cssi/SciSciGPT-SciSciNet huggingface dataset:
Habituating multiple model predictive control for blood glucose regulation in the ICU

A habituating multiple model predictive controller (MMPC) is developed by combining the habituating model predictive control law and multiple-model Kalman filter predictor. The habituating control is applied to blood glucose regulation in the intensive care unit, and includes both IV glucose input and IV insulin infusion in order to provide nutrition supply and improve disturbance rejection. The performance of Habituating MMPC is compared with Habituating MPC, SISO MMPC and SISO MPC on their ability to regulate BG for the fifteen in silico patients and to reject insulin sensitivity variation. The simulation results indicate that the Habituating MMPC strategy outperforms the other three control strategies by providing the tightest glucose control for a patient population, and producing the least amount of glucose variability while rejecting disturbances in insulin sensitivity.
Annular pancreas in adults.

OBJECTIVE. The purpose of this study was to review the CT, MRI, and ERCP findings of annular pancreas in adults.MATERIALS AND METHODS. A search of the radiology and ERCP databases at our institution for cases of annular pancreas in adults yielded the records of 42 patients who underwent 29 ERCP, 22 CT, and 13 MRI examinations. The CT and MR images were reviewed by two readers, and consensus agreement was reached regarding the shape of the pancreas, anatomic configuration of the ducts, and presence of disease. In addition, the degree of encirclement of the second part of the duodenum by the pancreatic head was evaluated in 24 patients with the CT or MRI finding of annular pancreas and in 30 control patients who were found not to have annular pancreas at ERCP.RESULTS. Nine of 24 (37.5%) cases of annular pancreas detected with CT or MRI did not have a radiologically complete ring of pancreatic tissue surrounding the second part of the duodenum. Three of the nine patients (33%) with radiologically incomplete ...
Dicer-substrate siRNA inhibits tumor necrosis factor alpha secretion in Kupffer cells in vitro: In vivo targeting of Kupffer cells by siRNA-liposomes

Tumor necrosis factor alpha (TNF-α) plays a major role in the pathogenesis of many inflammatory diseases. Neutralizing TNF-α by antibodies or antisense oligodeoxynucleotides, alleviate disease symptoms. In this study, we introduce the new generation of gene-silencing molecules, namely the small interfering RNAs (siRNAs) to reduce TNF-α. Although siRNAs of 19-21bp are commonly used, it is reported that longer siRNAs have much higher efficacies. Here, we report the identification of a 27-mer Dicer-substrate siRNA (DsiRNA) against TNF-α mRNA. Primary cells of rat Kupffer cells were transfected with five 27-mer siRNA constructs (si27-1, si27-2 si27-3, si27-4 and si27-5) for 24h, following which, TNF-α secretion was induced by exposure to LPS (0.1μg/ml) for 2h. TNF-α released to the medium was measured by ELISA. Of the five si27 constructs, si27-3 had the highest inhibitory effect on TNF-α secretion. At 10nM, si27-3 inhibited TNF-α secretion by 80% compared to a 60% inhibition by a 21-mer (SSL3). Following encapsulation in anionic liposomes, si27-3 at 100μg/kg body weight, on two successive days by intravenous administration, inhibited the secretion of TNF-α by 50%. These data demonstrate the identification of a highly efficacious siRNA formulation, which can be used in the treatment of TNF-α mediated diseases.
Comparative control strategies for roller shades with respect to daylighting and energy performance

Abstract Traditionally, automated shading operation includes open-closed strategies trying to maintain a comfortable environment while controlling glare and solar gains. Four different dynamic shading control strategies with constant and variable set points were developed and studied in this paper using year-round transient integrated thermal and lighting simulation, to investigate their impact on outdoor view, daylighting metrics, thermal loads and energy consumption as well as on excessive illuminance that can cause visual discomfort in private offices. The strategies and generic and can be applied to any location, orientation and climate if appropriate set points are selected. The results showed that: (i) shades remain open for a significant portion of working hours depending on orientation and weather conditions (ii) controlling shades based on solar radiation as suggested in previous studies might not be an effective method; instead, illuminance thresholds are probably more appropriate (iii) the third control strategy leads to reduced source energy consumption and maximized daylight utilization; however, careful consideration of interior illuminances is needed to avoid the risk of glare; (iv) differences in annual source energy consumption between control strategies range from 10.1% to 34.4% depending on glazing and shading properties and (v) different strategies should be used in different orientations. Validation of results with full-scale experiments is presented for representative cases. The interactions and integration between daylighting benefits and thermal requirements need to be studied through the interplay between lighting energy use, solar and internal heat gains, while considering comfort parameters that vary depending on the shading control strategy used.
Lipschitz spaces and Suslin sets

Every bounded Suslin set in the plane is the set of eigenvalues of some bounded operator in a separable B-space.
Convergence of immunoreceptor and integrin signaling.

