Miracle-dz/UniFAR-FTUs huggingface dataset:
Iowa State University From the SelectedWorks of Zengyi Shao 2009 DNA assembler , an in vivo genetic method for rapid construction of biochemical pathways

The assembly of large recombinant DNA encoding a whole biochemical pathway or genome represents a significant challenge. Here, we report a new method, DNA assembler, which allows the assembly of an entire biochemical pathway in a single step via in vivo homologous recombination in Saccharomyces cerevisiae. We show that DNA assembler can rapidly assemble a functional D-xylose utilization pathway (~9 kb DNA consisting of three genes), a functional zeaxanthin biosynthesis pathway (~11 kb DNA consisting of five genes) and a functional combined D-xylose utilization and zeaxanthin biosynthesis pathway (~19 kb consisting of eight genes) with high efficiencies (70–100%) either on a plasmid or on a yeast chromosome. As this new method only requires simple DNA preparation and one-step yeast transformation, it represents a powerful tool in the construction of biochemical pathways for synthetic biology, metabolic engineering and functional genomics studies.
Pulmonary function and long‐term follow‐up of children with tracheobronchomalacia

Primary tracheobronchomalacia (TBM) is a disease of the large airways. Long‐term follow‐up studies of TBM patients have not been reported. This study was undertaken to further elicit the natural history of this condition and the presence of concomitant reactive airways disease through clinical profiling and pulmonary function testing.
Number of distal limb and brachial pressure measurements required when diagnosing peripheral arterial disease by laser Doppler flowmetry

We examine the reliability of single and repeated blood pressure measurements at ankle, toe, and arm levels for the diagnosis of peripheral arterial disease (PAD) by laser Doppler flowmetry. Segmental pressures were measured in 200 patients with known or suspected PAD. Segmental indices were calculated using (1) one measurement [M-1], two measurements [M-2], or by a predefined reproducibility criterion (RC) as well as (2) by using one brachial blood-pressure (BBP-one) or correspondent to each segmental pressure (BBP-all) as reference. The agreement in diagnosis of PAD by Cohen's Kappa was κ = 0.930 when comparing RC to M-1, and κ = 0.977 when comparing RC to M-2. The same comparison showed excellent relative reliability for segmental indices (all intra-class correlation coefficients (ICC) ≥ 0.980). Diagnostic classification agreement for BBP-all versus BBP-one were κ = 0.831 for RC, κ = 0.804 for M-1, and κ = 0.847 for M-2. The relative reliability analysis showed excellent correlation in segmental indices (all ICC ≥ 0.957). The study shows minimal difference in segmental indices and diagnostic classification when comparing calculations based on the listed strategies. However, the study indicated that it is important to measure BBPs correspondent to each segmental pressure.
Drinking-Water Distribution, Sewage, and Rainfall Collection, Third Edition

Drinking Water Distribution, Sewage, and Rainfall Collection is the first textbook produced in French and English entirely devoted to practical hydraulic problems as they occur in modern cities. It looks at the design and application of equipment for drinking water distribution, runoff and sewage collection. Fundamental hydraulic principles are presented clearly and their application is illustrated in examples representative of real-world situations. Exercises and problems enable students to test their knowledge in each chapter. Specific topics include the measurement of sewage flow, sewage pumping stations, pump selection, inverted siphon, and characteristics of pipes available on the market in a wide variety of materials. The textbook also covers issues such as water hammer and other overpressures, dead and live loads, underground pipe installation, water supply to high rise buildings, the design of sewer and water service connections, water flows and volumes for fire fighting, water intake and intake pipes, fire hydrants, water inlets and valve settings on water networks, sewage outfall, pipe freezing and corrosion, thrust blocks and restrained joints, culverts, etc. One chapter is entirely devoted to waterborne diseases, chemical contaminants and dangerous gases that accumulate in enclosed spaces. Engineers, technicians and scientists can use the textbook to learn the basic requirements for designing and evaluating sanitary storm networks, sewage networks and water distribution networks.
Is anthropogenic sea level fingerprint already detectable in the Pacific Ocean?

