bluuebunny/crossref_metadata_2025 huggingface dataset:
The American Dream: Its Echoes and Possibilities in Literary Discourse
Authors: Kalu Obasi Kalu,
Published: January 2018

The American Dream stems from the inaugural speech of President Franklin Roosevelt’s “Four Freedoms”(1941). The Four Freedoms envisaged an American society where the freedom of worship, freedom of speech, freedom of movement and the rights to life are enshrined, guaranteed, and accommodated. America has been clouded with numerous yearnings from all angles – politics, academic, economic, among other social upheavals for the enthronement of the Four Freedoms. Literary scholars have diminutively expressed the horrors of African Americans in various forms and shades, and have hopefully waited for the day it will be implemented. This paper attempts to relay the horrors, echoes, and possibilities of the American Dream as expressed by literary scholars, and the mass media. It also attempts to unveil the measures the African Americans have tried to live within the face of the horrors that have attained their existence among the White Americans. The possibilities of their struggles to live above subjugations, oppressions, the Jim Crow Laws, and racial discrimination that have rocked the American society for decades are also within the wavelength of this work.
Adjustment of Lactation Curves of Holstein Cows from Herds of Minas Gerais, Brazil
Authors: Azevedo Junior Jairo , Gonçalves Tarcisio De Moraes , De Souza José Camisão , Rodriguez Mary Ana Petersen , Costa Cláudio Nápolis , Carvalheira Júlio Gil Vale
Published: January 2018

Random regression models (RRM) differ in terms of the functions used to describe the shape of lactation curves. The aim was to compare random regression models under different functions to describe the lactation curves from Holstein cows in herds of the state of Minas Gerais. A database of 28,118 production records was analyzed using the test-day records of 4,230 first parity cows from five herds. The Wilmink, Ali & Schaeffer and Legendre polynomial (orders 4, 5 and 6) functions were adjusted in RRM to model the mean production trend (fixed) and genetic and permanent environmental (random) effects. The residual variances were assumed to be constant throughout lactation. Analyses were performed using the AIREMLF90 program. Except for the model with the polynomial function of order 5, all models converged. The Wilmink function showed lower values for criteria based on the -2log (L), AIC and BIC. The model with the Legendre polynomial of order 6 showed lower residual variance. Heritability estimates were similar between functions, ranging from 0.07 to 0.18 and were higher from 215 days of lactation. From 155 days of lactation, genetic and permanent environmental correlations between successive controls are of high magnitude. The Wilmink function is the most suitable for the study of milk yields from primiparous Holstein cows. The selection of animals is possible from 155 days of lactation on. Permanent environmental effects have greater influence on the milk production at the end of lactation of primiparous cows and should be considered since they are important and may be cumulative throughout lactation.
Climatic and Soil Water Balances for the Melon Crop
Authors: Mota Jaedson Cláudio Anunciato , Libardi Paulo Leonel , Assis Júnior Raimundo Nonato , Brito Alexsandro Santos , Lobato Márcio Godofrêdo Rocha , Alencar Thiago Leite , Freire Alcione Guimarães , Lima Júnior Juarez Cassiano
Published: January 2018

The correct estimate of the water requirements of a crop, besides favoring its full development, also allows the rational use of water. In this context, this study aimed to evaluate water balance in the soil and estimated through climatic methods for the melon crop. Field water balance was daily determined along a period of 70 days. Climatic water balance was determined based on the reference evapotranspiration estimated by the methods of Penman-Monteith, Thornthwaite and Hargreaves-Samani. It was concluded that climatic methods do not estimate correctly water storage in the soil and, consequently, also the balance. Therefore, they should not substitute the soil water balance method to determine these variables. The water management for the melon crop based on evapotranspiration estimated through climatic methods results in overestimation of the water depth to be applied in the soil, in the initial growth stage, and underestimation in the periods of highest water demand.
Fatty Acid Composition, Acetylcholinesterase and Bacterial Inhibition by Inga cinnamomea Pulp
Authors: Abreu Herliana Damelys Flores , Melo Filho Antonio Alves de , Ribeiro Pedro Rômulo Estevam , Linhares Bernardo de Morais , Campêlo Maria da Conceição Freitas , Takahashi Jacqueline Aparecida , Barreto Debora Luiza Costa , Duarte Nathália Barroso Almeida , Ferraz Vany Perpetua , Costa Habdel Nasser Rocha da
Published: January 2018