Summary: A common signaling pathway is known to operate downstream of immunoreceptors, such as the T-cell, B-cell, or Fc receptors, following engagement by their respective ligands. This pathway involves Src family kinase-mediated tyrosine phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) that recruit and activate spleen tyrosine kinase (Syk) or Zap70 (ζ-associated protein of 70 kDa) kinases, which in turn activate a variety of downstream signals. Evidence has been building from a variety of sources, particularly mouse models, that molecules involved in the immunoreceptor signaling pathway are also required for signals initiated by integrins. Integrins are the major cell surface receptors that mediate adhesion of leukocytes to a variety of extracellular matrix proteins and counter-receptors expressed on endothelial cells. Integrin ligation is a critical step in the activation of leukocyte effector functions (such as neutrophil degranulation or lymphocyte proliferation). Integrin signaling through pathways common to those utilized by immunoreceptors provides a mechanism by which leukocyte adhesion can regulate activation of cellular responses. In animal models, integrin-mediated signal transduction plays a critical role in inflammatory disease. In this review, we discuss the convergence of immunoreceptor and integrin signaling, focusing on how these pathways modulate leukocyte activation.
Photorefractive Keratectomy for Severe Postkeratoplasty Astigmatism

We performed cylindric corneal ablations with the excimer laser on 12 patients to correct severe, disabling astigmatism after keratoplasty. In some patients, an additional ablation was performed to correct myopia. Patients were followed up for an average of eight months (range, six to 14 months). Uncorrected visual acuity improved in nine patients, and nine of the 12 patients had a decrease in refractive cylinder at last follow-up. The mean preoperative refractive cylinder was 7.0 ± 3.6 diopters, which decreased to a mean of 3.1 ± 2.6 diopters at one month (P = .0003) and 4.3 ± 2.9 diopters at last follow-up (P = .03). Keratometric astigmatism decreased from 7.5 ± 3.9 diopters preoperatively to 5.2 ± 3.9 diopters at the last follow-up (P = .001). Mean spherical equivalent was reduced from -7.4 ± 4.2 diopters preoperatively to —3.3 ± 4.4 diopters postoperatively (P = .003). Postoperative corneal haze, when present, did not reduce visual acuity. Excimer laser superficial keratectomy thus appears to be safe when used for postkeratoplasty ametropia, although substantial regression may limit its effectiveness in some patients.
ProgXe: progressive result generation framework for multi-criteria decision support queries

We demonstrate ProgXe, a practical approach to support Multi-Criteria Decision Support (MCDS) applications that need to report results as they are being generated to enable the user to make competitive decisions. ProgXe transforms the execution of MCDS queries involving skyline over joins to be non-blocking by progressively generating results early and often. The demonstration highlights key features of our progressive execution framework that optimizes for early output generation by: (1) evaluating the query at multiple levels of abstraction, (2) exploiting the skyline knowledge gained from both input as well as mapped output spaces. The audience will be able to submit MCDS queries. We provide visualization tools that enable the user to make quick decisions, compare alternative techniques, and provide capability to fine-tune the query predicates based on the early output results.
Early emerging nicotine dependence symptoms in adolescence predict daily smoking in young adulthood

Purpose The present study evaluated the predictive validity of individual early emerging nicotine dependence symptoms in adolescence on smoking behavior in young adulthood.
Role of current oscillations in ac-dc interference effects in NbSe 3

We investigate the relation between rf-induced Shapiro steps and current oscillations in the charge-density-wave (CDW) state of ${\mathrm{NbSe}}_{3}$. The Shapiro step magnitude is independent of the oscillation amplitude, and a rich spectrum of harmonic and subharmonic steps is observed. These results provide evidence for phase homogenization or excitation of internal modes of the CDW condensate.
The use of synthetic peptides for defining the specificity of typrosine protein kinases

Abstract The tyrosine protein kinases are a large family of enzymes that may be involved in regulating cell growth and differentiation. An important property of these enzymes is their substrate specificity. Defining the specificity of these enzymes will contribute to a greater understanding of their biological functions. Synthetic peptides provide a useful means for studying the specificities of protein kinases. The utility of synthetic peptides for specificity studies is exemplified by the results obtained with the cyclic nucleotide-dependent protein kinases. A large number of synthetic peptides have been tested as substrates for these enzymes. There are three important conclusions from this work. First, in terms of primary sequence, the two cyclic nucleotide-dependent protein kinases both require the presence of a pair of basic residues on the N-terminal side of the phosphorylatable residue. Second, recognition of a specific secondary structure of these enzymes. Third, the specificities of the two cyclic nucleotide-dependent protein kinases are remarkably similar in terms of both primary and secondary structure recognition. Sequences at the sites of tyrosine phosphorylation often show the presence of numerous acidic residues on the N-terminal side of the tyrosine. This result led to the suggestion that these acidic residues might be important for the recognition of these sites by the tyrosine protein kinases. Specificity studies using synthetic peptidese have provided some experimental verification of this concept. In the case of four tyrosine protein kinases, LSTRA cell tyrosine protein kinase, epidermal growth factor receptor kinase, insulin receptor kinase and pp60gag-yes tyrosine protein kinase, the presence of acidic residues on the N-terminal side of the tyrosine in a synthetic peptide was a favorable determinant. In the case of a fifth member of the tyrosine protein kinase family, namely pp60src kinase, the data are less clear that the presence of acidic residues is involved in substrate recognition. This enzyme readily phosphorylated several peptides that did not have acidic residues on the N-terminal side of the tyrosine. Although there is some indication that the presence of acidic residues on the N-terminal side of the tyrosine is a factor in substrate recognition by several of the tyrosine protein kinases, the changes in kinetic parameters with the various peptide substrates were rather small. In addition, some sites phosphorylated in proteins do not have any acidic residues on the N-terminal side of the phosphorylated tyrosine residue. The presence of acidic residues on the primary sequence near the tyrosine is not an absolute determinant for the recognition of sites of phosphorylation by the tyrosine protein kinases. As in the case of the cyclic nucleotide-dependent protein kinases, secondary structure is probably also important for the recognition of sites of phosphorylation by the tyrosine protein kinases.
Microdermabrasion: A Clinical and Histopathologic Study

