bluuebunny/crossref_metadata_2025 huggingface dataset:
Frost Dynamics of Sagebrush Steppe Soils
Authors: Roundy Bruce A. , Madsen Matthew D.
Published: September 2016

Core Ideas

Rangeland restoration seedings may sometimes fail due to frost damage.

Seed coatings could delay seed germination until spring.

Frost dynamics were characterized by soil temperatures on 14 sagebrush steppe sites.

More than 60 frost periods occurred at 2‐cm depth from fall to spring.

Freezing began in late October and ended in March.

Sagebrush (Artemisia spp.) steppe rangelands in the western United States are converting to weedy landscapes after large‐scale wildfires. To restore ecosystem function, perennial grasses, shrubs, and forbs are sown in fall after summer wildfires or in association with mechanical fuel reduction projects. Recent research has indicated that seeds may germinate too soon after fall sowing and seedlings suffer high mortality from frost during the winter. To help determine the length of germination delay needed to avoid seedling frost mortality and to help guide frost‐tolerance experiments, we analyzed fall to spring soil temperatures from 2010 to 2014 on six sagebrush–bunchgrass sites and eight woodland sites where conifers had invaded sagebrush communities. Soil temperatures were measured using thermocouples attached to microloggers, with stations placed in untreated, prescribed burned, and mechanically treated plots. Soil freezing differed with site, year of measurement, and soil depth but was relatively unaffected by fire and mechanical fuel reduction treatments. The 2‐cm depth experienced much more freezing than lower depths (14–29 cm) and had >60 freeze–thaw cycles from late October into late March. Although maximum continuously frozen periods ranged from 11 to 45 d, most frost periods were <1 d long. Additional field and laboratory research is needed to determine the effects of different seed coatings on germination delay and frost dynamics on seedling mortality to best avoid frost mortality.
Infiltration under Confined Air Conditions: Impact of Inclined Soil Surface
Authors: Mizrahi Guy , Furman Alex , Weisbrod Noam
Published: September 2016

Core Ideas

A non‐flat surface geometry may lead to preferential release of confined air.

There is a clear difference in the air‐pressure dynamics in an inclined soil surface.

The infiltration rate increased for an inclined surface by about 50%.

Entrapped air effects on infiltration under ponding condition are important in many engineered systems such as soil aquifer treatment and managed aquifer recharge. Earlier studies found that under ponding conditions, air is compressed until it reaches a pressure that enables it to be released, typically by intermittent bubbling through the surface. Entrapped air can reduce infiltration by 70 to 90%. Previous studies considered a flat soil surface topography and mostly vertical one‐dimensional flow. The objective of this study was to investigate the effect of irregular, inclined surface topography on infiltration, hypothesizing that non‐flat surface geometry may lead to preferential release of the confined air and subsequently increase infiltration. In a series of column experiments, we investigated the infiltration rates of flat and inclined soil surfaces. Our results indicate a clear infiltration rate increase of about 50% for an inclined surface. Further, we observed a clear difference in the air‐pressure dynamics, indicating that under an inclined surface, air is being released continuously, while under flat surface conditions, air is being released intermittently. This behavior is explained by differences in the air‐breaking and air‐closing values across the soil column, while the air pressure is practically uniform beneath the wetting front.
A glance behind and a look ahead: history and future of a regional biosolids authority
Authors: Vis Aaron
Published: September 2016

Regional utility, water or wastewater partnerships have existed for many years with varying degrees of success. In the early 2000's, leaders from two west Michigan communities came together with the idea of forming a regional biosolids program. Drivers for this effort primarily included increasing costs of existing programs, loss of land application sites, and age/condition of existing facilities. A project team was formed, a consultant was hired, and by 2004 the Cities of Grand Rapids and Wyoming formally signed the Articles of Incorporation forming the Grand Valley Regional Biosolids Authority (GVRBA). In 2009, a regional dewatering facility became operational. The economic downturn of 2007–2011 resulted in significant deviance from projected volume and costs, yet each community remains committed to the GVRBA and has recently begun incorporating the concept of sustainability into the program. The history, key drivers, benefits, disadvantages, and future of the GVRBA are further explored in this paper.
Retracted: Prediction and optimization of volumetric power draw in an aerated and stirred vessel used in wastewater biological plant: a mathematical model developed by using central composite rotatable design analysis (CCRD)
Authors: Issa Hayder Mohammed
Published: September 2016

In this study, the volumetric power draw P/V was determined as a factor in designing and identifying the optimal condition a successful aeration for stirred wastewater biological treatment vessels. The study was performed to characterize the volumetric power draw in the aerated stirred vessels by optimizing the operation variables. The concerning factors were improved by conjugating stirring and aeration with efficient and economic volumetric power draw condition. The drawn volumetric power was tested and analyzed for three independent parameters; impellers rotation speed (100–200 rpm), turbine blades submergence ratio S/W (0.33–1.67) and wastewater height level ratio H/D (1.37–1.58). A mathematical model was developed in the form of a nonlinear polynomial mathematical model to predict the P/V. The optimal values of the P/V and of relevant parameters were computed through the application of the Box–Wilson technique by application of the central composite rotatable design (CCRD) model. The volumetric power draw P/V and the relevant independent parameters are presented in optimal conditions surface plots that obtained from the nonlinear mathematical model. Optimum analysis result for the independent parameters showed low levels of impellers rotation speed and turbine submergence ratio draw lower P/V while wastewater height did not have a clear effect on P/V.
Consumer satisfaction on quantity and quality of water supply: a study in Matara, Southern Sri Lanka
Authors: Ellawala K. C. , Priyankara D. P. M. P.
Published: September 2016