Sea level rates up to three times the global mean rate are being observed in the western tropical Pacific since 1993 by satellite altimetry. From recently published studies, it is not yet clear whether the sea level spatial trend patterns of the Pacific Ocean observed by satellite altimetry are mostly due to internal climate variability or if some anthropogenic fingerprint is already detectable. A number of recent studies have shown that the removal of the signal corresponding to the Pacific Decadal Oscillation (PDO)/Interdecadal Pacific Oscillation (IPO) from the observed altimetry sea level data over 1993–2010/2012 results in some significant residual trend pattern in the western tropical Pacific. It has thus been suggested that the PDO/IPO-related internal climate variability alone cannot account for all of the observed trend patterns in the western tropical Pacific and that the residual signal could be the fingerprint of the anthropogenic forcing. In this study, we investigate if there is any other internal climate variability signal still present in the residual trend pattern after the removal of IPO contribution from the altimetry-based sea level over 1993–2013. We show that subtraction of the IPO contribution to sea level trends through the method of linear regression does not totally remove the internal variability, leaving significant signal related to the non-linear response of sea level to El Niño Southern Oscillation (ENSO). In addition, by making use of 21 CMIP5 coupled climate models, we study the contribution of external forcing to the Pacific Ocean regional sea level variability over 1993–2013, and show that according to climate models, externally forced and thereby the anthropogenic sea level fingerprint on regional sea level trends in the tropical Pacific is still too small to be observable by satellite altimetry.
Iterative fireworks algorithm with fuzzy coefficients

Themain aim of this paper is to use fuzzy inference systems for controlling the relevant parameters within the equations of the FWA algorithm. In other words, parameters that are considered constant in the traditional FWA and are now made dynamic by using fuzzy logic. It is worth mentioning that we also made a small modification to the algorithm with the goal of having a better performance and the modification was to change the stopping criteria of the algorithm. In the conventional fireworks algorithm (FWA) the stopping criteria is based on the function evaluations, including, some variations or modifications of the FWA but they also manage this in the same way. We propose a stopping criteria based on the iterations with the goal of having a more precise control and consequently, have a better way to control the output variables in a Fuzzy Inference System (FIS) of Mamdani type, since the number of iterations is used as the input variable. To demonstrate the validity of this modification we tested the algorithm with 12 benchmark functions with good results, and we call the proposed algorithm as Iterative Fuzzy Fireworks Algorithm and we denoted as IFFWA.
Factors that influence the detection of psychological problems in adolescents attending general practices.

BACKGROUND Epidemiological studies indicate that the prevalence of psychological problems in patients attending primary care services may be as high as 25%. AIM To identify factors that influence the detection of psychological difficulties in adolescent patients receiving primary care in the UK. DESIGN OF STUDY A prospective study of 13-16 year olds consecutively attending general practices. SETTING General practices, Norfolk, UK. METHOD Information was obtained from adolescents and parents using the validated Strengths and Difficulties Questionnaire (SDQ) and from GPs using the consultation assessment form. RESULTS Ninety-eight adolescents were recruited by 13 GPs in Norfolk (mean age = 14.4 years, SD = 1.08; 38 males, 60 females). The study identified psychological difficulties in almost one-third of adolescents (31/98, 31.6%). Three factors significant to the detection of psychological disorders in adolescents were identified: adolescents' perceptions of difficulties according to the self-report SDQ, the severity of their problems as indicated by the self-report SDQ, and whether psychological issues were discussed in the consultation. GPs did not always explore psychological problems with adolescents, even if GPs perceived these to be present. Nineteen of 31 adolescents with psychological difficulties were identified by GPs (sensitivity = 61.2%, specificity = 85.1%). A management plan or follow-up was made for only seven of 19 adolescents identified, suggesting that ongoing psychological difficulties in many patients are not being addressed. CONCLUSIONS GPs are in a good position to identify psychological issues in adolescents, but GPs and adolescents seem reluctant to explore these openly. Open discussion of psychological issues in GP consultations was found to be the most important factor in determining whether psychological difficulties in adolescents are detected by GPs.
Renale Sympathikusdenervierung 2014 in Österreich: Update der Empfehlungen der Öster- reichischen Gesellschaft für Hypertensiologie

Renal Sympathetic Denervation in Austria 2014: Update of the Recommen- dations of the Austrian Society of Hyperten- sion. If elevated blood pressure cannot be con- trolled, short- and mid-term cardiovascular prog- noses are poor in patients with resistant hyper- tension (blood pressure uncontrolled with  3 antihypertensive, adequately dosed drugs), but in particular in patients with refractory hypertension (blood pressure uncontrolled with  5 antihyper- tensive drugs in adequate dose). Renal sympathetic denervation (RSD) is a novel interventional technique to deliver radiof- requency or ultrasound energy into the lumen of the renal arteries to ablate sympathetic fibers lo- cated in the adventitia of the vessel. Presumably mediated by a reduction in sympa- thetic tone, pronounced reductions in office blood pressure could be observed following RSD in the initial, uncontrolled, clinical trials, in one small randomised trial, and in registries. A small ran- domized trial showed a smaller, but clinically rel- evant reduction in 24-hour blood pressure. A new randomized, double-blind, controlled trial (sham treatment in the control group) showed a lower reduction in office and 24-hour blood pressure at 6 months following RSD, as compared to previous studies, with no significant differences in blood pressure reduction between the RSD group and the sham group in the over- all study population (but with a significant differ- ence favoring RSD in caucasian patients). In this trial, RSD was free of relevant side effects at 6 months. The present position paper of the Austrian So- ciety of Hypertension's working group on RSD recommends the following considerations with respect to RSD, amending previous statements of the Society: due to the high risk of refractory hypertension (uncontrolled blood pressure with  5 drugs), RSD can be discussed for selected patients of this group and performed, following careful cost-benefit analysis. Conditio sine qua non is a 24-hour mean blood pressure > 145/90 mmHg and consideration of the requirements as outlined in this article. J Hypertonie 2014; 18 (2): 54-60.
AIS Electronic