Background. Microdermabrasion is a widely performed skin rejuvenation procedure. Few studies have examined its efficacy. Objective. To evaluate the clinical and histopathologic effects of microdermabrasion. Methods. Fourteen patients underwent microdermabrasion treatments over 12–14 weeks. Self-rated questionnaires were given before and after the treatment series and were evaluated by a paired t-test. Three of the 14 patients were treated for moderate to severe acne scarring. Acute histologic effects were assessed ex vivo on human abdominal skin. Chronic histopathologic effects were examined in three volunteers who underwent skin biopsies before and after a treatment series on the dorsal forearms. Results. By patient assessment, there was statistically significant improvement in roughness, mottled pigmentation, and overall improvement of skin appearance, but not in rhytides. Acne scarring sometimes improved, but required deeper ablation. Acutely the stratum corneum was homogenized and focally compacted. Chronically there was epidermal hyperplasia, decreased melanization, and some increase in elastin. Conclusion. Microdermabrasion improves some aspects of photoaging and select cases of acne scarring.
Methyl proton NMR shifts of coordinated methanol in a series of Co(CH3OH)5X2+ compounds

Abstract The isotropic contact NMR shifts of the coordinated cis and trans methanol methyl proton resonances of a series of Co(CH 3 OH) 5 X 2+ complexes were measured, where the ligand X was pyridine, β- and α-picoline, DNIF, DNISO, acetonitrile, and water. The question of how to separate the observed shifts into their respective Fermi contact and dipolar (pseudocontact) contributions was examined in detail with the result that a new procedure for carrying out the separation was proposed. The dipolar shifts for these complexes were found to vary widely, with the acetonitrile complex exhibiting the largest dipolar shift. For the DMSO and water complexes the sign of the dipolar shift was reversed relative to the others. Qualitatively this sign reversal may be related to the difference in ligand field strengths of methanol and X relative to the spin orbit soupling constant for cobalt (II). It was also concluded that the Fermi contact shift varied between complexes.
Path-based edge activation for dynamic run-time scheduling

We present a tool that performs real time analysis and dynamic execution of software tasks in a mixed hardware-software system with a custom run time scheduler. The tasks in hardware and software have control flow constraints (precedence and alternative execution), resource constraints, relative timing constraints, and a rate constraint. The custom run time scheduler dynamically executes tasks in different orders, based on the conditional execution path, such that a hard real time rate constraint can be predictably met. We describe the task modelling, run time scheduler implementation, and real time analysis. We introduce the concept of path based edge activation utilizing conditional edges. We show how our approach fits into an overall tool flow and target architecture. Finally, we conclude with a sample application of the system to a design example.
THE ET INTERVIEW: PROFESSOR C.R. RAO: Interviewed by Anil K. Bera University of Illinois at Urbana-Champaign

It was June 1940. The Second World War was already raging in full swing in its devastation. A young man not yet 20 set out on a 500-mile train journey from the coastal city of Vishakapatnam, India, to Calcutta, the second largest city of the British Empire, after obtaining a first-class first degree in mathematics and with a glimmer of hope of finding a job in the military. The young man was not so lucky; he was deemed too young for the job. However, while in Calcutta, through a chance encounter, he visited the Indian Statistical Institute (ISI) founded in 1931 by Professor Prasanta Chandra Mahalanobis, a Cambridge-trained physicist. As a last resort he applied for a one-year training program in statistics there. Very promptly he received a positive reply from Professor Mahalanobis admitting him to the Training Section of the ISI from January 1, 1941. This young man was none other than perhaps the most well known statistician in the world today, Calyampudi Radhakrishna Rao (or simply Dr. Rao, as he was universally known to his students and colleagues at the ISI. The “professor” title was reserved for Mahalanobis). Such was the beginning of his spectacular career in statistics, a field chosen as a last resort, and he never looked back.
Saturation throughput of IEEE 802.11 DCF in multi-hop ad hoc networks

IEEE 802.11 DCF has been widely used in wireless multi-hop ad hoc networks as the medium access control protocol. However, how well it can perform has not been well studied. In this paper, we first propose a new Markov chain model to analyze the per-node throughput by taking into consideration three important issues in multi-hop networks, i.e., physical carrier sensing threshold, signal-to-interference plus noise ratio threshold, and hidden terminal problems. Then, we validate our analytical model by simulations. We find the simulation results match our theoretical results well.
Differential effects of cholera toxin pre-treatment on in vitro vs. in vivo immunocyte responses.