Inga cinnamomea, a species from Fabaceae family, posses a convex-cylindrical fruit that has a white, slightly sweet, edible pulp, which is very appreciated in Brazil. The present study seeks to expand the knowledge about this fruit. The vegetable oil of the fruit’s pulp, extracted in a Soxhlet extractor using hexane as solvent, was studied. Fatty acids were determined, after oil hydrolysis and methylation, using gas chromatography with flame ionization detector (GC-FID). Additionally, the oil was tested to determine its potential as acetylcholinesterase inhibitor using Eserine as positive control. Bactericidal potential of the oil was also determined. Both assays were accomplished using Elisa spectrophotometer. Eight major fatty acids were detected in the following concentrations: linoleic (ω6) (31.7%), palmitic (26.2%), linolenic (ω3) (13.6%), oleic (ω9) (12.5%), stearic (6.5%), palmitoleic (ω7) (2.0%), myristic (0.6%) and arachidic (0.6%) acids. The oil inhibitory activity towards acetylcholinesterase enzyme was 54.81%, being classified as a potent effect. Finally, the oil presented a modest inhibitory activity against the following bacterial strains: Staphylococcus aureus (24.68%), Citrobacter freundii (20.46%), Listeria monocytogenes (27.26%) and Pseudomonas aeruginosa (26.89%).
Integral-cultural definition of a criminal punishment
An integral-cultural definition: source and application
Authors: Utrat-Milecki Jarosław
Published: January 2018

Many scholars feel, like the legal philosopher Joelberg, that "punishment from a theoretical point of view is something mysterious, and from a moral point of view - disturbing" .
The mystery and disturbing ambiguity of the punishment makes the formulation of its definition, and the definition of a criminal punishment in particular, which would be satisfactory, an extremely difficult task. A way out of an embarrassing situation of defining a criminal punishment is to indicate the most important circumstances and conditions that must be met in order for some social action to be called a punishment. This involves an exhaustive and comprehensive indication of the components ("constituent elements of punishment"), and at the same time a sharp cut-off of all other types of activities The question about constituent elements that give particular teams behaviour, carried out by authorized persons, the character of a criminal punishment does not concern the description of patterns of such a behaviour and their fulfilment, such as the action related to the enforcement of the obligation to pay a certain amount, physical deprivation of liberty or fulfilment of the obligation to work. It is important, however, to define the conditions in which the legal formulas of such behavior and the specific actions taken on their basis and the situations resulting from them can be described as a criminal punishment.
Treatment Optimization of Electrocoagulation (EC) in Purifying Palm Oil Mill Effluents (POMEs)
Authors: Rusdianasari R. , Taqwa Ahmad , Jaksen Jaksen , Syakdani Adi
Published: January 2018

Palm oil mill effluents (POMEs) can contaminate soil, groundwater, and also the water environment. The increasing production of crude palm oil in Indonesia produces an enormous amount of POME waste. Therefore, a method is needed that can be used to purify POMEs. In this paper, an electrocoagulation (EC) method for purification of wastewater and a design to optimize this method are presented. An optimization experiment was performed by varying voltage and process time. The applied voltages were 6, 9, and 12 V and the process time was varied between 30 and 150 minutes. The measured parameters were: COD, BOD5, pH, TSS, lipids, and NH3-N. The result shows that optimum conditions were achieved at a voltage of 12 V and a process time of 150 minutes with COD at 8000 mg/L, BOD5­ at 12000 mg/L, pH at 7.46, TSS at 324 mg/L, lipids at 17.8 mg/L, and NH3-N at 0.65 mg/L. The results are in accordance with environmental quality standards for pure water. This study proves that the proposed EC method is effective in purifying POMEs from pollutants.
Confirmatory factor analysis and psychometric properties of the Revised Child Anxiety and Depression Scale−30 (RCADS-30) in clinical and non-clinical samples
Authors: Piqueras Jose Antonio , Pineda David , Martin-Vivar María , Sandín Bonifacio
Published: January 2018