The aim of every water supply scheme (WSS) is to meet the demand qualitatively and quantitatively. Although quality can be maintained with appropriate operation and maintenance strategies, supplying increasing demand in terms of quantity is a problem, because large-scale investments are sought for water supply utilities. However, satisfaction of consumer cannot be neglected under these circumstances. Hence the objective of the current study is to examine the influence of the level of service supplied, water quality variations and the geographical location of consumers on their perceptions on service delivery, satisfaction and risk perception. The study was limited to Matara WSS, Southern Sri Lanka. Results of the logistic regression analysis show that the area of residence is the most influential parameter on the taste satisfaction and risk perception. Satisfaction on safety, odour and clarity is more than 95% of the respondents. However, satisfaction on the service delivery is poor and perceived pressure has a major impact on the satisfaction on service delivery and consumption, hence indicating that perceived pressure has a close relationship with the discharge. Further, the study confirms that socio-economic parameters are influential on the risk perception and satisfaction of the consumers. It can be concluded that proper management of available water quantity will increase the level of satisfaction in terms of service delivery.
Renal Toxicities of Novel Agents Used for Treatment of Multiple Myeloma
Authors: Wanchoo Rimda , Abudayyeh Ala , Doshi Mona , Edeani Amaka , Glezerman Ilya G. , Monga Divya , Rosner Mitchell , Jhaveri Kenar D.
Published: September 2016

Survival for patients with multiple myeloma has significantly improved in the last decade in large part due to the development of proteasome inhibitors and immunomodulatory drugs. These next generation agents with novel mechanisms of action as well as targeted therapies are being used both in the preclinical and clinical settings for patients with myeloma. These agents include monoclonal antibodies, deacetylase inhibitors, kinase inhibitors, agents affecting various signaling pathways, immune check point inhibitors, and other targeted therapies. In some cases, off target effects of these therapies can lead to unanticipated effects on the kidney that can range from electrolyte disorders to AKI. In this review, we discuss the nephrotoxicities of novel agents currently in practice as well as in development for the treatment of myeloma.
Effect of celebrity endorsement in marketing of musicals: Poster versus social networking site
Authors: Kim Hyeon-Cheol , Jeong Jae-Yeob
Published: September 2016

We investigated the effect of the message sender, communication type, and recipient's involvement in the marketing of a musical show. This study had a 2 (sender: celebrity vs. noncelebrity) × 2 (communication type: poster advertisement vs. Twitter word-of-mouth [WOM]) ×
2 (recipient involvement: high vs. low) design. Data were collected from 259 Korean university students. Results showed that a celebrity poster advertisement had a more positive effect on consumer attitude than did a noncelebrity poster advertisement. In contrast, with Twitter WOM, the noncelebrity
message sender was more effective in eliciting a positive response from consumers. The interaction of sender, communication type, and recipient involvement for musical ticket purchase intention was significant. Our findings will help marketers strategically allocate resources, as the effect
of celebrity endorsement differed according to communication type and recipient characteristics. Specifically, in the social networking site promotion condition, the similarity or social connection between the message sender and recipient was more influential than was the power of a celebrity
to attract consumers.
Tax Collector or Tax Avoider? An Investigation of Intergovernmental Agency Conflicts
Authors: Tang Tanya , Mo Phyllis Lai Lan , Chan K. Hung
Published: September 2016

Local governments play dual, but conflicting, roles in China's tax system. That is, they are both tax collectors and controlling shareholders of firms subject to tax payments. We investigate how local governments balance their tax collection and tax avoidance incentives. We find that the conflicts between central and local governments arising from the 2002 tax sharing reform have led to more tax avoidance by local government-controlled firms, particularly when the local government's ownership percentage of the firms is higher than the tax sharing ratio. We also find evidence that the overall level of tax avoidance by local government-controlled firms in a region is positively associated with local fiscal deficits. As a high level of government ownership of corporations and intergovernmental tax sharing are common phenomena in many transitional economies, this study offers valuable insights into how the dual roles played by local governments affect tax policy enforcement in these economies.