SummaryCholera toxin is known to affect antibody responsiveness, both in vivo and in vitro. In the present study spleen cells from mice pretreated with cholera toxin were markedly deficient in their ability to respond to sheep red blood cells by forming hemolytic antibodies in vitro, whereas splenocytes from mice treated with toxin on the day of immunization or 1 day earlier, showed marked enhancement of antibody responsiveness upon in vitro challenge immunization. Spleen cells from normal mice treated in vitro with cholera toxin at the same time as immunization also showed a marked enhancement of the immune response. Furthermore, normal spleen cell cultures first treated with cholera toxin in vitro and then immunized 2 days later with sheep erythrocytes showed an increased rather than decreased PFC response. These results indicate that depression of antibody formation observed in vivo or in vitro with spleen cells from cholera toxin pretreated animals may reflect an indirect effect, whereas increased res...
Single-narrative, multiple point-of-view dramatic experiences in augmented reality

Researchers and practitioners working on story-based experiences in virtual environments often make two assumptions. One assumption is that, to be compelling, such experiences must enable the user to make significant choices that alter the outcome of the story. Another is that virtual environments constitute a revolutionary new medium, and therefore that the techniques of earlier media, such as film and stage production, are no longer relevant. In designing story-based experiences in augmented reality, we have come to question these two assumptions. Three Angry Men, based on the teleplay and movie Twelve Angry Men, is an example of an augmented reality, dramatic experience with a fixed plot but multiple points of view.
The quick and the deadly: growth vs virulence in a seed bank pathogen.

Summary • We studied the relationship between virulence (ability to kill nondormant Bromus tectorum seeds) and mycelial growth index in the necrotrophic seed pathogen Pyrenophora semeniperda. Seed pathosystems involving necrotrophs differ from those commonly treated in traditional evolution-of-virulence models in that host death increases pathogen fitness by preventing germination, thereby increasing available resources. Because fast-germinating, nondormant B. tectorum seeds commonly escape mortality, we expected virulence to be positively correlated with mycelial growth index. • We performed seed inoculations using conidia from 78 pathogen isolates and scored subsequent mortality. For a subset of 40 of these isolates, representing a range of virulence phenotypes, we measured mycelial growth index. • Virulence varied over a wide range (3–43% seed mortality) and was significantly negatively correlated with mycelial growth index (R 2 = 0.632). More virulent isolates grew more slowly than less virulent isolates. • We concluded that there is an apparent tradeoff between virulence and growth in this pathogen, probably because the production of toxins necessary for necrotrophic pathogenesis competes with metabolic processes associated with growth. Variation in both virulence and growth rate in this pathosystem may be maintained in part by seasonal variation in the relative abundance of rapidly germinating vs dormant host seeds available to the pathogen.
Loosely-coordinated, distributed, packet-level simulation of large-scale networks

The complexity and dynamics of the Internet is driving the demand for scalable and efficient network simulation. In this paper, we describe a novel approach that partitions the networks into domains and simulation time into intervals. Each domain is simulated independently of and concurrently with the others with only local domain information over the same simulated time interval. At the end of each interval, global routing information, packet delays and drop rates for each inter-domain flow are exchanged between domain simulators. When the exchanged information converges to the value within a prescribed precision all simulators progress to the next simulated time interval. This approach allows the parallelization with infrequent synchronization, and achieves significant simulation speedups. Such a solution supports simulations of large-scale networks on distributed machines with modest memory size.
Solid-state fermentation plus extrusion to make biopesticide granules

Five fungal biocontrol agents useful in agriculture were grown on rice flour in plastic bags. The flour, infested with Colletotrichum truncatum, an Alternaria sp., Paecilomyces fumosoroseus, or atoxigenic Aspergillus flavus and A. parasiticus, was mixed with wheat flour, kaolin, and water and extruded into granules. The inoculum survived extrusion and fluid bed drying at 50°C 3–92 times better than inoculum produced in liquid fermentation. Depending on the agent, the high level of flour infestation permitted a 1:9 to 1:1600 dilution to yield the 1×106 cfu/g in the final product which is usually needed for biocontrol efficacy. © Rapid Science Ltd. 1998
Software Vulnerability Analysis for Web Services Software Systems

The use of Web Services has begun to significantly impact organizations and companies. Major business oriented objectives in reducing costs, shortening time, and improving quality and productivity can be achieved by using the Web Services technology. The Web Services software technology enables software components independently developed in disparate platforms to interact and collaborate in a seamless manner. They constitute a loosely-coupled, distributed system that is highly scalable. However, they also inherit the potential vulnerabilities of such systems. As Web Services increase in complexity and connectivity, the associated security risks also increase exponentially. Many of the security breaches can be traced back to poor verification and validation tasks. In this paper, a study on security related software vulnerabilities in SOAP-based Web Services is presented. The security context of traditional Web applications is compared to that of Web Services. An attempt has been made to map common attack patterns to security verification requirements with regard to Web Service software systems.
Rbms3 functions in craniofacial development by posttranscriptionally modulating TGF-β signaling.