Abstract: The 30-item shortened version of the Revised Child Anxiety and Depression Scale (RCADS-30) is a self-report instrument to assess symptoms of anxiety and depressive disorders. This study examined the factor structure, reliability, and construct validity of the RCADS-30, based on a sample of children and adolescents in clinical and community settings. Results provide evidence for (a) the six factors of the scale (separation anxiety disorder, generalized anxiety disorder, panic disorder, social phobia, obsessive-compulsive disorder, and major depressive disorder), (b) reliability (alpha and omega), and (c) convergent and discriminant validity against self-report and clinical interview criteria. The RCADS-30 demonstrated sound psychometric properties and that it is a suitable instrument to assess depression and anxiety disorder symptoms. Based on established cut-off scores, the scale also showed adequate capacity to differentiate emotional disorders from other mental disorders or the absence of diagnosis.Resumen: Análisis factorial confirmatorio y propiedades psicométricas de la Revised Child Anxiety and Depression Scale (RCADS-30) en muestras clínicas y no clínicas. La versión abreviada de 30 ítems de la Revised Child Anxiety and Depression Scale (RCADS-30) es un instrumento de autoinforme para evaluar síntomas de los trastornos de ansiedad y depresivos. Este estudio examinó la estructura factorial, la fiabilidad y la validez de constructo de la RCADS-30 en una muestra de niños y adolescentes procedentes de muestras clínicas y comunitarias. Los resultados aportan evidencia sobre (a) los seis factores de la escala (trastorno de ansiedad de separación, trastorno de ansiedad generalizada, trastorno de pánico, fobia social, trastorno obsesivo-compulsivo, y trastorno depresivo mayor), (b) fiabilidad (alfa y omega), y (c) validez convergente y discriminante sobre autoinformes y entrevista clínica. La RCADS-30 demostró poseer buenas propiedades psicométricas y ser adecuada para evaluar los síntomas de los trastornos de ansiedad y depresivos. Sobre la base de puntos de corte establecidos, la escala mostró adecuada capacidad para diferenciar los trastornos emocionales de otros problemas mentales o la ausencia de diagnóstico.
A cultural psychological analysis of collective memory as mediated action: Constructions of Indian history
Authors: Mukherjee Sahana , Adams Glenn , Molina Ludwin E.
Published: January 2018

The present research applies a cultural psychological perspective on collective memory as mediated action to examine how constructions of a national past serve as tools that both reflect and shape national identity concerns. We employ a situation-sampling method to investigate collective memory in a series of studies concerning intergroup relations in the Indian context. In Study 1, participants (N = 55) generated three historical events that they considered important/relevant for Indian history. In Study 2, participants (N = 95) rated the importance and relevance of these events in a within-participant design. Illuminating the psychological constitution of cultural reality, frequency of recall (Study 1) and ratings of importance/relevance (Study 2) were greater for nation-glorifying events celebrating ingroup triumph than for typically silenced, critical events acknowledging ingroup wrongdoing. Moreover, these patterns were stronger among participants who scored higher in national identification. In Studies 3 (N = 65) and 4 (N = 160), we exposed participants to different categories of events in a between-participants design. Illuminating the cultural constitution of psychological experience, participants exposed to typically silenced, critical events reported lower national identification and greater perception of injustice against marginalized groups than did participants exposed to nation-glorifying events. Together, results illuminate a conception of collective memory as mediated action. Producers invest memory products with an identity-interested charge that directs subsequent intergroup relations toward identity-consistent ends.
Introduction
Authors: Lund Jacob , Sejten Anne
Published: January 2018

Across philosophical traditions the question of taste has – at least paradigmatically since Kant’s third critique – been one of the most, perhaps the most central question within the discipline of aesthetics. The present issue of NJA explores ways in which this question can be addressed today; politically, analytically, historically, disciplinarily. The articles all stem from the inaugural conference of the research network Aesthetics Unlimited, which was held at Roskilde University, Denmark on 4–5 May 2017. Collaborating with Séminaire d’Esthétique Européen this new international research network for aesthetic studies is funded by the Danish Council for Independent Research and is led by Anne Elisabeth Sejten, Professor of Aesthetics at Roskilde University.
THE ORIGINS OF THE TRANSCENDENTAL JUSTIFICATION OF TASTE: KANT’S SEVERAL VIEWS ON THE STATUS OF BEAUTY
Authors: Pedersen Esther
Published: January 2018

The article follows Kant’s different views on aesthetics ranging from the pre-critical period to the Critique of the Power of Judgement. It argues that John Zammito’s psychological explanation of why Kant in the third Critique developed an argument for the transcendental justification of judgements of taste is unconvincing. As an alternative, the article shows how Kant in his published pre-critical discussions of aesthetics was relying upon empiricist sources while he in private comments turned to consider the culture critique of Rousseau. Kant’s preoccupation with questions of culture critique, it is argued, was an important reason to enlarge the doctrines of transcendental philosophy with a third Critique containing a transcendental aesthetics of beauty. Additionally, it is pointed out an interesting similarity throughout the development of Kant’s philosophy. In 1765 and in the third Critique Kant was concerned to keep philosophy and judgements of taste apart from science
Propuesta de un nuevo cuestionario de evaluación de los profesores de la Universidad del País Vasco. Estudio psicométrico, dimensional y diferencial
Authors: Lizasoain-Hernández Luis , Etxeberria-Murgiondo Juan , Lukas-Mujika José Francisco
Published: January 2018

