bluuebunny/crossref_metadata_2025 huggingface dataset:
Streaming stochastic variational Bayes; An improved approach for Bayesian inference with data streams
Authors: Jihan Nadheesh , Jayasinghe Malith , Perera Srinath
Published: June 2019

Online learning is an essential tool for predictive analysis based on continuous, endless data streams. Adopting Bayesian inference for online settings allows hierarchical modeling while representing the uncertainty of model parameters. Existing online inference techniques are motivated by either the traditional Bayesian updating or the stochastic optimizations. However, traditional Bayesian updating suffers from overconfidence posteriors, where posterior variance becomes too inadequate to adapt to new changes to the posterior. On the other hand, stochastic optimization of variational objective demands exhausting additional analysis to optimize a hyperparameter that controls the posterior variance. In this paper, we present ''Streaming Stochastic Variational Bayes" (SSVB)—a novel online approximation inference framework for data streaming to address the aforementioned shortcomings of the current state-of-the-art. SSVB adjusts its posterior variance duly without any user-specified hyperparameters while efficiently accommodating the drifting patterns to the posteriors. Moreover, SSVB can be easily adopted by practitioners for a wide range of models (i.e. simple regression models to complex hierarchical models) with little additional analysis. We appraised the performance of SSVB against Population Variational Inference (PVI), Stochastic Variational Inference (SVI) and Black-box Streaming Variational Bayes (BB-SVB) using two non-conjugate probabilistic models; multinomial logistic regression and linear mixed effect model. Furthermore, we also discuss the significant accuracy gain with SSVB based inference against conventional online learning models for each task.
Identification of compounds that rescue otic and myelination defects in the zebrafish adgrg6 (gpr126) mutant
Authors: Diamantopoulou Elvira , Baxendale Sarah , de la Vega de León Antonio , Asad Anzar , Holdsworth Celia J , Abbas Leila , Gillet Valerie J , Wiggin Giselle R , Whitfield Tanya T
Published: June 2019

Adgrg6 (Gpr126) is an adhesion class G protein-coupled receptor with a conserved role in myelination of the peripheral nervous system. In the zebrafish, mutation of adgrg6 also results in defects in the inner ear: otic tissue fails to down-regulate versican gene expression and morphogenesis is disrupted. We have designed a whole-animal screen that tests for rescue of both up- and down-regulated gene expression in mutant embryos, together with analysis of weak and strong alleles. From a screen of 3120 structurally diverse compounds, we have identified 68 that reduce versican b expression in the adgrg6 mutant ear, 41 of which also restore myelin basic protein gene expression in Schwann cells of mutant embryos. Nineteen compounds unable to rescue a strong adgrg6 allele provide candidates for molecules that may interact directly with the Adgrg6 receptor. Our pipeline provides a powerful approach for identifying compounds that modulate GPCR activity, with potential impact for future drug design.
Nanoresolution real-time 3D orbital tracking for studying mitochondrial trafficking in vertebrate axons in vivo
Authors: Wehnekamp Fabian , Plucińska Gabriela , Thong Rachel , Misgeld Thomas , Lamb Don C
Published: June 2019

We present the development and in vivo application of a feedback-based tracking microscope to follow individual mitochondria in sensory neurons of zebrafish larvae with nanometer precision and millisecond temporal resolution. By combining various technical improvements, we tracked individual mitochondria with unprecedented spatiotemporal resolution over distances of >100 µm. Using these nanoscopic trajectory data, we discriminated five motional states: a fast and a slow directional motion state in both the anterograde and retrograde directions and a stationary state. The transition pattern revealed that, after a pause, mitochondria predominantly persist in the original direction of travel, while transient changes of direction often exhibited longer pauses. Moreover, mitochondria in the vicinity of a second, stationary mitochondria displayed an increased probability to pause. The capability of following and optically manipulating a single organelle with high spatiotemporal resolution in a living organism offers a new approach to elucidating their function in its complete physiological context.
Short-term synaptic dynamics control the activity phase of neurons in an oscillatory network
Authors: Martinez Diana , Anwar Haroon , Bose Amitabha , Bucher Dirk M , Nadim Farzan
Published: June 2019

In oscillatory systems, neuronal activity phase is often independent of network frequency. Such phase maintenance requires adjustment of synaptic input with network frequency, a relationship that we explored using the crab, Cancer borealis, pyloric network. The burst phase of pyloric neurons is relatively constant despite a > two fold variation in network frequency. We used noise input to characterize how input shape influences burst delay of a pyloric neuron, and then used dynamic clamp to examine how burst phase depends on the period, amplitude, duration, and shape of rhythmic synaptic input. Phase constancy across a range of periods required a proportional increase of synaptic duration with period. However, phase maintenance was also promoted by an increase of amplitude and peak phase of synaptic input with period. Mathematical analysis shows how short-term synaptic plasticity can coordinately change amplitude and peak phase to maximize the range of periods over which phase constancy is achieved.
ANP32B, or not to be, that is the question for influenza virus
Authors: Baker Steven F , Mehle Andrew
Published: June 2019

The evolutionary history of ANP32 proteins impacts how influenza virus jumps from birds to mammals.
In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation
Authors: Hernández-Terán Alejandra , Wegier Ana , Benítez Mariana , Lira Rafael , Sosa Fuentes Tania Gabriela , Escalante Ana E.
Published: June 2019