Cranial neural crest cells form much of the facial skeleton, and abnormalities in their development lead to severe birth defects. In a novel zebrafish protein trap screen, we identified an RNA-binding protein, Rbms3, that is transiently expressed in the cytoplasm of condensing neural crest cells within the pharyngeal arches. Morphants for rbms3 displayed reduced proliferation of prechondrogenic crest and significantly altered expression for chondrogenic/osteogenic lineage markers. This phenotype strongly resembles cartilage/crest defects observed in Tgf-βr2:Wnt1-Cre mutants, which suggests a possible link with TGF-β signaling. Consistent with this are the findings that: (a) Rbms3 stabilized a reporter transcript with smad2 3′ untranslated region, (b) RNA immunoprecipitation with full-length Rbms3 showed enrichment for smad2/3, and (c) pSmad2 levels were reduced in rbms3 morphants. Overall, these results suggest that Rbms3 posttranscriptionally regulates one of the major pathways that promotes chondrogenesis, the transforming growth factor β receptor (TGF-βr) pathway.
Investigation of Urinary Water Reabsorption in the Cloaca and Rectum of the Hen

ABSTRACT EARLY work involving short periods of urine collection and extrapolation to a 24 hour basis led many workers studying water metabolism in the hen to conclude: (1) that the amount of ureteral urine entering the cloaca and rectum may be as much as 700 to 1,000 cc. in 24 hours and (2) that 240 to 720 cc. of water was reabsorbed from this urine in the cloaca and rectum in 24 hours (Sharpe, 1923; Davis, 1927; Korr, 1939; Hester, Essex and Mann, 1940; and others). The estimated volume of urine voided daily was extremely large and greatly exceeded the daily water consumption; water balance was thus believed to be maintained by reabsorption of water from the urine in the cloaca and rectum. Hart and Essex (1942) reported ureteral urine volumes of 50 to 180 cc. per day based on 24 hour quantitative collections. Their work suggested that the cloaca was . . .
Performance evaluation of AODVH: An Ad hoc networking scheme for hybrid nodes

Mobile Ad hoc networks (MANETs) are composed of a collection of independent nodes usually connected by low bandwidth Radio Frequency (RF) links which are challenging for transmitting video and high bandwidth applications for rescue workers in emergency situations. Earlier we proposed a routing protocol, called AODVH to use for high bandwidth communication for search and rescue operations in a disaster area which consists of hybrid nodes using Free Space Optical (FSO) and RF links, with FSO being the primary link and RF as backup in the case of failure of “FSO only” paths. The objective of this paper is to evaluate the performance of AODVH using ns-2 simulations with varying network size and compare with three other Ad hoc routing protocols. We also implemented and tested AODVH in the laboratory using a testbed consisting of Linux based Ad hoc nodes. Results show that AODVH performs better in terms of packet loss, end-to-end delay, overhead, packet delivery ratio, route discovery frequency and throughput when compared to with the other three protocols.
The Stab-in-the-Back Legend and the Vietnam War

Although associated with post-World War I Germany, the stab-in-the-back perspective is a common cultural response to defeat in war. An American, post-Vietnam War version maintains that the military could have won the war but for the activities of Democratic presidents, Congress, civilian strategists, the press, and antiwar protesters. The roots of the legend lie in arch-conservative assumptions, partisanship, wartime right-wing criticism of Lyndon Johnson's war, militant cold war attitudes, and attempts of purveyors of the myth to defend failed policies and strategies and to counter the "Vietnam syndrome." Seriously flawed historically, logically, and empirically regarding the possibility of victory and the role of the press and the antiwar movement, the stab-in-the-back argument nevertheless enjoys partial public acceptance because of the influence of its proponents and also because it is an essential component of a larger myth: the "Lost Cause."
Stability of NNO and NPO Nanotube Crystals

We combine the USPEX evolution searching method with density functional theory using dispersion corrections (DFT-ulg) to predict the crystal structure of the NNO extended solid at high pressures (from 100 to 500 GPa). We find that the NNO nanotube (with diameter ≈ 2.5 A) is the most stable form above 180 GPa. We report here the stability, electronic properties, and mechanical properties of this novel nanotube and show that it is stable above 20 GPa. To find a similar structure that might be stable at ambient conditions, we considered the NPO tube and show that it is stable at zero pressure. The NPO phase leads to an insulator to metal transition at 25 GPa, where the PP van der Waals distance approaches the covalent bond distance. The energy content of this NPO nanotube crystal is 10.6 kJ/g, which is 152% higher than that of TNT and 86% higher than that of the HMX energetic material. This is the first example of a structural energetic material, which could have important applications in igniters, incendiaries, screening smoke ammunition, and similar devices. This process illustrates how materials discovery in extreme conditions can be used to discover and stabilize novel structures.
Angular displacement patterns of leading and trailing limb joints during galloping in monkeys

The movement patterns of the joints of the right hind limbs and forelimbs of four vervet and one squirrel monkey were compared during right- and left-lead gallops. Although the overall displacement patterns were similar under both conditions, comparisons of the inflection points in the curves yielded consistent differences in the joints at various phases in the cycle. Some of these differences appear to reflect differing mechanical conditions, whereas others seem to represent variation in muscle activation patterns. Although some of the differences in the joints under the two conditions were consistent with those reported previously for other quadrupeds, others were not. This may reflect that different quadrupeds use slightly different biomechanical strategies during galloping.
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