El objetivo de este artículo es analizar el proyecto de nuevo cuestionario diseñado por la Universidad del País Vasco (UPV/EHU) para realizar la evaluación de sus docentes (SET). Se analizan las respuestas de una muestra de 941 estudiantes y se estudia la fiabilidad del cuestionario, la dimensionalidad, la validez de constructo y criterial, finalizando con un estudio diferencial tomando en cuenta variables como el género, el campo disciplinar, el nivel percibido de dificultad o el interés de las materias. Los resultados permiten afirmar que se trata de un instrumento de alta consistencia interna y esencialmente unidimensional pero que, a la vez, se ajusta a las dimensiones teóricas usadas para su diseño y construcción lo que posibilita un uso formativo de la información.
A Newly Discovered Roll Copy of Peter of Poitier‘s Compendium historiae in genealogia Christi (JRL Gaster MS 2037) and Alexander Nequam on the Immaculate Conception
Authors: O‘Daly Irene
Published: January 2018

This article investigates a series of additions made to JRL Gaster MS 2037, a
newly identified copy of Peter of Poitier‘s Compendium historiae in genealogia
Christi. Following a detailed description and dating of the manuscript, it
investigates two sets of additions to the roll in depth. It establishes that the
first motive behind the inclusion of such additions was educative – serving to
extend the historic information given in the Compendium, while the second motive
was devotional – elevating the status of the Virgin Mary through the enhancement
of her genealogical record. Given the fact that the manuscript was produced in
the mid-fifteenth century, this focus on the Virgin likely had a polemic
purpose, situating the manuscript in the context of debates over the Immaculate
Conception, and using Alexander Nequams Expositio super Cantica canticorumto
this end. In identifying the sources used, as well as the limits on the compiler
imposed by the physical form of the roll, this examination of Gaster MS 2037
offers an insight into the later reception of this popular text.
Zeta potential of bacteria cells: Effect of wash buffers
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy parameter for bacteria cell surface charge. Nonspecific adsorption of ions or polyelectrolytes onto the cell surface, however, alters the value and polarity of the measured zeta potential, leading to erroneous results. Multiple wash and centrifugation steps are commonly used in preparing cells for zeta potential analysis, where various wash buffers (such as 9 g/L NaCl, 0.001M KCl, and 0.1M NaNO3) are routinely used for removing (by charge screening) ions and charged molecules that bind nonspecifically to the cell surface. Using Escherichia coli DH5α grown in LB Lennox (with 2 g/L glucose, LBG hereafter), experiment data showed that the zeta potential-pH profile was not significantly different over the pH range from 2 to 12 for deionized water, 9 g/L NaCl, and phosphate buffer saline (PBS) wash buffers. As LBG is a low salt medium without a phosphate buffer, it was likely that the extent of nonspecific adsorption of ions on the cell surface was not severe, and the different wash buffers would correspondingly not exert much effect on measured zeta potential. Zeta potential-pH profiles for E. coli grown in a semi-defined medium (with a high capacity phosphate buffer system), on the other hand, was significantly different over the pH range from 1 to 12 for deionized water, 9 g/L NaCl, 0.1M NaNO3, 0.1M sodium acetate, and 0.1M sodium citrate wash buffers with the deviation positively correlated with wash buffer’s ionic strength. Furthermore, the point of zero charge (pHzpc) for E. coli grown in the semi-defined medium varies between 1.5 and 3, in an ionic strength-dependent manner, for the various wash buffers tested. Collectively, this preliminary study highlights the importance of wash buffer ionic strength in affecting removal efficiency of non-specifically absorbed ions on bacteria cell surface, where a threshold exists (0.15M) for charge screening to be effective. At the upper bound, however, 0.6M ionic strength might remove cations intrinsic to cell envelope, leading to possible cell surface damage and erroneous measurements.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flasks: Part 1
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Sufficient quantities of cells of consistent characteristics are needed for studying biological processes (at the population level) in many areas of applied microbiology. However, generating the requisite biomass by cell culture is usually the rate-limiting step of a project given the relatively low biomass yield of many commercial culture media in shake flasks. This work reports the formulation of a semi-defined medium that enabled aerobic high cell density cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. The formulated medium (FM) comprises: a buffer system (K2HPO4: 12.54 g/L and KH2PO4: 2.31 g/L); vitamins and trace elements (yeast extract: 12.0 g/L); salts (NaCl: 5.0 g/L and MgSO4: 0.24 g/L); and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium are: high buffer capacity (89 mM phosphate), 1:1 molar ratio between D-Glucose and NH4Cl, and yeast extract providing trace elements and a secondary source of carbon and nitrogen. Preliminary data revealed that an OD600nm of 9 was attained after 24 hours of cultivation at 37 oC, with glucose and NH4Cl as the main nutrients. At 48 hours, the OD600nm reached a maximum value of 11 with yeast extract providing the necessary nutrients for cell growth and biomass formation. The broth’s pH varied between 5.5 and 7.8 during cultivation. For comparison, the maximum OD600nm of E. coli grown in three commonly used complex media: Nutrient Broth, LB Lennox, and Tryptic Soy Broth (TSB) were 1.4, 3.2 and 9.2, respectively, under identical culture conditions. Finally, FM maintained the viability of a larger population of cells for three days - compared to a population collapse observed in TSB after one day. Collectively, the present findings suggested that the formulated medium might find use as a high cell density aerobic growth medium for E. coli in shake flasks. Part 2 of this work describes improvements in medium performance - specifically, higher cell yield as well as a shorter diauxic lag phase and total culture period – achieved through a small reduction in D-Glucose and NH4Cl concentrations in the medium composition. An abstract preprint of Part 2 is available at https://peerj.com/preprints/117/
Stress-induced production of lipids in oleaginous microalgae for biofuel optimization
Authors: Teichner Eric M
Published: January 2018