One of the best ex situ conservation strategies for wild germplasm is in vitro conservation of genetic banks. The success of in vitro conservation relies heavily on the micropropagation or performance of the species of interest. In the context of global change, crop production challenges and climate change, we face a reality of intensified crop production strategies, including genetic engineering, which can negatively impact biodiversity conservation. However, the possible consequences of transgene presence for the in vitro performance of populations and its implications for biodiversity conservation are poorly documented. In this study we analyzed experimental evidence of the potential effects of transgene presence on the in vitro performance of Gossypium hirsutum L. populations, representing the Mexican genetic diversity of the species, and reflect on the implications of such presence for ex situ genetic conservation of the natural variation of the species. We followed an experimental in vitro performance approach, in which we included individuals from different wild cotton populations as well as individuals from domesticated populations, in order to differentiate the effects of domestication traits dragged into the wild germplasm pool via gene flow from the effects of transgene presence. We evaluated the in vitro performance of five traits related to plant establishment (N = 300): propagation rate, leaf production rate, height increase rate, microbial growth and root development. Then we conducted statistical tests (PERMANOVA, Wilcoxon post-hoc tests, and NMDS multivariate analyses) to evaluate the differences in the in vitro performance of the studied populations. Although direct causality of the transgenes to observed phenotypes requires strict control of genotypes, the overall results suggest detrimental consequences for the in vitro culture performance of wild cotton populations in the presence of transgenes. This provides experimental, statistically sound evidence to support the implementation of transgene screening of plants to reduce time and economic costs in in vitro establishment, thus contributing to the overarching goal of germplasm conservation for future adaptation.
Stoichiometric ratios support plant adaption to grazing moderated by soil nutrients and root enzymes
Authors: Ma Wenjing , Li Jin , Jimoh Saheed Olaide , Zhang Yujuan , Guo Fenghui , Ding Yong , Li Xiliang , Hou Xiangyang
Published: June 2019

Background

Vegetation succession is one of the major driving processes of grassland degradation. Stoichiometry significantly contributes to vegetation dynamics. However, a knowledge gap exists in how soil nutrients and root enzymes influence the stoichiometric ratio to affect vegetation dynamics.

Methods

To address these questions, we selected a dominant species (Leymus chinensis (Trin.) Tzvel.) and a degraded-dominant species (Artemisia frigida Willd.) under different management regimes (enclosure and grazing) on the Inner Mongolia steppe. We measured (i) plant nutrient concentrations, (ii) root enzymes and (iii) soil nutrients to investigate how the selected plant species responded to grazing.

Results

The results show that: (i) N and P concentrations and the C:N:P ratio in different organs are significantly affected by grazing, and there is variation in the plant species’ response. Grazing significantly increased N and P in the leaves and stems of L. chinensis and the stems and roots of A. frigida. (ii) Grazing significantly increased the activities of glutamine synthase but decreased the activities of acid phosphatase in L. chinensis. The nitrate reductase and acid phosphatase activities significantly increased in A. frigida under grazing conditions. (iii) Grazing decreased the total nitrogen, total phosphorus, and available nitrogen, but increased the available phosphorus in the soil.

Conclusion

We conclude that A. frigida is better adapted to grazing than L. chinensis, possibly because of its relatively increased stem and root growth, which enhance population expansion following grazing. Conversely, L. chinensis showed increased leaf and stem growth, but suffered nutrient and biomass loss as a result of excessive foraging by livestock, which severely affected its ability to colonize. Root enzymes coupled with soil nutrients can regulate plant nutrients and stoichiometric ratios as an adaptive response to grazing. Thus, we demonstrated that stoichiometric ratios allow species to better withstand grazing disturbances. This study provides a new understanding of the mechanisms involved in grazing-resistance within a plant-soil system.
Genome-wide analysis of the WRKY gene family in drumstick (Moringa oleifera Lam.)
Authors: Zhang Junjie , Yang Endian , He Qian , Lin Mengfei , Zhou Wei , Pian Ruiqi , Chen Xiaoyang
Published: June 2019

WRKY proteins belong to one of the largest families of transcription factors. They have important functions in plant growth and development, signal transduction and stress responses. However, little information is available regarding the WRKY family in drumstick (Moringa oleifera Lam.). In the present study, we identified 54 MoWRKY genes in this species using genomic data. On the basis of structural features of the proteins they encode, the MoWRKY genes were classified into three main groups, with the second group being further divided into five subgroups. Phylogenetic trees constructed from the sequences of WRKY domains and overall amino acid compositions derived from drumstick and Arabidopsis were similar; the results indicated that the WRKY domain was the main evolutionary unit of WRKY genes. Gene structure and conserved motif analysis showed that genes with similar structures and proteins with similar motif compositions were usually clustered in the same class. Selective pressure analysis indicated that although neutral evolution and positive selection have happened in several MoWRKY genes, most have evolved under strong purifying selection. Moreover, different subgroups had evolved at different rates. The levels of expression of MoWRKY genes in response to five different abiotic stresses (salt, heat, drought, H2O2, cold) were evaluated by reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR), with the results indicating that these genes had different expression levels and that some may be involved in abiotic stress responses. Our results will provide a foundation for cloning genes with specific functions for use in further research and applications.
Prognosis predictive value of the Oxford Acute Severity of Illness Score for sepsis: a retrospective cohort study
Authors: Chen Qingui , Zhang Lishan , Ge Shanhui , He Wanmei , Zeng Mian
Published: June 2019

Background

The Oxford Acute Severity of Illness Score (OASIS) has shown fair prognosis predictive value in critically ill patients, but its predictive value has not been assessed in septic patients.