Information Systems (IS) have never been more important as digital technologies are essential for business model innovation by developing new digital products and services. Digital transformation not only affects business, but also IT. While digital transformation and digital technologies are well established research areas, the implications of digital transformation on IT are rarely in focus. Taking this topic as a reference, the paper contributes to general IS research by assessing to which extent digital innovation is already subject to mainstream IS research. A bibliometric study analyzing all 2,833 articles published in the AIS Senior Scholars’ 'basket' of eight leading IS journals between 2007 and 2016 reveals that a mere 0.2% address the impact of digital transformation on IT while 2.3% cover topics of digital transformation, innovation, or digital technologies. In contrast to previous work, this study finds that digital innovation research is already present in primarily high-ranked IS journals.
Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed.
Draft , August 21 2015 Expectation Driven Learning of Phonology *

Expectation Driven Learning of Phonology Gaja Jarosz Abstract This paper develops a novel approach to learning phonological hidden structure relying on underexplored expectation driven learning strategies rooted in the machine learning literature. A novel probabilistic grammatical representation that enables estimation of expectation driven learning updates, and two learning algorithms utilizing these updates, are introduced. The algorithms are shown to surpass the performance of existing error-driven learning models on a large test system with hidden metrical structure. The paper then shows that the learning strategies are fully general and can also be successfully applied to learning of an entirely different sort of hidden structure created by unknown underlying representations.
Discrete camera calibration from the information distance between pixel streams

We consider the problem of estimating the relative orientation of a number of individual photocells-or pixels-that hold fixed relative positions. The photocells measure the intensity of on a pencil of lines. We assume that the light-field thus sampled is changing, e.g. as the result of motion of the sensors and use the obtained measurements to estimate the orientations of the photocells. We explore an information-theoretic and geometric approach: based on real-world data, we build anon-parametric functional relation linking the information distance between the data streams of two photocells, and the angular separation between the photocells. Then, given data streams produced by arrays of pixels in similar conditions, we use the functional relation to estimate the angles between pixels. Finally, we embed the estimated angles in the unit 3D sphere to obtain the estimated layout of the array.
Use of Variable Selection in Modeling the Secondary Structural Content of Proteins from Their Composition of Amino Acid Residues

The possibility of prediction of protein secondary structure content from composition of their amino acid residues can help in bridging the gap between proteins of known primary sequence having an unknown secondary structure. Almost all recently published models for understanding the relationship between composition (frequency of occurrence) of amino acid residues and secondary structure content of proteins involved composition of all 20 amino acid residues. However, it is well-known that many amino acid residues are mutually similar according to their physicochemical properties (hydrophobicity, hydrophilicity, charge, size, etc.). Because of that, we were motivated to investigate the possibility of reduction of the total number of terms (frequencies of amino acid residues) in the models for describing the relation between the composition of amino acid residues and the percentage of residues belonging to alpha, beta, and coil secondary structure. For this purpose, the CROMRsel algorithm (J. Chem. Inf. Comput. Sci. 1999, 39, 121-132) for selection of a small subset of the most important variables/descriptors into the multiregression (MR) models, i.e., frequency of occurrence of amino acid residues in proteins, was used. Analysis was performed on a data set containing 475 proteins, taken from Proteins 1996, 25, 157-168. A complete data set was partitioned into a 317-protein training set and 158-protein test set. The best possible linear models containing I=1, . , 20 frequencies were selected among all 20 frequencies of occurrence of amino acid residues on the 317-protein training set, and were used for performing prediction of the corresponding percentage of secondary structure content on the 158-protein test set. For the 317-protein data set the best selected concise models for the alpha, beta, and coil secondary structure contain only 9, 5, and 8 frequencies, respectively. Selected concise models are of the same or better fitted, cross-validated, and predictive statistical parameters than the models containing all 20 frequencies. Additionally, for each I (I=1, ., 20) 30 the best possible random models were selected. In each case, the best possible real models are much better than each of the best possible random models, showing clearly that there is no risk of a chance correlation (what one could expect due to the application of an exhaustive search for the best model having I frequencies among all 20! /I! (20-I)! possible models). Finally, the best selected models on the complete 475-protein data set for the alpha, beta, and coil secondary structure contain only 7, 4, and 7 frequencies of amino acid residues, respectively. These models are much simpler and have better fitted and cross-validated errors than the corresponding models from the literature, that were obtained without using a procedure for selection of the most important frequencies of amino acid residues in proteins.
Abortion and women's roles in society: opinions from Tlaxcala, Mexico.