Emerging concerns over energy security and accelerating climate change have led to a global interest in developing a sustainable biofuel. Recently, it was determined that algal biofuels can be possibly cultured in a wastewater medium due to high levels of nutrients nitrogen, phosphorus, and potassium (NPK), reducing economic costs. Further efforts are needed in strain selection for cultivation in wastewater or inexpensive fertilizer. Common algal strains Nannochloropsis sp. and Chlorella sp. were studied to determine effects. Both strains were exposed to standard nutrients, which acted as controls, and high levels of NPK to simulate wastewater. The results revealed that NPK had a positive effect on turbidity and dissolved oxygen while decreasing the lipid productivities (measured via hexane solvent extraction) by an average of 36.5%. Specifically, Nannochloropsis sp. had overall higher values for all dependent variables. It is believed that under nutrient limiting conditions the cells deposited fatty acids in a triacylglycerol pathway. A follow-up experiment was performed using salinity as a novel method of decreasing biomass while maintaining lipid viability. Results revealed that freshwater algae can be cultivated in salinity levels between 10-15 ppt in order to increase lipid production. It is believed that while salinity osmotically interfered with the cell, lipid content increased, acting as a protective mechanism. Future research should focus on optimizing lipid production under stressed conditions using genetic manipulation of the TAG biosynthesis pathway.
Frequency distribution and mean comparisons of red light absorbance-transmittance of the e1 leaf sectors of five pipeline maize hybrids during early grain filling in subtropical winter
Authors: Adhikari Nav Raj , Ghimire Surya Kant , Sah Shrawan Kumar , Koirala Keshab Babu
Published: January 2018

Background: Crop scientist’s curiosities were to examine variation in photosynthetic sectors of grain filler leaf or flag leaf of any major crop species. Crop scientists including plant breeders too will be privileged from the findings. So it includes such precision evaluation of single cross pipeline hybrids of yellow maize before their release as cultivars. Materials and methods: For it, five pipeline hybrids were examined from two trials of RCBD trial that they were in a big research plot with uniform soil fertility level and with the same control environment. Each of the trials was conducted planting the seeds of the fifteen newly bred separate hybrids on October 3, 2012 exposing their flowering and early grain filling to the natural winter in the subtropical region in Nepal. Five plants of the pipeline hybrids of the fifteen plots of three replications were randomly selected and tagged from each of the fifteen plots of the five hybrids before tassel emergence. After about one month of anthesis, one hundred observations of red light absorbance-transmittance (RAT) measures were taken from chlorophyll meter ‘SPAD 502’ (Soil Plant Analysis Development) from the just-above-ear (e1) leaf of each of the selected plants of the hybrids in three days from 99 to 101 days after sowing (DAS). Results and discussion: From analysis of frequency distribution of the RAT SPAD measures of the e1 leaf sectors, it is not necessary that hybrids that demonstrates curve with high kurtosis always yield higher. Among the five hybrids, second highest grain yielding hybrid 112 had least leaf sectors of very low RAT SPAD measures. Besides, the hybrid 112 has been found least skewed and least peaked among the five hybrids. Furthermore, the hybrid 112 displayed least coefficient of variation and standard deviation among the 1500 RAT SPAD readings of its e1 leaf sectors. From the mean analysis through DMRT (Duncan Multiple Range Test), the twenty four averages have been found almost non-significant different among themselves inside each of the five hybrids. Single reading and four reading averages were non-significant different to one hundred reading average of each of the fifteen selected plants. Besides, the study also implies that a single reading from a leaf in the surrounding region of the topmost ear in five randomly selected plants can suffice to reflect the average SPAD measure of the particular leaf if the readings are from the e1 leaf. But, it can also be concluded that the similar non-significant nature of average central leaves around the top ear node. The mean comparison also gives useful information about the methodology of taking SPAD observations and how many readings are enough for the study of red light absorbance-transmittance, chl and N concentration in maize leaves. It also includes explanation why the e1 leaf is taken in the study.
PhilDB - The time series database with built-in change logging
Authors: MacDonald Andrew
Published: January 2018