JEL Classifications: H26; H71; M40; G38.
Rubber–Road Contact: Comparison of Physics-Based Theory and Indoor Experiments
Authors: Motamedi Mehran , Taheri Saied , Sandu Corina
Published: September 2016

For tire designers, rubber friction is a topic of pronounced practical importance. Thus, development of a rubber–road contact model is of great interest. In this research, to predict the effectiveness of the tread compound in a tire as it interacts with the pavement, the physics-based multiscale rubber-friction theories developed by B. Persson and M. Klüppel were studied. The strengths of each method were identified and incorporated into a consolidated model that is more comprehensive and proficient than any single, existing, physics-based approach. In the present work, the friction coefficient was estimated for a summer tire tread compound sliding on sandpaper. The inputs to the model were the fractal properties of the rough surface and the dynamic viscoelastic modulus of rubber. The sandpaper-surface profile was measured accurately using an optical profilometer. Two-dimensional parameterization was performed using one-dimensional profile measurements. The tire tread compound was characterized via dynamic mechanical analysis. To validate the friction model, a laboratory-based, rubber-friction test that could measure the friction between a rubber sample and any arbitrary rough surface was designed and built. The apparatus consisted of a turntable, which can have the surface characteristics of choice, and a rubber wheel in contact with the turntable. The wheel speed, as well as the turntable speed, could be controlled precisely to generate the arbitrary values of longitudinal slip at which the dynamic coefficient of friction was measured. The correlation between the simulation and the experimental results was investigated.
Assessment of plant diversity in homegardens of three ecological zones of Nepal
Authors: Pokhrel Chandra Prasad
Published: September 2016

Homegardens in Nepal have long been regarded as one of the most important multi-propose agroforestry systems with complex structure. The aim of the study was to assess the species diversity and richness in three different ecological regions, i.e., Mountain (Sub-alpine), Mid-hill (Temperate) and Terai (Tropical) of Nepal. In total 45 homegardens were randomly selected and examined from three different villages representing one from each ecological regions and the Shannon–wiener, Simpson index and evenness were assessed. Overall 147 species were identified mainly vegetable, fruit, fodder, spices or medicinal plants. The average size of homegardens were found to be bigger in Mid-hill (0.12 ha), however, the species number and diversity was found to be high in the Terai region (102). More similarity between plant species composition was between Terai and Mid-hill. The Shannonwiener index was found to be 1.316, 1.84 and 1.90 in the homegarden of Mountain, Mid-hill and Terai respectively. Simpson index was 0.052, 0.014 and 0.01 in homegarden of Mountain, Mid hill and Terai region, respectively. Similarly, evenness percentage was 56.29, 65.55 and 65.93 in homegarden of Mountain, Mid-hill and Terai region, respectively. Properly managed homegardens have high productivity and increased sustainability which helps in conserving agro-biodiversity, food sufficiency and economic supports including other ecological functions.ECOPRINT 22: 63-74, 2015
Assessment of python (Python bivittatus Kuhl.) habitats in Bardiya National Park, Nepal
Authors: Sharma Bhuvan Keshar , Kandel Ram Chandra
Published: September 2016

Habitats used by the Python (Python bivittatus) were studied in lowland areas of Bardiya National Park, Nepal. The main objective of the study was to assess the specific habitats used by Python in the Park. In association with key informants’ survey to identify the potential habitats areas, field investigation was conducted and found out the specific sites. Among twenty habitat sites of Python, three were currently used and remaining other were found as potential habitats. In total, six specific habitats such as burrow or holes were mostly preferred by Python.ECOPRINT 22: 85-90, 2015
The Novel Aminomethylcycline Omadacycline Has High Specificity for the Primary Tetracycline-Binding Site on the Bacterial Ribosome
Authors: Heidrich Corina , Mitova Sanya , Schedlbauer Andreas , Connell Sean , Fucini Paola , Steenbergen Judith , Berens Christian
Published: September 2016

Omadacycline is an aminomethylcycline antibiotic with potent activity against many Gram-positive and Gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. This makes it a promising candidate for therapy of severe infectious diseases. Omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. Its interactions with the 70S ribosome were, therefore, analyzed in great detail and compared with tigecycline and tetracycline. All three antibiotics are inhibited by mutations in the 16S rRNA that mediate resistance to tetracycline in Brachyspira hyodysenteriae, Helicobacter pylori, Mycoplasma hominis, and Propionibacterium acnes. Chemical probing with dimethyl sulfate and Fenton cleavage with iron(II)-complexes of the tetracycline derivatives revealed that each antibiotic interacts in an idiosyncratic manner with the ribosome. X-ray crystallography had previously revealed one primary binding site for tetracycline on the ribosome and up to five secondary sites. All tetracyclines analyzed here interact with the primary site and tetracycline also with two secondary sites. In addition, each derivative displays a unique set of non-specific interactions with the 16S rRNA.
Kinetic and Equilibrium Studies of Sorption of Ammonium in the Soil-Water Environment in Agricultural Areas of Central Poland
Authors: Sieczka Anna , Koda Eugeniusz
Published: September 2016

Sorption characteristics of nitrogen compounds is necessary in ascertaining their fate in the soil-water environment. This paper presents a laboratory “batch” experiment for determining the sorption parameters of ammonium in the soil-water environment. Three agricultural soils (silt loam, loam, and sand) with different contents of the clay fraction, significantly affecting the range of the adsorption of contaminants on the surface of solid particles, were chosen as research material. Considering the composition of ammonium nitrate (a commonly used fertilizer in Poland), ammonium solutions with a concentration of 0–52 mg NH4+/L were used as markers. Pseudo-first order, pseudo-second order, and intra-particle diffusion kinetic models were used to describe the mechanisms of ammonium adsorption. Experimental data obtained from the equilibrium tests have been analysed using two-parameter (Freundlich, Langmuir, Temkin) and three-parameter (Redlich-Peterson, Hill, Sips) models. In order to adjust the parameters of the considered isotherms to the experimental data, the method of minimization of the sum of squared errors was used. Additionally, the maximum sorption capacities and reduction ratios of ammonium versus time were assessed. It was observed that the presence of silt loam and loam in the soil profile can increase the possibility of ammonium adsorption up to almost 20%. Taking into consideration the results of the batch tests, it was concluded that ammonium adsorption attains equilibrium within 48 h. Experimental data was best followed by the pseudo-second order equation and the adsorption isotherm conformed to the Redlich-Peterson model for loam and sand.
Eventogram: A Visual Representation of Main Events in Biomedical Signals
Authors: Elgendi Mohamed
Published: September 2016