Objective

The aim of this study was to evaluate the performance of the OASIS for the assessment of mortality in septic patients, especially when compared with the Sepsis-related Organ Failure Assessment (SOFA) score.

Methods

A retrospective cohort study was conducted using data from a public database and septic patients were identified using the Sepsis-3 criteria. The primary outcome was hospital mortality. Data were mainly analyzed using multivariable logistic regression and receiver operating characteristic (ROC) curves. Sensitive analyses were performed in patients with an ICD-9-CM code for sepsis and ROC curves analyses were also conducted in septic patients stratified by the Simplified Acute Physiology Score (SAPS) II as subgroup analyses.

Results

A total of 10,305 septic patients were included. The OASIS was found to be significantly associated with hospital mortality (odds ratio 1.07 per one-point increase, 95% confidence interval [1.06–1.08]), while ROC curves analyses showed the discriminatory power of the OASIS for hospital mortality was statistically significantly lower than that of the SOFA score (area under the ROC curve: 0.652 vs 0.682, p < 0.001). Results of sensitive analyses were consistent, but the significant difference existed only when the SAPS II was higher than 50 according to results of the subgroup analyses.

Conclusions

The OASIS might serve as an initial predictor of clinical outcomes for septic patients, but one should be circumspect when it is applied to severer patients.
Produção de arroz e feijão em municípios com menores Índices de Desenvolvimento Humano na região do Matopiba, Brasil
Authors: Da Silva Osmira Fátima , Wander Alcido Elenor , Di Stéfano José Geraldo , Didonet Agostinho Dirceu
Published: June 2019

A produção de feijão da região do Matopiba foi de 255,6 mil toneladas, em 2014, colhidas em 430,9 mil hectares, com produtividade média de 593 kg/ha. Essa produção e área representaram, respectivamente, 9,5% e 22,2% do total nacional. A produção de 777,5 mil toneladas de arroz de sequeiro foi colhida em 533,0 mil hectares, que representam, respectivamente, 42,8% e 58,3% da produção e da área nacional do arroz em terras altas. A produtividade média do arroz de terras altas no Brasil foi de 1.986 kg/ha, e na região do Matopiba, de 1.459 kg/ha. O complexo Matopiba, considerado como última fronteira agrícola do Brasil, e compreendendo parte dos estados do Piauí, Maranhão, Tocantins e Bahia, evidencia municípios com produtores descapitalizados, sobretudo, na agricultura familiar, embora seja um reduto onde pode se desenvolver uma agricultura potencial em commodities, a exemplo da região dos cerrados do planalto central, na produção de soja, bioenergia e fibras. Este artigo tem por objetivo a análise comparativa da conjuntura da produção do arroz e do feijão, elementos básicos da alimentação da maior parte da população brasileira, contrapondo-os com os menores Índices de Desenvolvimento Humano Municipal, no complexo Mapotiba.Código JEL | O13; Q18; R11.
Meios de vida e produção de tabaco: uma análise das condições de vida na perspectiva do desenvolvimento humano
Authors: Freitas Tanise Dias , Rambo Anelise Graciele , Schneider Sérgio
Published: June 2019

Este artigo consiste num estudo sobre as condições de vida no meio rural a partir de um caso sobre a agricultura familiar produtora de tabaco, no município de Arroio do Tigre, Rio Grande do Sul, da perspectiva do desenvolvimento humano. O objetivo é analisar os meios de vida a partir de uma concepção de desenvolvimento que ultrapasse o mero crescimento econômico e considere seus aspectos multidimensionais. O presente artigo tem como base teórica a abordagem das capacitações de Amartya Sen, operacionalizada metodologicamente pela perspectiva da diversificação dos meios de vida (livelihoods) de Frank Ellis. Esta abordagem sustenta a proposição metodológica de cinco dimensões do desenvolvimento: natural, social, humano, físico e financeiro. Estas foram agregadas a partir de médias simples e resultaram em dois índices: meios de vida (IMV) e condições de vida (ICV). Os instrumentos foram aplicados a 38 famílias produtoras de tabaco. Os resultados iniciais apontaram que os meios de vida condicionam o desenvolvimento humano das famílias produtoras de tabaco; e os meios apresentam-se de forma diferente das percepções.Código JEL | L66; O13; Q12.
Euthanasia, Female Genital Mutilation, Children with Disabilities: A Review on Societal Issues and Their Scientific Implications
Authors: Ankeli Gabriel Odeh
Published: June 2019

This paper reviewed some societal challenges, their causes, possible scientific solutions to them and the controversies arising from each of them. Three societal problems were identified which are; Euthanasia, Female Genital Mutilation (FGM) and Children with Disabilities (CWDs). The different types of Euthanasia were identified as the active and passive ethanasia respectively also the FGM was discussed under three main types, namely; clitoridectomy, excision, infibulation  and others,  while  the  CWDs was also  discussed,  the causes and  challenges they go  through  such  as discrimination and institutional and environmental challenges. In each case their causes, effects and scientific solutions were proffered.
Effect of Sago Effluent on the Growth Hormone Levels in Clarias batrachus Blood Sample
Authors: Ramesh F.
Published: June 2019