Massively parallel sequencing technologies have made the generation of genomic data sets a routine component of many biological investigations. For example, Chromatin immunoprecipitation followed by sequence assays detect genomic regions bound (directly or indirectly) by specific factors, and DNase-seq identifies regions of open chromatin. A major bottleneck in the interpretation of these data is the identification of the underlying DNA sequence code that defines, and ultimately facilitates prediction of, these transcription factor (TF) bound or open chromatin regions. We have recently developed a novel computational methodology, which uses a support vector machine (SVM) with kmer sequence features (kmer-SVM) to identify predictive combinations of short transcription factor-binding sites, which determine the tissue specificity of these genomic assays (Lee, Karchin and Beer, Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011; 21:2167–80). This regulatory information can (i) give confidence in genomic experiments by recovering previously known binding sites, and (ii) reveal novel sequence features for subsequent experimental testing of cooperative mechanisms. Here, we describe the development and implementation of a web server to allow the broader research community to independently apply our kmer-SVM to analyze and interpret their genomic datasets. We analyze five recently published data sets and demonstrate how this tool identifies accessory factors and repressive sequence elements. kmer-SVM is available at http://kmersvm.beerlab.org.
An MAT tool and its effectiveness

Although automatic machine translation (MT) of unconstrained text is beyond the state of the art today, the need for increased translator productivity is urgent. The PANGLOSS system addresses this dilemma by integrating MT with machine-aided translation (MAT). The main measure of progress in the development of the PANGLOSS system is a gradual increase in the level of automation. The current PANGLOSS MT system typically generates sub-sentence-length units of the target text. Any remaining gaps are treated by lexicon lookup. A mixture of these two kinds of components is presented to the user using the CMAT (Component Machine-Aided Translation) editor, which was designed to facilitate the transformation of this output into a high-quality text. An experiment evaluating the utility of the CMAT editor demonstrated its usefulness in this task, and provides useful guidance for further development.
Taxol biosynthesis: Molecular cloning of a benzoyl- CoA:taxane 2α-O-benzoyltransferase cDNA from Taxus and functional expression in Escherichia coli

A cDNA clone encoding a taxane 2alpha-O-benzoyltransferase has been isolated from Taxus cuspidata. The recombinant enzyme catalyzes the conversion of 2-debenzoyl-7,13-diacetylbaccatin III, a semisynthetic substrate, to 7,13-diacetylbaccatin III, and thus appears to function in a late-stage acylation step of the Taxol biosynthetic pathway. By employing a homology-based PCR cloning strategy for generating acyltransferase oligodeoxynucleotide probes, several gene fragments were amplified and used to screen a cDNA library constructed from mRNA isolated from methyl jasmonate-induced Taxus cells, from which several full-length acyltransferases were obtained and individually expressed in Escherichia coli. The functionally expressed benzoyltransferase was confirmed by radio-HPLC, (1)H-NMR, and combined HPLC-MS verification of the product, 7, 13-diacetylbaccatin III, derived from 2-debenzoyl-7, 13-diacetylbaccatin III and benzoyl-CoA as cosubstrates in the corresponding cell-free extract. The full-length cDNA has an open reading frame of 1,320 base pairs and encodes a protein of 440 residues with a molecular weight of 50,089. The recombinant benzoyltransferase has a pH optimum of 8.0, K(m) values of 0.64 mM and 0.30 mM for the taxoid substrate and benzoyl-CoA, respectively, and is apparently regiospecific for acylation of the 2alpha-hydroxyl group of the functionalized taxane nucleus. This enzyme may be used to improve the production yields of Taxol and for the semisynthesis of drug analogs bearing modified aroyl groups at the C2 position.
In vitro characteristics of a gelling PEGDA‐QT polymer system with model drug release for cerebral aneurysm embolization

A liquid-to-solid gelling polymer system, such as the poly(ethylene glycol) diacrylate-pentaerythritol tetrakis (3-mercaptopropionate) (PEGDA-QT) system, can fill cerebral aneurysms more completely than current embolization materials, reducing the likelihood of aneurysm recurrence. PEGDA-QT gels were formulated using PEGDA of different molecular weights (PEGDA575 and PEGDA700), and their characteristics were examined in vitro. Experiments examined gel time, mass change, crosslink integrity, cytotoxicity, and protein release capabilities. In general, PEGDA575-QT gels were more hydrophobic, requiring an initiating solution with a higher pH (pH 9.5) to achieve a gel time comparable to PEGDA700-QT gels, which used an initiating solution at pH 9.19. The mass change and crosslink integrity of gels were analyzed over time after gels were submerged in 150 mM phosphate buffered saline. After 380 days, PEGDA575-QT gels achieved a maximum mass increase of 72% due to water uptake, while PEGDA700-QT gels doubled their initial mass (100% increase) by 165 days. Compression tests showed that PEGDA700-QT gels hydrolyzed more quickly than PEGDA575-QT gels. Cytotoxicity assays showed that in general, PEGDA575-QT negatively affected cell growth, while PEGDA700-QT gels promoted cell viability. Sustained, controlled release of lysozyme, a 14.3 kDa protein, was achieved over an 8-week period when loaded into PEGDA700-QT gels, but PEGDA575-QT gels did not show sustained release. These studies show that although they are similar in composition, these PEGDA-QT gel formulations behave considerably differently. Although PEGDA700-QT gels swell more and degrade faster than PEGDA575-QT gels, their cytocompatibility and protein release characteristics may prove to be more beneficial for in vivo aneurysm treatment. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 101B: 1477–1488, 2013.
Computed Tomography Angiography of the Lower Extremities