Biomedical signals carry valuable physiological information and many researchers have difficulty interpreting and analyzing long-term, one-dimensional, quasi-periodic biomedical signals. Traditionally, biomedical signals are analyzed and visualized using periodogram, spectrogram, and wavelet methods. However, these methods do not offer an informative visualization of main events within the processed signal. This paper attempts to provide an event-related framework to overcome the drawbacks of the traditional visualization methods and describe the main events within the biomedical signal in terms of duration and morphology. Electrocardiogram and photoplethysmogram signals are used in the analysis to demonstrate the differences between the traditional visualization methods, and their performance is compared against the proposed method, referred to as the “eventogram” in this paper. The proposed method is based on two event-related moving averages that visualizes the main time-domain events in the processed biomedical signals. The traditional visualization methods were unable to find dominant events in processed signals while the eventogram was able to visualize dominant events in signals in terms of duration and morphology. Moreover, eventogram-based detection algorithms succeeded with detecting main events in different biomedical signals with a sensitivity and positive predictivity >95%. The output of the eventogram captured unique patterns and signatures of physiological events, which could be used to visualize and identify abnormal waveforms in any quasi-periodic signal.
The Effect of Computerized Testing on Sun Bear Behavior and Enrichment Preferences
Authors: Perdue Bonnie
Published: September 2016

The field of comparative cognition investigates species’ differences and similarities in cognitive abilities, and sheds light on the evolutionary origins of such capacities. Cognitive testing has been carried out in a variety of species; however, there are some taxa that are underrepresented in this field. The current work follows on a recent increase in cognitive research in the order Carnivora with a specific focus on sun bears. Sun bears are the smallest existing bear species and live in tropical regions of Southeast Asia. They have an omnivorous diet and use their tongues to forage for insects and sap. Little is known about sun bear cognition, although much like other bear species, anecdotes suggest a high level of intelligence. The current work explored training sun bears to use a touchscreen computer. This effort allows for insight into cognitive abilities as well as providing a complex source of enrichment for the bears. The bears use their tongues to respond to a touchscreen computer, and the effects on stereotypic behaviors on exhibit and preference for this over other forms of enrichment were examined. Overall, bears performed well on the task and showed a preference for the computer.
Catalytic Conversion of Biomass
Authors: Luque Rafael , De Sudipta , Balu Alina
Published: September 2016

Petroleum, natural gas and coal supply most of the energy consumed worldwide and their massive utilization has allowed our society to reach high levels of development in the past century.[...]
A Permutation Importance-Based Feature Selection Method for Short-Term Electricity Load Forecasting Using Random Forest
Authors: Huang Nantian , Lu Guobo , Xu Dianguo
Published: September 2016

The prediction accuracy of short-term load forecast (STLF) depends on prediction model choice and feature selection result. In this paper, a novel random forest (RF)-based feature selection method for STLF is proposed. First, 243 related features were extracted from historical load data and the time information of prediction points to form the original feature set. Subsequently, the original feature set was used to train an RF as the original model. After the training process, the prediction error of the original model on the test set was recorded and the permutation importance (PI) value of each feature was obtained. Then, an improved sequential backward search method was used to select the optimal forecasting feature subset based on the PI value of each feature. Finally, the optimal forecasting feature subset was used to train a new RF model as the final prediction model. Experiments showed that the prediction accuracy of RF trained by the optimal forecasting feature subset was higher than that of the original model and comparative models based on support vector regression and artificial neural network.
Helicase Lymphoid-Specific Enzyme Contributes to the Maintenance of Methylation of SST1 Pericentromeric Repeats That Are Frequently Demethylated in Colon Cancer and Associate with Genomic Damage
Authors: Samuelsson Johanna , Dumbovic Gabrijela , Polo Cristian , Moreta Cristina , Alibés Andreu , Ruiz-Larroya Tatiana , Giménez-Bonafé Pepita , Alonso Sergio , Forcales Sonia-V. , Perucho Manuel
Published: September 2016