The aim of the study was to determine the effect of Sago effluent on the levels of growth hormone in the blood samples of the fresh water fish Clarias batrachus. The fish were exposed to control and different concentrations of treated sago effluents. The concentrations chosen were 25%, 50% and 75% of treated sago effluent. The levels of the growth hormone were increased in the blood sample of the experimental fish Clarias batrachus, when compared with that of controls.
Biological Synthesis of Cobalt Nanoparticles from Mangifera indica Leaf Extract and Application by Detection of Manganese (II) Ions Present in Industrial Wastewater
Authors: Okwunodulu Felicia Uchechukwu , Chukwuemeka-Okorie Helen Ogechi , Okorie Francis Chijioke
Published: June 2019

This study was focused on the synthesis of cobalt nanoparticles using Mangifera indica leaf extract and the characterization of the particles via UV–Vis spectroscopy, XRD, FT-IR and SEM. The XRD results showed the formation of cobalt nanoparticles that was crystalline in nature, with an average size of 25—40 nm. The FT-IR analysis of the leaf extract reviewed some functional groups responsible for the reduction of cobalt ions to cobalt nanoparticles while the SEM indicates that the synthesised cobalt nanoparticles possess a cubic, pentagonal and irregular in shape with a smooth surface. Application of colloidal cobalt nanoparticles in detecting Mn2+ ions was discussed which indicated that the absorption of the Mn (II) ions decreased at increased concentration of Mn (II) ions indicating that Mn (II) ion can be detected even at a very low concentration. The minimum and maximum detection limit was found to be 5 and 25 mM of Mn (II) ions, respectively. The obtained results encourage the use of economical synthesis of cobalt nanoparticles in the development of nanosensors to detect the pollutants present in industrial efﬂuents.
Effect of Grape Seed Oil on Chronic Carbon Tetrachloride-Induced Hepatic Injury and Determination of Hepatic Apoptosis in Rats
Authors: Atasever Ayhan , Alpay Ahmet , Ekebas Gorkem , Gram Duygu Yaman
Published: June 2019

Aims: The present study was designed to evaluate the hepatoprotective activity of grape seed oil (GSO) on liver lesions induced by carbon tetrachloride (CCl4) in rats. The effects on hepatic injury were investigated by measuring serum levels of ALT, triglyceride, total protein, total cholesterol and liver levels of MDA. Furthermore, caspase -3, -8 and -9 activities in cellular apoptosis were determined.

Place and Duration of Study: Faculty of Veterinary Medicine, Department of Pathology, Erciyes University, Kayseri, between November 2017 and September 2018.

Methodology: In this study 40 male Wistar albino rats were divided into four groups including 10 animals in each. Control group administered with 0.9% NaCl. The second group was administered with 4 mL/kg GSO for twelve weeks. Third group were given CCl4 (0.2 mL/kg) twice for 8-weeks. Fourth group was administered with 4 mL/kg GSO, for 12 weeks and also given CCl4 (0.2 mL/kg) twice for 8 weeks, starting from the 5th week.

Results: Histopathological examination of CCl4 group showed intense macro and micro vesicular steatosis in hepatocytes, necrosis, and lymphocytes rich mononuclear cell infiltration in portal area and mild portal fibrosis in the parenchyma. The grape seed oil applications have partially normalized the altered histological changes and the activity of caspase -3, -8 and -9. Administration of GSO led to a decline in the activities of ALT and MDA levels while this treatment elevated serum triglycerides levels which are not significantly important.

Conclusion: The results indicate that the antioxidant properties of GSO have not ameliorative effect in either the histopathological lesions or biochemical parameters against CCl4-induced hepatotoxicity in rats. Also, it has been concluded that duration‐dependent further research results are needed to determine the effects of grape seed oil in high doses which can give the best results without side effects.
Capture Efficiency of Some Artisanal Fishing Gears Employed At Upper Benue River Basin, Nigeria
Authors: Bonjoru R. , Abubakar K. A. , Bonjoru F. H. , Ndeham V. R. , Amadu S. O.
Published: June 2019

This study was carried out to compare the capture efficiency of some artisanal fishing gears employed at Upper Benue Basin, Nigeria. The study was carried out for a 6 months period running from July to December 2017. Sampling was by Direct observation of the Fish at the landing sites and the gears used by the fishermen. Coefficient of Variation is used for the assessment of variability in the Catch Per Unit Effort (CPUE) by gear types. Other data were analyzed using Analysis of Variance (ANOVA).  A total of 5 different gear types were identified to include: Gill net – Taru; Malian trap – Gura/Malia; Lift net – Akauji; Cast net – Birgi; Longline – Rincha. The result further indicated that Coefficient of Variations (C.V) differ with the gear used. The study therefore recommends that further investigation on the efficiency of the nets over a longer period (for at least 2 seasons) should be carried out; government should take immediate action through public awareness and education to regulate fishing activities such that adequate numbers of fishermen should be licensed to fish in a particular water body, together with their gear and craft nets; and a minimum of 3” mesh size has been recommended for all inland net fishing. This is to protect the spawning stock of commercially valued species.
Antibiotic Susceptibility Testing, Plasmid Detection and Curing of Clinically Isolated Enterococcus Species
Authors: Ezeah G. A. C. , Ugwu M. C. , Ekundayo A. O. , Odo O. F. , Ike O. C. , Akpe R. A.
Published: June 2019