CT angiography (CTA) of the lower extremities is an important and versatile, noninvasive tool for diagnosis as well as surgical or endovascular interventional planning. Although lower extremity CTA is most commonly performed in patients with peripheral artery disease or trauma affecting the lower extremities, it also plays a role in the workup of nonischemic etiologies such as vasculitis, aneurysms, and congenital vascular malformations. CT scan protocols should adjust bolus timing and multiphasic imaging to account for the clinical question of interest, and 3-dimensional postprocessing plays an important role in the visualization and interpretation of these high-resolution imaging examinations.
The mouse Ulnaless mutation deregulates posterior HoxD gene expression and alters appendicular patterning

The semi-dominant mouse mutation Ulnaless alters patterning of the appendicular but not the axial skeleton. Ulnaless forelimbs and hindlimbs have severe reductions of the proximal limb and less severe reductions of the distal limb. Genetic and physical mapping has failed to separate the Ulnaless locus from the HoxD gene cluster (Peichel, C. L., Abbott, C. M. and Vogt, T. F. (1996) Genetics 144, 1757-1767). The Ulnaless limb phenotypes are not recapitulated by targeted mutations in any single HoxD gene, suggesting that Ulnaless may be a gain-of-function mutation in a coding sequence or a regulatory mutation. Deregulation of 5' HoxD gene expression is observed in Ulnaless limb buds. There is ectopic expression of Hoxd-13 and Hoxd-12 in the proximal limb and reduction of Hoxd-13, Hoxd-12 and Hoxd-11 expression in the distal limb. Skeletal reductions in the proximal limb may be a consequence of posterior prevalence, whereby proximal misexpression of Hoxd-13 and Hoxd-12 results in the transcriptional and/or functional inactivation of Hox group 11 genes. The Ulnaless digit phenotypes are attributed to a reduction in the distal expression of Hoxd-13, Hoxd-12, Hoxd-11 and Hoxa-13. In addition, Hoxd-13 expression is reduced in the genital bud, consistent with the observed alterations of the Ulnaless penian bone. No alterations of HoxD expression or skeletal phenotypes were observed in the Ulnaless primary axis. We propose that the Ulnaless mutation alters a cis-acting element that regulates HoxD expression specifically in the appendicular axes of the embryo.
Evidence for Eumelanin and Pheomelanin Producing Genotypes in the Arabian Horse

The ultrastructural imaging of melanocytes coupled with analyses to detect sulfur-containing melanosomes by energy-dispersive X-ray spectroscopy were used to test the hypothesis that the yellowish-red and black pigments found in Arabian horses result from pheomelanogenesis and eumelanogenesis, respectively. These procedures detected pheomelanosomes in follicles at the base of hairs in chestnut horses and eumelanosomes in follicles at the base of hairs in black horses. By analyzing tissue obtained by skin biopsy, these procedures also demonstrated that skin melanocytes in a chestnut horse produce eumelanosomes, and follicular melanocytes in the same horse produce pheomelanosomes. It was also shown that the type of follicular melanosome present in light bay horses is correlated with the color of the hair. The results of this study give experimental evidence for the Odriozola-Adalsteinsson hypothesis that the e allele is responsible for the chestnut phenotype; they also give fine structure and chemical confirmation of the action of the A and E loci in the Arabian horse as currently proposed for the mouse and other mammals.
Neoliberalism, logistics and the treadmill of production in metropolitan waste management: A case of Turkish firms

This paper examines the domestic growth and overseas expansion of Turkish firms as part of the treadmill of production. The treadmill of production is an environmental and political-economy approach to society’s insatiable hunger for material goods. In this approach, economic growth leads to withdrawals of natural resources, and the addition of waste to the environment that stresses both nature and society. Drawing on the treadmill of production approach, I argue that logistical service providers are a coping and modernisation mechanism for accelerated urban growth and economic expansion. This process is visible in the expansion of privatised waste management, and even more so in rapidly urbanising regions where growth and modernisation are of great importance to policy-makers. Owing to the importance of growth and expansion, logistics firms in newly industrialised countries, like their counterparts in the Global North, increasingly export logistical services overseas. This, in turn, accelerates the tread...
The residual fate of N,N,N',N'-tetramethyl-p-piperidinophosphonic diamide after injection, tarsal contact, and topical application to the boll weevil.