DNA hypomethylation at repetitive elements accounts for the genome-wide DNA hypomethylation common in cancer, including colorectal cancer (CRC). We identified a pericentromeric repeat element called SST1 frequently hypomethylated (>5% demethylation compared with matched normal tissue) in several cancers, including 28 of 128 (22%) CRCs. SST1 somatic demethylation associated with genome damage, especially in tumors with wild-type TP53. Seven percent of the 128 CRCs exhibited a higher (“severe”) level of demethylation (≥10%) that co-occurred with TP53 mutations. SST1 demethylation correlated with distinct histone marks in CRC cell lines and primary tumors: demethylated SST1 associated with high levels of the repressive histone 3 lysine 27 trimethylation (H3K27me3) mark and lower levels of histone 3 lysine 9 trimethylation (H3K9me3). Furthermore, induced demethylation of SST1 by 5-aza-dC led to increased H3K27me3 and reduced H3K9me3. Thus, in some CRCs, SST1 demethylation reflects an epigenetic reprogramming associated with changes in chromatin structure that may affect chromosomal integrity. The chromatin remodeler factor, the helicase lymphoid-specific (HELLS) enzyme, called the “epigenetic guardian of repetitive elements”, interacted with SST1 as shown by chromatin immunoprecipitation, and down-regulation of HELLS by shRNA resulted in demethylation of SST1 in vitro. Altogether these results suggest that HELLS contributes to SST1 methylation maintenance. Alterations in HELLS recruitment and function could contribute to the somatic demethylation of SST1 repeat elements undergone before and/or during CRC pathogenesis.
Menopausal Age and Chronic Diseases in Elderly Women: A Cross-Sectional Study in Northeast China
Authors: Fu Yingli , Yu Yaqin , Wang Shibin , Kanu Joseph , You Yueyue , Liu Yingyu , Zhang Yangyu , Liu Yawen , Li Bo , Tao Yuchun , Kou Changgui
Published: September 2016

Many factors affect menopausal age, and early or late onset of menopause may be associated with many chronic health problems. However, limited data are available regarding this phenomenon in the Northeast China population. For this study, 2011 elderly women were selected as a sample from participants in a cross-sectional survey performed using stratified, clustered multistage, and random sampling methods. Early menopause was more prevalent in subjects born from 1943 to 1947 (OR = 1.708, 95% CI = 1.205, 2.420) and 1933 to 1937 (OR = 2.445, 95% CI: 1.525, 3.921) and in physical laborers (OR = 1.413, 95% CI = 1.021, 1.957). Women with less than nine years of education (OR = 0.515, 95% CI: 0.327, 0.812) and who were current smokers (OR = 0.577, 95% CI: 0.347, 0.959) were less likely to have late menopause. BMIs between 25 and 30 (OR = 1.565, 95% CI: 1.152, 2.125) and greater than 30 (OR = 2.440, 95% CI: 1.482, 4.016) were associated with later menopausal age. Late menopause was positively associated with diabetes (OR = 1.611, 95% CI: 1.142, 2.274) but protective against chronic gastroenteritis/peptic ulcers (OR = 0.533, 95% CI: 0.333, 0.855). Results showed that (1) Being born in an earlier year, having a lower education, and engaging in physical labor were associated with an earlier menopausal age, while a higher BMI was associated with a later menopausal age; and that (2) menopausal age was associated with diabetes and gastroenteritis in elderly women living in Northeast China.
Data Autodiscovery—The Role of the OPD
Authors: Cox Adrian , Milsted Andrew , Gutteridge Christopher
Published: September 2016

The importance of open data and the benefits it can offer have received recognition on the international stage with the signing of the G8 Open Data Charter in June 2013. The charter has an early focus on 14 high value areas, including transport and education, where governments have greater influence. In the UK, we have seen the funding of the Open Data Institute (ODI) with a remit to support small and medium sized enterprises (SMEs) in identifying benefits from using open data, whereas, within HE, open data discussion is in its infancy although is acknowledged as a sector challenge by the Russell Group of universities. There is an evident need for the academic community to influence the adoption of applications using linked open data techniques in data management and service delivery. This article introduces the concept of “data autodiscovery”, highlighting the role of the Organisation Profile Document (OPD) and its contribution to the early success of the UK National Equipment Portal, equipment.data, along with discussing the need for greater dialogue in linked and open data standards development.
Inducible Expression of both ermB and ermT Conferred High Macrolide Resistance in Streptococcus gallolyticus subsp. pasteurianus Isolates in China
Authors: Li Meixia , Cai Chao , Chen Juan , Cheng Changwei , Cheng Guofu , Hu Xueying , Liu Cuiping
Published: September 2016

Streptococcus gallolyticus subsp. pasteurianus is an under-recognized pathogen and zoonotic agent causing opportunistic infections in humans. Despite increasing recognition of this subspecies as a cause for human infectious diseases, limited information is known about its antibiotic resistance mechanism. In this study, we aim to identify the molecular mechanism underlying the high macrolide resistance of six S. gallolyticus subsp. pasteurianus isolates from dead ducklings collected in several natural outbreaks in China during 2010–2013. All isolates exhibited multi-drug resistance including high macrolide resistance (MIC ≥ 1024 mg/L for erythromycin, and 512 mg/L for clarithromycin). Efflux-encoding mefA and mefE genes were not detectable in these isolates. The presence of 23S rRNA mutations in specific isolates did not significantly change macrolide MICs. No nucleotide substitutions were found in genes encoding ribosomal proteins L4 or L22. The ermB and ermT genes were found in the genomes of all isolates. These two genes were acquired independently in one highly virulent isolate AL101002, and clustered with Tn916 and IS1216, respectively. The expression of both ermB and ermT in all isolates was erythromycin inducible and yielded comparable macrolide MICs in all six isolates. Taken together, inducible expression of both ermB and ermT conferred high macrolide resistance in these S. gallolyticus subsp. pasterianus isolates. Our findings reveal new macrolide resistance features in S. gallolyticus subsp. pasteurianus by both ermB and ermT.
Designing Efficient Double RNA trans-Splicing Molecules for Targeted RNA Repair
Authors: Hüttner Clemens , Murauer Eva , Hainzl Stefan , Kocher Thomas , Neumayer Anna , Reichelt Julia , Bauer Johann , Koller Ulrich
Published: September 2016