Vancomycin resistant enterococci (VRE) are a major medical concern globally. Their significantly greater prevalence and the ability to transfer resistance to vancomycin from other bacteria made them an object of interest and intense research. The isolates of Enterococcus sp. were subjected to antibiotic susceptibility testing before curing. The three Enterococcus species exhibited different antibiotic resistance profile. Pre-curing antibiotic resistance of nosocomial isolates compared with community acquired isolates revealed that high percentage of the nosocomial isolates were resistant to antibiotics compared to community isolate. Post-curing antibiograms of the isolates showed different resistant and susceptibility pattern. Also, DNA plasmid pre-curing and post curing analysis of the isolates showed different resistance pattern. Six of the 15 representative isolates selected on the basis of their high pre-curing antibiotic resistance for plasmid analysis with 0.8% agarose electrophoresis were positive for plasmid DNA. Four (4) of the positive isolates (E. faecium, E. faecium, E. faecalis, and E. avium) had plasmid fragment of greater than 1000 bp while two (2) of them (E. faecalis and E. faecalis) had fragments of between 100 and 500 bp. The remaining nine (9) had no plasmid DNA. The study revealed the pathogenicity factors demonstrated with the enterococcal isolates.
Parametric Bootstrapping Predictive Estimator for Logistic Regression
Authors: Takezawa Kunio
Published: June 2019

This paper proposes a method for constructing a predictive estimator for logistic regression. We make a provisional assumption that the predictive estimator is given by multiplying the maximum likelihood estimators by constants, which are estimated using a parametric bootstrap method. The relative merits of the maximum likelihood estimator and the predictive estimator produced by this method are determined by cross-validation. The results show that the predictiveestimators derived by this method lead to a smaller deviance than that obtained by the maximum likelihood estimator in many instances.
Efficacy of the Peganum Harmala Oil Versus 1% Permethrin Shampoo on the Treatment of Head Louse Infestation
Authors: Maarefvand Mina , Kenari Hoorieh Mohammadi , Ghobadi Ali , Soleymani Alireza , Hashem-Dabaghian Fataneh Hashem-Dabaghian
Published: June 2019

Introduction: Head louse infestation is one of the major public health problems among children worldwide. Several drugs have been developed to treat the infestation. Side effects and drug resistance associated with these drugs limit their applicability. Increasing attention of scientific committees to alternative drugs along with greater effects and lower complications and costs, increase the hope of success for alternative drugs.

Materials and Methods: 93 participants (11 men and 82 women) with positively diagnosed with head lice infestation were allocated into two groups using the stratified randomization method. The intervention in one group comprised of Peganum harmala oil applied onto the patient’s hair and scalp and the hair and scalp being washed after 20 minutes once a day. The procedure was performed on the first three days of week one of intervention (phase 1) and reiterated on the subsequent week (phase 2) in a similar manner. The other group applied permethrin shampoo once in the first week of intervention and once in the second week.

Results: Permethrin shampoo recovered 7 (29.2%) in day 1, 2 (15.4%) in day 2, 2 (25.0%) in day 3 and 28 (73.7%) in day 11 but Peganum harmala oil recovered 17 (70.8%) in day 1, 11 (84.6%) in day 2, 6 (75.0%) in day 3 and 10 (26.3%) in day 11 (P-value <0.005).  

Conclusion: The clearing effects and side effects of Peganum harmala oil and permethrin shampoo are approximately similar in the two-phase application although the oil’s clearing and protective effect is greater than that of the shampoo with its effect occurring earlier than that of the shampoo.
Bioremediation
Authors: Prince Roger C.
Published: June 2019

Bioremediation is the process of thoughtfully exploiting biological processes to minimize an unwanted environmental impact; usually the aim is the removal of a contaminant from the biosphere. Like most definitions in biology, that of bioremediation is the subject of some debate. A narrow definition might focus on the conversion of contaminating organic molecules to CO
2
, water, and inorganic ions, and the oxidation or reduction of contaminating inorganic ions such as nitrate or ammonia to harmless forms, in this case nitrogen gas. A broader definition would include biological processes for ameliorating extremes of pH, concentrating contaminants so that they can be more easily removed by physical techniques, converting toxic species to less toxic or less bioavailable forms that pose less of a threat to the environment, and restoring functional ecosystems to contaminated or disturbed sites when the contaminants or disturbance cannot be removed.
Urea
Authors: Brouwer Mark
Published: June 2019

Urea was discovered in urine by Rouelle in 1773 and first synthesized from ammonia and cyanic acid by Wöhler in 1828. Commercially, urea is produced by the direct dehydration of ammonium carbamate at elevated temperature and pressure. Ammonium carbamate is obtained by direct reaction of ammonia and carbon dioxide. Most urea plants are licensed by Saipem, Stamicarbon, or Toyo Engineering Corporation. Their processes are discussed in detail. Urea's biggest use is as a fertilizer. Further, it is also used in animal feeds, in the manufacture of resins, and in reducing NO

x

emissions by catalytic reduction. Urea is classified as a nontoxic compound.
S
porichthyales
Authors: Trujillo Martha E. , Normand Philippe
Published: June 2019

Spor.ich.thy.a'les
. (N.L. fem. n.
Sporichthya
, type genus of the order; ‐
ales
, ending to denote an order; N.L. fem. pl. n.
Sporichthyales
, the
Sporichthya
order).