PhilDB is an open-source time series database. It supports storage of time series datasets that are dynamic, that is recording updates to existing values in a log as they occur. Recent open-source systems, such as InfluxDB and OpenTSDB, have been developed to indefinitely store long-period, high-resolution time series data. Unfortunately they require a large initial installation investment before use because they are designed to operate over a cluster of servers to achieve high-performance writing of static data in real time. In essence, they have a ‘big data’ approach to storage and access. Other open-source projects for handling time series data that don’t take the ‘big data’ approach are also relatively new and are complex or incomplete. None of these systems gracefully handle revision of existing data while tracking values that changed. Unlike ‘big data’ solutions, PhilDB has been designed for single machine deployment on commodity hardware, reducing the barrier to deployment. PhilDB eases loading of data for the user by utilising an intelligent data write method. It preserves existing values during updates and abstracts the update complexity required to achieve logging of data value changes. PhilDB improves accessing datasets by two methods. Firstly, it uses fast reads which make it practical to select data for analysis. Secondly, it uses simple read methods to minimise effort required to extract data. PhilDB takes a unique approach to meta-data tracking; optional attribute attachment. This facilitates scaling the complexities of storing a wide variety of data. That is, it allows time series data to be loaded as time series instances with minimal initial meta-data, yet additional attributes can be created and attached to differentiate the time series instances as a wider variety of data is needed. PhilDB was written in Python, leveraging existing libraries. This paper describes the general approach, architecture, and philosophy of the PhilDB software.
Phylogenetics and population genetics of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
Authors: Khalili Samani Nima , Esa Yuzine , Mohd Ikhsan Natrah Fatin , Amin S.M Nurul
Published: January 2018

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of more COI genes and nuclear hypervariable markers.
FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models
Authors: Christensen Anders Steen , Jensen Jan H , Hamelryck Thomas
Published: January 2018

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.
Microbes in deionized water: Implications for maintenance of laboratory water production system
Authors: Ng Wenfa
Published: January 2018

Microbes, with their vast metabolic capabilities and great adaptability, occupy almost every conceivable ecological niche on Earth. Thus, could they survive in the oligotrophic (i.e., nutrient poor) deionized (DI) water that we use for experiments? Observations of white cauliflower-like lumps and black specks in salt solutions after months of storage in plastic bottles prompted the inquisition concerning the origin and nature of the “contaminants”. Hypothesizing that the “contaminants” may be microbes from DI water, a series of growth experiments was conducted to detect and profile the diversity of microbes in fresh DI water, produced on a just-in-time basis by a filter cum ion exchange system with tap water as feed. While microbes could also be present on the surfaces and headspace of the unsterilized polyethylene bottles, investigating whether microbes are present in freshly produced DI water provides a more stringent performance test of the production system. Inoculation of DI water on R2A agar followed by multi-day aerobic cultivation revealed the presence of a wide variety of microbes (total viable cell concentration of ~103 colony forming units (CFU) per mL) with differing pigmentations, growth rates, as well as colony sizes and morphologies. Additionally, greater abundance and diversity of microorganisms was recovered at 30 oC compared to 25 and 37 oC; most probably due to adaptation of microbes to tropical ambient water temperatures of 25 to 30 oC. Comparative experiments with tap water as inoculum recovered a significantly smaller number and diversity of microorganisms; thus, suggesting that monochloramine residual disinfectant in tap water was effective in inhibiting cell viability. In contrast, possible removal of monochloramine by adsorption onto ion exchange resins (and thus, alleviation of a source of environmental stress) might explain the observed greater diversity and abundance of viable microbes in DI water. Collectively, this study confirmed the presence of microbes in fresh DI water, and suggested a possible source of the “contaminants” in prepared salt solutions. Propensity of microbes in forming biofilm on various surfaces suggested that intermittent flow in just-in-time DI water production provided opportunities for cell attachment and biofilm formation during water stagnation, and subsequent dislodgement and resuspension of cells upon water flow. Thus, regular maintenance and cleaning of the production system should help reduce DI water’s microorganism load. In addition, simple and low cost culture experiments on solid medium can provide a qualitative and semi-quantitative estimate of microbial diversity and viable cell concentration in DI water, respectively. The above, together with regular monitoring of water resistivity or conductivity, comprise a trio of tests useful for detecting possible contamination, or deterioration of DI water’s chemical and microbiological quality.
Animal-oriented Virtual Environments: illusion, dilation, and discovery
Authors: Alicea Bradly
Published: January 2018