RNA trans-splicing is a promising tool for mRNA modification in a diversity of genetic disorders. In particular, the substitution of internal exons of a gene by combining 3′ and 5′ RNA trans-splicing seems to be an elegant way to modify especially large pre-mRNAs. Here we discuss a robust method for designing double RNA trans-splicing molecules (dRTM). We demonstrate how the technique can be implemented in an endogenous setting, using COL7A1, the gene encoding type VII collagen, as a target. An RTM screening system was developed with the aim of testing the replacement of two internal COL7A1 exons, harbouring a homozygous mutation, with the wild-type version. The most efficient RTMs from a pool of randomly generated variants were selected via our fluorescence-based screening system and adapted for use in an in vitro disease model system. Transduction of type VII collagen-deficient keratinocytes with the selected dRTM led to accurate replacement of two internal COL7A1 exons resulting in a restored wild-type RNA sequence. This is the first study demonstrating specific exon replacement by double RNA trans-splicing within an endogenous transcript in cultured cells, corroborating the utility of this technology for mRNA repair in a variety of genetic disorders.
The Role of Anisotropic Exchange in Single Molecule Magnets: A CASSCF/NEVPT2 Study of the Fe4 SMM Building Block [Fe2(OCH3)2(dbm)4] Dimer
Authors: Lunghi Alessandro , Totti Federico
Published: September 2016

The rationalisation of single molecule magnets’ (SMMs) magnetic properties by quantum mechanical approaches represents a major task in the field of the Molecular Magnetism. The fundamental interpretative key of molecular magnetism is the phenomenological Spin Hamiltonian and the understanding of the role of its different terms by electronic structure calculations is expected to steer the rational design of new and more performing SMMs. This paper deals with the ab initio calculation of isotropic and anisotropic exchange contributions in the Fe(III) dimer [Fe 2 (OCH 3 ) 2 (dbm) 4 ]. This system represents the building block of one of the most studied Single Molecule Magnets ([Fe 4 RC(CH 2 O) 3 ) 2 (dpm) 6 ] where R can be an aliphatic chain or a phenyl group just to name the most common functionalization groups) and its relatively reduced size allows the use of a high computational level of theory. Calculations were performed using CASSCF and NEVPT2 approaches on the X-ray geometry as assessment of the computational protocol, which has then be used to evinced the importance of the outer coordination shell nature through organic ligand modelization. Magneto-structural correlations as function of internal degrees of freedom for isotropic and anisotropic exchange contributions are also presented, outlining, for the first time, the extremely rapidly changing nature of the anisotropic exchange coupling.
Comparison of Model Predictions and Laboratory Observations of Transgene Frequencies in Continuously-Breeding Mosquito Populations
Authors: Valerio Laura , North Ace , Collins C. , Mumford John , Facchinelli Luca , Spaccapelo Roberta , Benedict Mark
Published: September 2016

The persistence of transgenes in the environment is a consideration in risk assessments of transgenic organisms. Combining mathematical models that predict the frequency of transgenes and experimental demonstrations can validate the model predictions, or can detect significant biological deviations that were neither apparent nor included as model parameters. In order to assess the correlation between predictions and observations, models were constructed to estimate the frequency of a transgene causing male sexual sterility in simulated populations of a malaria mosquito Anopheles gambiae that were seeded with transgenic females at various proportions. Concurrently, overlapping-generation laboratory populations similar to those being modeled were initialized with various starting transgene proportions, and the subsequent proportions of transgenic individuals in populations were determined weekly until the transgene disappeared. The specific transgene being tested contained a homing endonuclease gene expressed in testes, I-PpoI, that cleaves the ribosomal DNA and results in complete male sexual sterility with no effect on female fertility. The transgene was observed to disappear more rapidly than the model predicted in all cases. The period before ovipositions that contained no transgenic progeny ranged from as little as three weeks after cage initiation to as long as 11 weeks.
Statistical Interpolation of Tidal Datums and Computation of Its Associated Spatially Varying Uncertainty
Authors: Shi Lei , Myers Edward
Published: September 2016