Actinobacteria / Actinobacteria / Sporichthyales

Soil‐inhabiting actinobacteria with a unique morphology. Short aerial mycelium forms rod‐shaped to coccoid spores that may develop polar flagella in liquid media. Aerial hyphae form upright on the surface of the medium by holdfasts, which are outgrowths of the wall of the basal cell. Substrate mycelium is not formed. Gram‐stain‐variable, with young cells staining Gram‐negative and older cells showing a Gram‐positive reaction. Aerobic or facultatively anaerobic. Mesophilic with a growth range between 10 and 42°C. Chemoorganotrophic. Cell walls contain large amounts of LL‐diaminopimelic acid. Iso‐branched, unsaturated, and saturated are common components of fatty acid profiles. The order
Sporichthyales
was recently created to accommodate the family
Sporichthyaceae
previously assigned to the order
Frankiales
. It is phylogenetically related to the orders
Frankiales
and
Acidothermales
.

Type genus
:
Sporichthya
Lechevalier, Lechevalier and Holbert 1968, 279
AL
.
Compound heterozygosity for a frameshift mutation and an upstream deletion that reduces expression of SERPINH1 in siblings with a moderate form of osteogenesis imperfecta
Authors: Schwarze Ulrike , Cundy Tim , Liu Yajuan J. , Hofman Paul L. , Byers Peter H.
Published: June 2019

SERPINH1 encodes the collagen chaperone HSP47 that binds to arginine‐rich sequences in the type I procollagen trimers and provides the final steps in the folding and stabilization of the triple helical domain. Loss of both alleles in mice results in very early embryonic lethality. SERPINH1 mutations have been associated with one of the rarest forms of recessively inherited osteogenesis imperfecta (OI) with a moderate to severe phenotype. We identified a family with non‐consanguineous unaffected parents who had two children with moderate short stature, low bone density, and fractures. Both children were compound heterozygotes for two mutations: a frameshift in the last exon that deleted the RER retention signal, and a 5,274 bp deletion 2.37 kb upstream from the transcription start site. The maternally‐inherited frameshift allele was expressed at normal levels, but the protein was unstable. The mRNA encoded by the second allele represented about 50% of that from the frameshift‐containing allele. The upstream deletion was inherited from the father, and the mRNA encoded by that allele in his cultured dermal fibroblasts was also expressed at a low level, which confirmed that this domain had a regulatory function for SERPINH1. Regulatory mutations are uncommon causes of human genetic disorders, and the ability to measure expression levels in appropriate cells is key to their identification.
Synthesis of four series of quinoline‐based heterocycles by reacting 2‐chloroquinoline‐3‐carbonitriles with various types of isocyanides
Authors: Tanbakouchian Zahra , Zolfigol Mohammad Ali , Notash Behrouz , Ranjbar Maryam , Shiri Morteza
Published: June 2019

Four distinct sets of functionalized quinolines were synthesized by reacting 2‐chloroquinoline‐3‐carbonitriles with various types of isocyanides under appropriate conditions. The palladium‐catalysed reaction of less hindered aliphatic and aromatic isocyanides with 2‐chloroquinoline‐3‐carbonitriles yielded 2‐alkyl(aryl)‐1‐imino‐1H‐pyrrolo[3,4‐b]quinolin‐3(2H)‐one derivatives; however, the catalysed reaction of more hindered isocyanides such as tert‐butyl isocyanide produced the corresponding 3‐cyanoquinoline‐2‐carboxamides. Interestingly, chloroquinoline‐3‐carbonitriles reacted with ethyl isocyanoacetate in the presence of Cs2CO3 to generate imidazo[1,5‐a]quinoline derivatives; notably, tosylmethyl isocyanide under the same conditions formed unprecedented 2‐tosyl‐3‐cyanoquinolines.
Effect of natural toxins and adipokinetic hormones on the activity of digestive enzymes in the midgut of the cockroach Periplaneta americana
Authors: Karbusová Nikola , Gautam Umesh K. , Kodrík Dalibor
Published: June 2019

This study examined the effect of two natural toxins (a venom from the parasitic wasp Habrobracon hebetor and destruxin A from the entomopathogenic fungus Metarhizium anisopliae), and one pathogen (the entomopathogenic fungus Isaria fumosorosea) on the activity of basic digestive enzymes in the midgut of the cockroach Periplaneta americana. Simultaneously, the role of adipokinetic hormones (AKH) in the digestive processes was evaluated. The results showed that all tested toxins/pathogens elicited stress responses when applied into the cockroach body, as documented by an increase of AKH level in the central nervous system. The venom from H. hebetor showed no effect on digestive enzyme activities in the ceca and midgut in vitro. In addition, infection by I. fumosorosea caused a decrease in activity of all enzymes in the midgut and a variable decrease in activity in the ceca; application of AKHs did not reverse the inhibition. Destruxin A inhibited the activity of all enzymes in the midgut but none in the ceca in vitro; application of AKHs did reverse this inhibition, and no differences between both cockroach AKHs were found. Overall, the results demonstrated the variable effect of the tested toxins/pathogens on the digestive processes of cockroaches as well as the variable ability of AKH to counteract these effects.
Detection of intraseasonal oscillations in the Bay of Bengal using altimetry
Authors: Trott Corinne B. , Subrahmanyam Bulusu
Published: June 2019

