bluuebunny/crossref_metadata_2025 huggingface dataset:
High Incidence of Herpes Simplex Virus-1 in Cord Blood and Placenta Infection of Women in Southern Brazil
Authors: Avila Emiliana Claro , Finger-Jardim Fabiana , Gonçalves Carla Vitola , da Hora Vanusa Pousada , Soares Marcelo Alves , Martínez Ana Maria Barral de
Published: February 2020

Objective Estimate the prevalence of human herpesvirus type 1 HSV-1 DNA in placental samples, its incidence in umbilical cord blood of newborns and the associated risk factors.

Methods Placental biopsies and umbilical cord blood were analyzed, totaling 480 samples, from asymptomatic parturients and their newborns at a University Hospital. Nested polymerase chain reaction (PCR) and gene sequencing were used to identify the virus; odds ratio (OR) and relative risk (RR) were performed to compare risk factors associated with this condition.

Results The prevalence of HSV-1 DNA in placental samples was 37.5%, and the incidence in cord blood was 27.5%. Hematogenous transplacental route was identified in 61.4% from HSV-1+ samples of umbilical cord blood paired with the placental tissue. No evidence of the virus was observed in the remaining 38.6% of placental tissues, suggesting an ascendant infection from the genital tract, without replication in the placental tissue, resulting in intra-amniotic infection and vertical transmission, seen by the virus in the cord blood. The lack of condom use increased the risk of finding HSV-1 in the placenta and umbilical cord blood.

Conclusion The occurrence of HSV-1 DNA in the placenta and in cord blood found suggests vertical transmission from asymptomatic pregnant women to the fetus.
Análise comparativa do efeito de dois protocolos de ultrassom terapêutico para regeneração de defeito ósseo crítico
Authors: Daltro Ana Flávia Calmon , Barreto Isabela Cerqueira , Almeida Renata dos Santos , Ribeiro Iorrana Índira dos Anjos , Barbosa Junior Aryon de Almeida , Rosa Fabiana Paim
Published: February 2020

Objetivo Comparar o efeito de dois protocolos de ultrassom terapêutico com diferentes tempos de exposição para regeneração de defeito ósseo crítico.

Métodos Foram utilizados 45 ratos, machos, distribuídos em três grupos: grupo ultrassom terapêutico 5 minutos (GUS 5); grupo ultrassom terapêutico 10 minutos (GUS 10); e grupo controle (GC). Em todos os grupos, confeccionou-se um defeito ósseo crítico, com 8,5 mm de diâmetro, na região da calvária. O protocolo foi iniciado no 1° dia do pós-operatório, no GUS 5 e no GUS 10, com ultrassom terapêutico na frequência de 1,0 MHz, modo pulsado, 5 vezes por semana, nos períodos de 15, 30, e 60 dias.

Resultados Dentre os grupos experimentais, houve maior neoformação de matriz osteoide no GUS 10, seguido do GUS 5 quando comparados ao GC, no qual a neoformação foi restrita à região de borda. O uso do ultrassom promoveu aumento na espessura da matriz conjuntiva, proliferação de capilares, alinhamento das fibras colágenas, redução do edema e do processo inflamatório, tendo sido mais significativo no tempo de 10 minutos.

Conclusão O ultrassom terapêutico estimulou o reparo do defeito ósseo crítico, e o maior tempo de exposição promoveu maior estímulo osteogênico.
Posturographic Analysis in the Elderly with and without sensorineural Hearing Loss
Authors: Ciquinato Daiane Soares de Almeida , Doi Marcelo Yugi , Silva Rubens A. da , Oliveira Márcio Rogério de , Gil André Wilson de Oliveira , Marchiori Luciana Lozza de Moraes
Published: February 2020

Introduction Sensorineural hearing loss (SNHL) is a serious public health problem. Some evidence suggests a significant relationship between SNHL and balance disorders. The inability to maintain balance associated with SNHL while standing further increases the risk of falls among older people.

Objective To investigate the association between SNHL on the postural balance in elderly individuals of both genders.

Methods The sample consisted of 247 (166 women) physically independent elderly individuals, (mean age = 68.4 ± 6.0). The instruments used were the anamnesis and the pure tone audiometry for hearing loss, and for balance a force platform based in measures of center of pressure area and of sway velocity in the anteroposterior and mediolateral directions.

Results Presence of hearing loss (HL) was observed in 68% of the participants. We observed a significant association between SNHL and characteristics of balance between the groups with and without HL for center of pressure (COP) area (p = 0.010), anteroposterior velocity (p = 0.001) and mediolateral velocity (p = 0.020). There was a significant difference between the gender groups for center of pressure area (p = 0.004), anteroposterior velocity (p = 0.001) and mediolateral velocity (p = 0.001) with better performance in the female group. Amongst men, there was a difference between the ones with HL and those without it, for COP area (p = 0.049).