Tidal datums are key components in NOAA’s Vertical Datum transformation project (VDatum). In this paper, we propose a statistical interpolation method, derived from the variational principle, to calculate tidal datums by blending the modeled and the observed tidal datums. Through the implementation of this statistical interpolation method in the Chesapeake and Delaware Bays, we conclude that the statistical interpolation method for tidal datums has great advantages over the currently used deterministic interpolation method. The foremost, and inherent, advantage of the statistical interpolation is its capability to integrate data from different sources and with different accuracies without concern for their relative spatial locations. The second advantage is that it provides a spatially varying uncertainty for the entire domain in which data is being integrated. The latter is especially helpful for the decision-making process of where new instruments would be most effectively placed. Lastly, the test case results show that the statistical interpolation reduced the bias, maximum absolute error, mean absolute error, and root mean square error in comparison to the current deterministic approach.
A Convenient Four-Step Synthesis of 1-{β-[3-(4-Methoxy-phenyl)Propoxy]-4-Methoxyphenethyl}-1H-Imidazole Hydrochloride as a Probing Tool for SOCE Assays
Authors: Dago Camille , Messé Estelle , Mignen Olivier , Brigaudeau Christophe , Békro Yves-Alain , Bazureau Jean-Pierre
Published: September 2016

1-{β-[3-(4-Methoxy-phenyl)propoxy]-4-methoxyphenethyl}-1H-imidazole hydrochloride 7, or SKF-96365, was synthesized in four steps with an overall yield of 9%. The structure of 7 was confirmed by 1H-, 13C-NMR, HRMS, and elemental analysis. The intermediates 3 and 4 were also isolated and characterized by 1H-, 13C-NMR, and HRMS.
Marine Microbiological Enzymes: Studies with Multiple Strategies and Prospects
Authors: Wang Yan , Song Qinghao , Zhang Xiao-Hua
Published: September 2016

Marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. Both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. In this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (AHL) lactonase, which is an important but largely unexplored enzyme. We also detail the status and catalytic mechanism of the main types of polysaccharide-degrading enzymes that broadly exist among marine microorganisms but have been poorly explored. In order to facilitate understanding, the regulatory and synthetic biology strategies of terrestrial microorganisms are also mentioned in comparison. We anticipate that this review will provide an outline of multiple strategies for promising marine microbial enzymes and open new avenues for the exploration, engineering and application of various enzymes.
Bioactivity of a Novel Glycolipid Produced by a Halophilic Buttiauxella sp. and Improving Submerged Fermentation Using a Response Surface Method
Authors: Marzban Abdolrazagh , Ebrahimipour Gholamhossein , Danesh Abolghasem
Published: September 2016

An antimicrobial glycolipid biosurfactant (GBS), extracted and identified from a marine bacterium, was studied to inhibit pathogenic microorganisms. Production of the GBS was optimized using a statistical method, a response surface method (RSM) with a central composite design (CCD) for obtaining maximum yields on a cost-effective substrate, molasses. The GBS-producing bacterium was identified as Buttiauxella Species in terms of biochemical and molecular characteristics. This compound showed a desirable antimicrobial activity against some pathogens such as E. coli, Bacillus subtilis, Bacillus cereus, Candida albicans, Aspergilus niger, Salmonella enterica. The rheological studies described the stability of the GBS at high values in a range of pH (7–8), temperature (20–60) and salinity (0%–3%). The statistical optimization of GBS fermentation was found to be pH 7, temperature 33 °C, Peptone 1%, NaCl 1% and molasses 1%. The potency of the GBS as an effective antimicrobial agent provides evidence for its use against food and human pathogens. Moreover, favorable production of the GBS in the presence of molasses as a cheap substrate and the feasibility of pilot scale fermentation using an RSM method could expand its uses in food, pharmaceutical products and oil industries.
Silver Nanoparticle-Embedded Thin Silica-Coated Graphene Oxide as an SERS Substrate
Authors: Pham Xuan-Hung , Hahm Eunil , Kim Hyung-Mo , Shim Seongbo , Kim Tae , Jeong Dae , Lee Yoon-Sik , Jun Bong-Hyun
Published: September 2016

A hybrid of Ag nanoparticle (NP)-embedded thin silica-coated graphene oxide (GO@SiO2@Ag NPs) was prepared as a surface-enhanced Raman scattering (SERS) substrate. A 6 nm layer of silica was successfully coated on the surface of GO by the physical adsorption of sodium silicate, followed by the hydrolysis of 3-mercaptopropyl trimethoxysilane. Ag NPs were introduced onto the thin silica-coated graphene oxide by the reduction of Ag+ to prepare GO@SiO2@Ag NPs. The GO@SiO2@Ag NPs exhibited a 1.8-fold enhanced Raman signal compared to GO without a silica coating. The GO@SiO2@Ag NPs showed a detection limit of 4-mercaptobenzoic acid (4-MBA) at 0.74 μM.
Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers
Authors: Najafi Saeed , Podgornik Rudolf , Potestio Raffaello , Tubiana Luca
Published: September 2016

Knots appear frequently in semiflexible (bio)polymers, including double-stranded DNA, and their presence can affect the polymer’s physical and functional properties. In particular, it is possible and indeed often the case that multiple knots appear on a single chain, with effects which have only come under scrutiny in the last few years. In this manuscript, we study the interaction of two knots on a stretched semiflexible polymer, expanding some recent results on the topic. Specifically, we consider an idealization of a typical optical tweezers experiment and show how the bending rigidity of the chain—And consequently its persistence length—Influences the distribution of the entanglements; possibly more importantly, we observe and report how the relative chirality of the otherwise identical knots substantially modifies their interaction. We analyze the free energy of the chain and extract the effective interactions between embedded knots, rationalizing some of their pertinent features by means of simple effective models. We believe the salient aspect of the knot–knot interactions emerging from our study will be present in a large number of semiflexible polymers under tension, with important consequences for the characterization and manipulation of these systems—Be they artificial or biologica in origin—And for their technological application.
Operator Training Simulator for an Industrial Bioethanol Plant
Authors: Gerlach Inga , Tholin Sören , Hass Volker , Mandenius Carl-Fredrik
Published: September 2016