Air–sea and mixed layer dynamics in the Bay of Bengal (BoB) respond strongly to Intraseasonal Oscillations (ISOs) that primarily operate on three observed time scales: the 30–90 day Madden‐Julian Oscillation, the 10–20 day quasi‐biweekly oscillation, and the synoptic‐scale 3–7 day oscillation of the monsoon trough. In this research, we focus on local and basin‐wide signals, zonal and meridional propagation, and variability of ISOs with respect to the strength of the summer monsoon season over a multi‐decadal period (1993–2016). For the first time, this study examines the relationship between larger‐ and shorter‐period ISOs in SLA and shows the usefulness of altimetry data in Indian monsoon studies. We compare ISOs in SLA during years with summer monsoons of varying strengths, finding notably stronger circulation and larger amplitude of all ISOs in years with stronger summer monsoons theorized in part to be due to the first‐baroclinic mode forcing from low‐level winds (R2 values of 0.61, 0.67, and 0.64 in the northern, central, and southern Bay, respectively), although it is important to note the influence of other local forcings, such as mesoscale eddies and coastal Kelvin waves. We demonstrate that 30–90 day variability of SLA is initially forced by equatorial processes and strengthened by local processes in the BoB, as higher‐amplitude SLA ISOs were consistently observed in the southern and eastern Bay. Local processes like coastal Kelvin waves were found to strongly influence the 10–20 day quasi‐biweekly signal, as was seen in the high‐amplitude 10–20 day SLA ISOs found in the eastern BoB. The synoptic signal also revealed a zonal pattern consistent with coastal Kelvin wave intensification and eddy generation.
Collecting and utilising crowdsourced data for numerical weather prediction: Propositions from the meeting held in Copenhagen, 4–5 December 2018
Authors: Hintz Kasper S. , O'Boyle Katharine , Dance Sarah L. , Al‐Ali Saja , Ansper Ivar , Blaauboer Dick , Clark Matthew , Cress Alexander , Dahoui Mohamed , Darcy Rónán , Hyrkkanen Juhana , Isaksen Lars , Kaas Eigil , Korsholm Ulrik S. , Lavanant Marion , Le Bloa Gwenaelle , Mallet Emilie , McNicholas Callie , Onvlee‐Hooimeijer Jeanette , Sass Bent , Siirand Valeria , Vedel Henrik , Waller Joanne A. , Yang Xiaohua
Published: June 2019

In December 2018, the Danish Meteorological Institute organised an international meeting on the subject of crowdsourced data in numerical weather prediction (NWP) and weather forecasting. The meeting, spanning 2 days, gathered experts on crowdsourced data from both meteorological institutes and universities from Europe and the United States. Scientific presentations highlighted a vast array of possibilities and progress being made globally. Subjects include data from vehicles, smartphones, and private weather stations. Two groups were created to discuss open questions regarding the collection and use of crowdsourced data from different observing platforms. Common challenges were identified and potential solutions were discussed. While most of the work presented was preliminary, the results shared suggested that crowdsourced observations have the potential to enhance NWP. A common platform for sharing expertise, data, and results would help crowdsourced data realise this potential.
The misallocation of students to academic sets in maths: A study of secondary schools in England
Authors: Connolly Paul , Taylor Becky , Francis Becky , Archer Louise , Hodgen Jeremy , Mazenod Anna , Tereshchenko Antonina
Published: June 2019

Drawing upon data gathered from 9301 Year 7 students (12–13 years old) from 46 secondary schools in England, this study represents the first larger‐scale attempt to compare their actual set allocations in maths with the counterfactual position where their allocation to sets is based solely on their prior attainment at the end of primary school [using their Key Stage 2 (KS2) fine‐grained scores in maths]. Through such an analysis, the study found that nearly a third of students (31.2%) had been misallocated to lower or higher sets than their KS2 results would have warranted. Beyond this, school setting practices were found to exacerbate differences in set allocation in relation to gender and ethnicity, but not socioeconomic background. The odds of girls being misallocated to lower sets in maths than their prior attainment would warrant was found to be 1.5 times higher than that for boys. Similarly, the odds of Black students being misallocated to lower sets was 2.4 times higher than for White students, whilst the odds of Asian students being misallocated to lower maths sets was 1.7 times higher than for White students. The article concludes by reflecting on the significant role that setting by attainment in secondary school can play in exacerbating already established patterns of educational inequalities in gender and ethnicity.
Increased 3′‐Phosphoadenosine‐5′‐phosphosulfate Levels in Engineered Escherichia coli Cell Lysate Facilitate the In Vitro Synthesis of Chondroitin Sulfate A
Authors: Badri Abinaya , Williams Asher , Xia Ke , Linhardt Robert J. , Koffas Mattheos A. G.
Published: June 2019

