely explanation for the increased terbutaline-stimulated alveolar ﬂuid clearance in heart failure rats. These data provide evidence for previously unrecognized mechanisms that can protect against or hasten resolution of alveolar edema in heart failure.
Adder circuits with transistors using independently controlled gates

Circuits with transistors using independently controlled gates have been proposed to reduce the number of transistors and to increase the logic density per area. So far only small building blocks have been presented. This paper investigates for the first time the use of independent double gate transistors in 16 bit ripple carry and parallel prefix adders. New adder circuits and the trade-off between area reduction, delay and power consumption are presented. Area and transistor count reduction by one third can be achieved.
Crystallographic evidence for dual coordination around zinc in the T3R3 human insulin hexamer.

The T3R3 human insulin hexamer (T and R referring to extended and alpha-helical conformations, respectively, of the first eight residues of the B-chain), complexed to two zinc ions, crystallizes in space group R3 with hexagonal cell constants a = 80.64 and c = 37.78 A. The structure has been refined to a residual of 0.172 using 9225 independent data to 1.6-A resolution. The asymmetric unit consists of a TR dimer, and the insulin hexamer is generated by the action of the crystallographic 3-fold axis. The conformation of one insulin trimer is nearly identical to that of the T6 hexamer, while the other trimer approximates that of the R6 hexamer, except for the three N-terminal B-chain residues that adopt an extended rather than an alpha-helical conformation. Each of the two zinc ions, which lie on the crystallographic 3-fold axis and exhibit two different, disordered coordination geometries, is coordinated by the imidazole groups of three symmetry-related B10 histidine residues. The coordination sphere of the zinc in the T3 trimer is either tetrahedral, with the fourth site filled by a chloride ion, or octahedral, completed by three water molecules. The coordination of the zinc in the 12-A narrow channel in the R3 trimer is tetrahedral, with either a second chloride ion or a water molecule completing the coordination sphere. The putative off-axial zinc binding sites that result from the T-->R transition of monomer II do not contain zinc ion, but instead are filled with clusters of ordered water molecules. (ABSTRACT TRUNCATED AT 250 WORDS)
Inferring Landmarks for Pedestrian Navigation from Mobile Eye-Tracking Data and Google Street View

While it has been well established that incorporating landmarks into route descriptions enhances understanding and performance of wayfinding, only a very few available systems make use of them. This is primarily due to the fact that landmark data is often not available, and the creation of the data is connected to tedious manual labor. Prior work explored crowd-sourced approaches to collect landmark data, but most of that work focused on explicit user input to gather the data. In this paper, we presented our work towards a system to automatically infer suitable landmarks for pedestrian navigation instructions from mobile eye-tracking data. By matching the video feed of the scene camera of a head-mounted eye tracker to Google Street View imagery, our system is able to cluster the visual attention of the users and extract suitable landmarks from it. We present early results of a field study conducted with six participants to highlight the potential of our approach.
Throw In Attempt Card Corner Free Kick Goal

Detection of concepts, or actions, within a video is a challenging and important task. Detecting concepts as simple as a person walking or as subtle as a wheel turning is challenging for many reasons. We introduce a method to improve concept detection through the use of known temporal relationships between concepts. We compare our approach with baseline concept detection accuracies to show that the notion of temporal relationships is beneficial to the task of concept detection. We apply our method to two datasets TRECVID and a self-annotated soccer dataset. Each dataset shows varying levels of improvement and helps to indicate the generality of our approach.