OBJECTIVE We aim to assess the opinions of Mexicans in the state of Tlaxcala on abortion and other topics concerning women's reproductive health and status in society. MATERIAL AND METHODS We summarize opinions on abortion and women's roles in society and perform logit regressions to assess characteristics correlated with support for abortion rights. RESULTS A majority of respondents were against a woman's right to abortion when asked generally, but when asked about specific circumstances, a majority supported the right to abortion in five of the nine hypothetical circumstances proposed. In multivariate analysis, age, education, religion, religious service attendance, and views regarding women's roles in society had significant effects on support for the right to abortion. CONCLUSIONS Our results demonstrate that residents of Tlaxcala view abortion as a personal decision and support a woman's right to abortion in more circumstances than currently allowed under state law.
Audiovisual speech inversion by switching dynamical modeling governed by a Hidden Markov process

We propose a unified framework to recover articulation from audiovisual speech. The nonlinear audiovisual-to-articulatory mapping is modeled by means of a switching linear dynamical system. Switching is governed by a state sequence determined via a Hidden Markov Model alignment process. Mel Frequency Cepstral Coefficients are extracted from audio while visual analysis is performed using Active Appearance Models. The articulatory state is represented by the coordinates of points on important articulators, e.g., tongue and lips. To evaluate our inversion approach, instead of just using the conventional correlation coefficients and root mean squared errors, we introduce a novel evaluation scheme that is more specific to the inversion problem. Prediction errors in the positions of the articulators are weighted differently depending on their relevant importance in the production of the corresponding sound. The applied weights are determined by an articulatory classification analysis using Support Vector Machines with a radial basis function kernel. Experiments are conducted in the audiovisual-articulatory MOCHA database.
Factors affecting the electrofusion of mouse and ferret oocytes with ferret somatic cells

The domestic ferret, Mustela putorius furos, holds great promise as a genetic model for human lung disease, provided that key technologies for somatic cell nuclear transfer (SCNT) are developed. In this report, we extend our understanding of SCNT in this species by defining conditions for efficient cell fusion by electrical pulse. Two experimental systems were employed in this study. First, in vivo‐matured mouse oocytes and ferret somatic cells were used to establish general parameters for fusion. One fibroblast, or cumulus cell, was agglutinated to nucleate, zona pellucida‐free, mouse oocytes, and subjected to an electrical pulse. Similar electrical pulse conditions were also tested with 1 or 2 somatic cells inserted into the perivitelline space (PVS) of intact mouse oocytes. The fusion rate for a single fibroblast with a zona‐free oocyte was 80.2%, significantly higher (P < 0.05) than that observed for 1, or 2, fibroblasts placed in the PVS (52.0% and 63.8%, respectively). The fusion rate (44.1%) following insertion of two cumulus cells was significantly higher (P < 0.05) than that following insertion of one cumulus cell (25.1%). Second, in vitro‐matured ferret oocytes were enucleated, and one to three fibroblasts or cumulus cells were inserted into the PVS. Zona pellucida‐free ferret oocytes were fragile and excluded from the study. The fusion rates with two or three fibroblasts were 71.4% and 76.8%, respectively; significantly higher (P < 0.05) than that for one fibroblast (48.6%). This cell number‐dependent difference in fusion efficiency was also observed with cumulus cells. Fusion‐derived (ferret–ferret) NT embryos cleaved, formed blastocysts in vitro, and underwent early‐stage fetal development following embryo transfer. The rate of development was cell type‐independent, in contrast to the cell type‐dependent differences observed in fusion efficiency. In conclusion, fibroblasts fused more efficiently than cumulus cells and the efficiency of single cell fusions was improved when two or more cells were inserted into the PVS. These studies define conditions for efficient cell fusion with ferret oocytes and should facilitate SCNT and the development of genetically defined animal models in this species. © 2005 Wiley‐Liss, Inc.