Chondroitin sulfates (CSs) are linear glycosaminoglycans that have important applications in the medical and food industries. Engineering bacteria for the microbial production of CS will facilitate a one‐step, scalable production with good control over sulfation levels and positions in contrast to extraction from animal sources. To achieve this goal, Escherichia coli (E. coli) is engineered in this study using traditional metabolic engineering approaches to accumulate 3′‐phosphoadenosine‐5′‐phosphosulfate (PAPS), the universal sulfate donor. PAPS is one of the least‐explored components required for the biosynthesis of CS. The resulting engineered E. coli strain shows an ≈1000‐fold increase in intracellular PAPS concentrations. This study also reports, for the first time, in vitro biotransformation of CS using PAPS, chondroitin, and chondroitin‐4‐sulfotransferase (C4ST), all synthesized from different engineered E. coli strains. A 10.4‐fold increase is observed in the amount of CS produced by biotransformation by employing PAPS from the engineered PAPS‐accumulating strain. The data from the biotransformation experiments also help evaluate the reaction components that need improved production to achieve a one‐step microbial synthesis of CS. This will provide a new platform to produce CS.
Optogenetic neuronal stimulation promotes axon outgrowth and myelination of motor neurons in a three‐dimensional motor neuron–Schwann cell coculture model on a microfluidic biochip
Authors: Hyung Sujin , Lee Seung‐Ryeol , Kim Yeon Jee , Bang Seokyoung , Tahk Dongha , Park Jong‐Chul , Suh Jun‐Kyo Francis , Jeon Noo Li
Published: June 2019

Axonal regeneration and remyelination of peripheral motor neurons (MNs) are critical for restoring neuromuscular motor function after injury or peripheral neuropathy. We examined whether optogenetically mediated light stimulation (OMLS) could enhance the axon outgrowth and myelination of MNs using three‐dimensional motor neuron–Schwann cell (MN–SC) coculture on a microfluidic biochip. The biochip was designed to allow SCs to interact with the axons of MNs, while preventing direct contact between SCs and the cell bodies of MNs. Following coculture with SCs on the microfluidic biochip, MNs were transfected with a light‐sensitive channelrhodopsin gene. Transfected MNs subjected to repeated light stimulation (20 Hz, 1 hr) produced significantly longer axons than nontransfected MNs. OMLS of MNs greatly increased the number of myelin basic protein (MBP)‐expressing SCs, promoting the initiation of myelination of MNs. Ultrastructurally, OMLS of MNs markedly enhanced the thickness of the compact myelin sheath around the MN axons such that the average thickness was closer to that of the theoretical estimates in vivo. Thus, the MN–SC coculture model on a microfluidic biochip augmented by OMLS of MNs is a feasible platform for studying the relationship of neuronal activity with regrowth and remyelination.
Construction of a sensitive pyrogen‐testing cell model by site‐specific knock‐in of multiple genes
Authors: Hu Ruobi , Li Hui , Lei Zhen , Han Qing , Yu Xiuyan , Zhou Na , Zhang Xuehui , Mao Yiqing , Wang Xi , Irwin David M. , Niu Gang , Tan Huanran
Published: June 2019

A pyrogen test is crucial for evaluating the safety of drugs and medical equipment, especially those involved in injections. As existing pyrogen tests, including the rabbit pyrogen test, the limulus amoebocyte lysate (LAL) test and the monocyte activation test have limitations, development of new models for pyrogen testing is necessary. Here we develop a sensitive cell model for pyrogen test based on the lipopolysaccharides (LPS) signal pathway. TLR4, MD2, and CD14 play key roles in the LPS‐mediated pyrogen reaction. We established a new TLR4/MD2/CD14‐specific overexpressing knock‐in cell model using the CRISPR/CAS9 technology and homologous recombination to detect LPS. Stimulation of our TLR4/CD14/MD2 knock‐in cell line model with LPS leads to the release of the cytokines IL‐6 and TNF‐alpha, with a detection limit of 0.005 EU/ml, which is greatly lower than the lower limit of 0.015 EU/ml detected by the Tachypleus amebocyte lysate (TAL) assay.
iTest: A novel online testing system based on the WeChat platform
Authors: Xu Jia , Wang Junbin , Wang Xiaoxin , Lv Pin
Published: June 2019

Timely feedback is important for both teachers and students in teaching and learning practice. Teachers rely on feedback from students to gain a better understanding of their learning effects. Students also need feedback to identify gaps in their knowledge. Conducting in‐class tests is considered an effective way to obtain such feedback. However, traditional testing methods are inflexible and inefficient. In this paper, we introduce iTest, a novel online testing system developed on the popular WeChat platform. With the help of iTest, the teacher organizes an in‐class test conveniently, and the students take the test with their smartphones regardless of which operating systems the smartphones use. When the student answers questions in a test, abundant behavior data for the student are collected. According to the analysis of the behavior data and the testing results, the teacher gains a deeper insight into the learning effect for each student. A weighted knowledge graph is also constructed for each student by virtue of the prerequisite relationships among the knowledge points and the behavior data. On the basis of the weighted knowledge graph, iTest recommends personalized exercises in an appropriate order to each student after the test, which helps to improve the learning effect. Teaching practice in five courses verifies that iTest is effective and efficient in promoting teaching and learning. Both teachers and students have high praise for iTest.