As a research tool, virtual environments hold immense promise for brain scientists. Yet to fully realize this potential in non-human systems, theoretical and conceptual perspectives must be developed. When selectively coupled to nervous systems, virtual environments can help us better understand the functional architecture of animals brains during naturalistic behaviors. While this will no doubt allow us to further our understanding of the neural bases of behavior, there is also an opportunity to uncover the diversity inherent in brain activity and behavior. This is due to two properties of virtual environments: the ability to create sensory illusions, and the ability to dilate space and/or time. These issues will be presented in the context of three types of neurobehavioral phenomena: sensorimotor integration, spatial navigation, and interactivity. For each of these behaviors, a combination of illusory and time dilation examples will be reviewed. Once these applications have been reviewed, implications for improving upon virtual models for inducing the mental phenomena of illusion and time dilation will be considered. To conclude, future directions for this research area will be presented, particularly with relevance to gene-environment interactions.
Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?
Authors: Silva Pedro J
Published: January 2018

1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozymeand has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the very sluggish C4-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere.
Modeling potential distribution of Indo-Pacific humpback dolphins (Sousa chinensis) in the Beibu Gulf, China
Authors: Chen Mei , Song Yuqin , Qin Dagong
Published: January 2018

Mapping key habitats of marine mega-vertebrates with high mobility is crucial for establishing Marine Protected Area (MPA) networks. Due to difficulties in achieving sound data in the field, Species Distribution Modeling (SDM) provide an efficient alternative. As a keystone and flagship species in inshore waters in southern China, Indo-Pacific humpback dolphins (Sousa chinensis) play an important role in coastal ecosystems. We used a maximum entropy (Maxent) modeling approach to predict potential habitats for the dolphins in the Beibu Gulf of China. Models was based on eight independent oceanographic parameters derived from Google Earth Digital Elevation Model (DEM) and Landsat images, and presence-only data from boat-based surveys between 2003 and 2013. Three variables, distance from major estuaries, from coast and from 10-m isobaths, were the strongest predictors, consistent with previous studies. Apart from known areas, a new area, Beilunhe Estuary (BE) close to the boundary of China and Vietnam was predicted. Based on our findings, we proposed a regional MPA network for humpback dolphins in the Beibu Gulf of China.
Head motion in children with ADHD during resting-state brain imaging
Authors: Kong Xiang-zhen
Published: January 2018

Resting-state functional MRI (rs-fMRI) has become an important method for analyzing the neural mechanisms underlying mental disorders. But studies targeting head motion during an rs-fMRI examination are rare. Since head motion may pollute the data in the neural imaging studies and further mislead the understanding of the causes of some disorders, systematic investigations on this topic were badly needed. To this end, in this study, children with attention-deficit/hyperactivity disorder (ADHD) and demographically-matched typically developing control (TDC) participants underwent an rs-fMRI examination. We obtained a summary motion index and six mean single head motion parameters (three translational and three rotational) for each participant. With the summary index, we found that motion was significantly increased in the ADHD group and the results showed that the increase was mainly contributed by the motion around and along the superior-to-inferior direction. Moreover, the classification analysis showed that these head motion parameters during scanning could accurately distinguish children with ADHD from the healthy control group. These results suggest that accounting for head motion during scanning may be helpful for ADHD diagnosis and treatment with neuroimaging.
High School Pupils’ Academic Achievement, Self-regulation (Locomotion and Assessment), and Psychological Well-Being
Authors: Garcia Danilo , Jimmefors Alexander , Adrianson Lillemor , Mousavi Fariba , Rosenberg Patricia , Archer Trevor
Published: January 2018

Background: Education plays an important role on a personal level because it is related to personal control, a healthy lifestyle, greater income, employment, interpersonal relations, and social support (Mirowsky & Ross, 2003). Self-regulation is the procedure implemented by an individual striving to reach a goal and consists of two inter-related strategies: (1) the identification of the desired out-come and the appraisal of procedures to reach the desired goal (i.e., assessment), and (2) the selection between available approaches to reach the goal and the commitment to the chosen approaches until the goal is reached (i.e., locomotion) (Kruglanski et al, 2000). Self-regulation plays an essential role in academic achievement (Kruglanski et al 1994, 2000). Psychological well-being is a multi-faceted concept composed of six different intra-personal characteristics that describe the fully functional individual (Ryff, 1989). These factors are: positive relationships with others, self-acceptance, environmental mastery, autonomy, purpose in life, and personal growth. We aimed to study the relationship between academic achievement and self-regulation and psychological well-being in Swedish high school pupils.