N, N, N', N' -Tetramethyl-p-piperidinophosphonic diamide (ENT-5I007) was applied to boll weevils, Anthonomus Grandis Bohemian, topically, by tarsal contact, and by injection. Gas chromatographic analysis of the residues remaining in or on the boll weevil at various times after treatment showed that the greater part of the residues disappeared after 24 hr regardless of the method of application. The rate of disappearance of the parent compound from males injected with 20 µg was extremely rapid: only 20% of the original dose remained 1 hr after injection.
Hybrid ray-mode formulation of SH motion in a two-layer half-space

A hybrid ray-mode formulation is presented as an attractive alternative to the generalized ray formulation or normal mode formulation for the construction of synthetic seismograms. By the hybrid method, the motion is expressed as a combination of ray fields, modal fields, and a remainder. The number of retained ray fields can be chosen at will, and the required number of modes is thereby determined. Thus, the hybrid method quantifies the truncation effect of a ray series in terms of a certain number of modes, plus a remainder, and vice versa. The remainder field provides the fine tuning that ensures continuity of the total motion; its effect is greatest near the arrival time of the last retained ray and diminishes soon thereafter. The hybrid scheme incorporates within a single concise framework the advantages of a ray description for early observation times and of a modal description for later observation times. Therefore, over a prolonged range of observation times, it is numerically more efficient and physically more appealing than either the pure ray or pure mode formulations. These aspects are demonstrated on the simple example of a two-layer (sediment atop bedrock) half-space excited by a line source of SH waves in the semi-infinite bedrock. Numerical results are presented for parameters employed in a similar calculation by Heaton and Helmberger and by Swanger and Boore.
Municipal Wastewater Treatment by A Two-Stage, Submerged Membrane Bioreactor

A two-stage, submerged membrane bioreactor with Kubota flat-plate microfiltration membrane was designed for the treatment of municipal domestic waste water. The results of the operation showed that the two-stage, submerged membrane bioreactor helped the growth of the energy-rich worms and reduced the yield of sludge. When the sludge loading was 0.35 ~ 0.65g/(g·d)and the volumetric loading was 2 ~ 5g/(L·d), the mass concentrations of COD and NH3-N of the effluent water were 18.67 mg/L and 0.24 mg/L respectively, and the sludge yield was 0.1 kg/kg.
The comparative risks of bacterial contamination between a venturi atomizer and a positive displacement atomizer.

INTRODUCTION This laboratory study determined the incidence of internal contamination of Venturi principle atomizers and positive displacement atomizers exposed to high external concentrations of Staphylococcal aureus (Staph). METHODS Atomizer device nozzle tips were immersed into a Staph solution and I ml of spray was atomized via compressed wall air (Venturi) or hydraulic pump (positive displacement). The Venturi nozzle was then wiped with 70% isopropyl alcohol while the disposable positive displacement nozzle was replaced. After 30 minutes, 1 ml of atomized fluid was collected and cultured and the process was repeated. After sixteen uses the fluid remaining in the bottles was cultured. The Venturi atomizer also was subjected to a single use trial to determine the location of device contamination. RESULTS Venturi atomizers sprays grew Staph in every case (144/144), while positive displacement atomizer sprays never grew contaminants (0/144; p < 0.0001). At the end of 16 uses, 7/9 of Venturi atomizers had Staph within their medication reservoirs while none (0/9; p = 0.002) existed in the positive displacement atomizers. After a single use of the Venturi atomizer, the medication reservoir, the air lumen and the medication lumen of the nozzle were all contaminated with Staph. CONCLUSIONS External bacterial contamination of the atomizer nozzle tip results in internal bacterial contamination of Venturi devices in as little as one use but not of positive displacement devices. These results warrant further investigation to determine whether a risk of cross-contamination exists in a clinical setting.
GC/ITMS measurement of carbonyls and multifunctional carbonyls in PM2.5 particles emitted from motor vehicles.

A method was developed and tested to identify and quantitate carbonyls and multifunctional carbonyls in fine particulate matter (PM 2.5 ; methylene chloride > toluene-isopropanol (2 + 1, v/v). Water provided the highest recovery for dihydroxy acetone, pyruvic acid, and hydroxy acetone, compared to methylene chloride, and toluene-isopropanol. Lowering the ultrasonication bath temperature from 0° to -8°C improved the recoveries of the less water soluble and more volatile species-methacrolein, methyl vinyl ketone, 2,3-butanedione, and tolualdehyde. The power of the method was demonstrated by identification and quantitation of carbonyls and multifunctional carbonyls in sample extracts of fine particulate matter (PM 2.5 ) collected in the Caldecott tunnel, CA. The identities of crotonaldehyde, 2,3-butanedione, glyoxal, 9H-fluoren-9-one, glycolaldehyde, glyoxylic acid, levulinic acid, and 3-hydroxybenzaldehyde were confirmed by comparing the relative retention time and mass spectra of the analyte in the sample extract with an authentic standard. Quantitation of crotonaldehyde, glyoxal, 2,3-butanedione, glyoxylic acid, and levulinic acid was accomplished. This is the first report of glyoxylic acid, levulinic acid, and 3-hydroxybenzaldheyde in PM 2.5 particles sampled in a roadway tunnel. It is also the first report of a C 10 carbonyl with the molecular formula of C 10 H 16 O 2 , a hydroxy carbonyl with the molecular formula of C 17 H 21 NO 2 , and a hydroxy or dihydroxy carbonyl with the molecular formula of C 16 H 14 O 2 or C 9 H 10 O 3 . The high-molecular weight hydroxy carbonyls, which were found only in the heavy-duty (diesel) bore, may be tracers of diesel emissions in air.