Operator training simulators (OTS) are software tools for training process operators in large-scale industrial applications. Here, we describe the development, implementation and training of an OTS for a large-scale industrial plant for bioethanol production. The design of the OTS is based on conceptual analysis (previously reported by us in this journal) of various configuration alternatives and training procedures at the plant. In this article, we report on how the conceptual design is used in simulation models and graphical user interfaces and how the design is applied for training of operators in the real plant environment. The results imply that OTS would be time- and cost-efficient tools for application in the biotechnological industry.
Land Surface Temperature Differences within Local Climate Zones, Based on Two Central European Cities
Authors: Geletič Jan , Lehnert Michal , Dobrovolný Petr
Published: September 2016

The main factors influencing the spatiotemporal variability of urban climate are quite widely recognized, including, for example, the thermal properties of materials used for surfaces and buildings, the mass, height and layout of the buildings themselves and patterns of land use. However, the roles played by particular factors vary from city to city with respect to differences in geographical location, overall size, number of inhabitants and more. In urban climatology, the concept of “local climate zones” (LCZs) has emerged over the past decade to address this heterogeneity. In this contribution, a new GIS-based method is used for LCZ delimitation in Prague and Brno, the two largest cities in the Czech Republic, while land surface temperatures (LSTs) derived from LANDSAT and ASTER satellite data are employed for exploring the extent to which LCZ classes discriminate with respect to LSTs. It has been suggested that correctly-delineated LCZs should demonstrate the features typical of LST variability, and thus, typical surface temperatures should differ significantly among most LCZs. Zones representing heavy industry (LCZ 10), dense low-rise buildings (LCZ 3) and compact mid-rise buildings (LCZ 2) were identified as the warmest in both cities, while bodies of water (LCZ G) and densely-forested areas (LCZ A) made up the coolest zones. ANOVA and subsequent multiple comparison tests demonstrated that significant temperature differences between the various LCZs prevail. The results of testing were similar for both study areas (89.3% and 91.7% significant LST differences for Brno and Prague, respectively). LSTs computed from LANDSAT differentiated better between LCZs, compared with ASTER. LCZ 8 (large low-rise buildings), LCZ 10 (heavy industry) and LCZ D (low plants) are well-differentiated zones in terms of their surface temperatures. In contrast, LCZ 2 (compact mid-rise), LCZ 4 (open high-rise) and LCZ 9 (sparsely built-up) are less distinguishable in both areas analyzed. Factors such as seasonality and thermal anisotropy remain a challenge for future research into LST differences.
Gateway-Assisted Retransmission for Lightweight and Reliable IoT Communications
Authors: Chang Hui-Ling , Wang Cheng-Gang , Wu Mong-Ting , Tsai Meng-Hsun , Lin Chia-Ying
Published: September 2016

Message Queuing Telemetry Transport for Sensor Networks (MQTT-SN) and Constrained Application Protocol (CoAP) are two protocols supporting publish/subscribe models for IoT devices to publish messages to interested subscribers. Retransmission mechanisms are introduced to compensate for the lack of data reliability. If the device does not receive the acknowledgement (ACK) before retransmission timeout (RTO) expires, the device will retransmit data. Setting an appropriate RTO is important because the delay may be large or retransmission may be too frequent when the RTO is inappropriate. We propose a Gateway-assisted CoAP (GaCoAP) to dynamically compute RTO for devices. Simulation models are proposed to investigate the performance of GaCoAP compared with four other methods. The experiment results show that GaCoAP is more suitable for IoT devices.
Approaches to Sampling Gay, Bisexual, and Other Men Who Have Sex with Men from Geosocial-Networking Smartphone Applications: A Methodological Note
Authors: Goedel William , Brooks Forrest , Duncan Dustin
Published: September 2016

Geosocial-networking smartphone applications utilize global positioning system (GPS) technologies to connect users based on their physical proximity. Many gay, bisexual, and other men who have sex with men (MSM) have smartphones, and these new mobile technologies have generated quicker and easier modes for MSM to meet potential partners. In doing so, these technologies may facilitate a user’s ability to have multiple concurrent partners, thereby increasing their risk for acquiring HIV or other sexually transmitted infections. Researchers have sought to recruit users of these applications (e.g., Grindr, Jack’d, Scruff) into HIV prevention studies, primarily through advertising on the application. Given that these advertisements often broadly targeted large urban areas, these approaches have generated samples that are not representative of the population of users of the given application in a given area. As such, we propose a method to generate a spatially representative sample of MSM via direct messaging on a given application using New York City and its geography as an example of this sampling and recruitment method. These methods can increase geographic representativeness and wider access to MSM who use geosocial-networking smartphone applications.