Method: Participants were 160 Swedish high school pupils (111 boys and 49 girls) with an age mean of 17.74 (sd = 1.29). We used the Assessment and Locomotion Scales (Kruglanski et al., 2000) to measure self-regulation and Ryff’s Psychological Well-Being Scales short version (Clark et al., 2001) to measure well-being. Academic achievement was operationalized through pupils’ final grades in Swedish, Mathematics, English, and Physical Education. The courses take place during either one or two semesters and the grading scale ranges from F = fail to A = pass with distinction.

Results: Final grades in Swedish were positively related to two psychological well-being scales: self-acceptance and personal growth; and to the self-regulation strategy of assessment. Final grades in Mathematics were positively related to three psychological well-being scales: self-acceptance, autonomy, and personal growth; and also to assessment. Final grades in English were positively related to one psychological well-being scale: personal growth; and also to assessment. Final grades in Physical Education were positively related to four psychological well-being scales: environmental mastery, self-acceptance, autonomy, and personal growth; and also to the self-regulation strategy of locomotion.

Conclusions: A profile consisting of assessment orientation combined with self-acceptance and personal growth leads to the best study results. This understanding is important when supporting pupils in achieving the best possible results in school and thus lay the formation for a continued successful life.
Castration modulates singing patterns and electrophysiological properties of RA projection neurons in adult male zebra finches
Authors: Li Dongfeng , Wang Songhua , Liao Congshu , Liu Shaoyi , Li Fengling , Meng Wei
Published: January 2018

Castration can change levels of plasma testosterone. Androgens such as testosterone play an important role in stabilizing birdsong. The robust nucleus of the arcopallium (RA) is an important premotor nucleus critical for singing. In this study, we investigated the effect of castration on singing patterns and electrophysiological properties of projection neurons (PNs) in the RA of adult male zebra finches.Adult male zebra finches were castrated and the changes in bird song assessed. We also recorded the electrophysiological changes from RA PNs using patch clamp recording. We found that the plasma levels of testosterone were significantly decreased, song syllable’s entropy was increased and the similarity of motif was decreased after castration. Spontaneous and evoked firing rates, membrane time constants, and membrane capacitance of RA PNs in the castration group were lower than those of the control and the sham groups. Afterhyperpolarization（AHP）time to peak of spontaneous action potential (AP) was prolonged after castration.These findings suggest that castration decreases song stereotypy and excitability of RA PNs in male zebra finches.
DNA methylation marks inter-nucleosome linker regions throughout the human genome
Authors: Berman Benjamin P. , Liu Yaping , Kelly Theresa K.
Published: January 2018

Nucleosome organization and DNA methylation are two epigenetic mechanisms that are important for proper control of mammalian transcription. Numerous lines of evidence suggest an interaction between these two mechanisms, but the nature of this interaction in vivo remains elusive. Whole-genome DNA methylation sequencing studies have shown that human methylation levels are periodic at intervals of approximately 190 bp, suggesting a genome-wide relationship between the two marks. A recent report (Chodavarapu et al., 2010) attributed this to higher methylation levels of DNA within nucleosomes. Here, we propose an alternate explanation for these nucleosomal periodicities. By examining methylation patterns in published datasets, we find that genome-wide methylation levels are highest within the linker regions that occur between nucleosomes in multi-nucleosome arrays. This effect is most prominent within long-range Partially Methylated Domains (PMDs) and the strongly positioned nucleosomes that flank CTCF binding sites. The CTCF-flanking nucleosomes retain positioning even in regions completely devoid of CpG dinucleotides, suggesting that DNA methylation is not required for proper positioning. We propose that DNA methylation is inhibited by histone proteins at CTCF and other unknown classes of nucleosomes within PMDs.
In a fit of pique: Analyzing microbial ChIP-Seq data with Pique
Authors: Neches Russell Y , Facciotti Marc T , Seitzer Phillip M , Wilbanks Elizabeth G
Published: January 2018

While numerous effective peak finders have been developed for eukaryotic systems, we have found that the approaches used can be error prone when run on high coverage bacterial and archaeal ChIP-Seq datasets. We have developed Pique, an easy to use ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. The software is cross-platform and Open Source, and based on only freely licensed dependencies. Output is provided in standardized file formats, and may be easily imported by the Gaggle Genome Browser (Bare et al. 2010) for manual curation and data exploration, or into statistical and graphics software such as R (R Core Team 2013) for further analysis. The software is available under the BSD-3 license, and tutorial and test data are included with the documentation.

http://github.com/ryneches/pique.