Conclusion In the present study, elderly individuals with SNHL exhibited more instability on the postural balance, and elderly men presented worse results in the test.
Generalized Peierls–Nabarro model for studying misfit dislocation in a BN/AlN heterostructure
Authors: Zhang Shujun , Wang Shaofeng
Published: February 2020

Based on the solution of the balance problem for a semi-infinite lattice, we propose a generalization of the Peierls–Nabarro equation that is applicable to an interfacial misfit dislocation array. We obtain a relationship between the mass center displacement and the relative displacement. Under the assumption that the change in the interfacial layer spacing is sufficiently small that it can be ignored, this relationship allows us to reveal the core structure of the misfit dislocation and determine the interfacial atomic coordinates. As an example, a boron nitride/aluminum nitride heterostructure with a large lattice mismatch is studied using the equation. We find a good match between the theoretically predicted interfacial atomic configuration and that obtained from a first-principles calculation. Furthermore, the adhesion energy of the heterostructure is also evaluated, and the theoretical result coincides with that obtained from first-principles simulations.
Inlet swirl decay and mixing in a laminar micro-pipe flow with wall slip
Authors: Kumar Dhananjay , Shakya Shavitur Mukesh Kumar , Kaushik P.
Published: February 2020

In this work, the decaying laminar inlet swirl flow in a straight circular micro-pipe with wall slip is solved analytically and the solution is verified numerically. Based on a fully developed parabolic axial velocity profile, the swirl velocity equation is solved by the separation of variables technique. The solution is expressed as a function of the flow Reynolds number, the axial distance within the circular micro-pipe from the inlet, the wall slip, and the inlet swirl velocity profile. The effects of the parameters on the swirl velocity distribution and the swirl decay are analyzed along the flow. The addition of swirling velocity to the flow of a fluid in a pipe is of great importance in the enhancement of transport characteristics. The current results offer analytical equations to estimate the swirl velocity distribution with slip at the walls for the design of swirl flow devices. Furthermore, to quantify mixing, the change in the average distance traveled by fluid particles from the inlet in a swirl flow is compared with the average distance traveled by the fluid particles in the case of no swirl. A clear enhancement of the average distance traveled is obtained for flows with the interaction of both swirl and slip effects. In our opinion, the present work is useful to researchers looking for the enhancement of transport characteristics in circular micro-pipes.
Luminescence study in InGaAs/AlGaAs multi-quantum-well light emitting diode with p–n junction engineering
Authors: Han Lili , Zhao Minglong , Tang Xiansheng , Huo Wenxue , Deng Zhen , Jiang Yang , Wang Wenxin , Chen Hong , Du Chunhua , Jia Haiqiang
Published: February 2020

Overlapping between the quantum-well structure and p–n junction plays an important role in the development of high-efficiency GaAs-based light-emitting diodes (LEDs). In this work, we apply p–n junction engineering to study electro-photoluminescence spectra under open-circuit, forward voltage, and reverse voltage conditions. Through modifying the doping of p-layer or n-layer, luminescent characteristics are apparently improved as a result of the more effective overlapping of the quantum-well structure and p–n junction caused by energy band modification, with the more balanced carrier and stronger confinement in quantum wells. Furthermore, the electroluminescence spectra of all LEDs studied herein are consistent with the photoluminescence results. This work provides an explicit way to tune p- and n-doping to increase emission efficiency, which is important for research and industrial applications.
Magneto-electric antiferromagnetic spin–orbit logic devices
Authors: Dowben P. A. , Nikonov D. E. , Marshall A. , Binek Ch.
Published: February 2020

As electronic integrated circuits are scaled to ever smaller sizes, they run into the obstacle of excessive power dissipation. Spintronic devices hold the promise of alleviating this problem via improved energy efficiency. Research effort around a promising class of such devices based on antiferromagnetic materials and magnetoelectric switching is reviewed.
A high-strength Co–Fe–Ta–B metallic-glass phase enabled tensile plasticity in Co–Fe–Ta–B–O oxide glass matrix nanocomposites
Authors: Huang Longchao , Tang Xinkai , Jiang Guochen , Fang Kaixuan , Yao Kefu , Zhang Zhengjun , Chen Na , Shan Zhiwei
Published: February 2020

Oxide glasses are intrinsically brittle at room temperature when loaded under tension. In this study, a high-strength CoFe-based metallic glass was used as a strengthening phase to make a Co–Fe–Ta–B–O oxide glass become stronger and ductile in tension. The developed metallic-glass-reinforced oxide glass matrix nanocomposite possessed a supra-nanometer-sized dual-phase structure. Owing to the dispersion strengthening effects, the nanocomposite showed a tensile strength σb of ∼2.7 GPa, about 29% higher than that of the single-phase oxide glass. Meanwhile, its tensile plasticity εp was enhanced from zero to ∼2.7%. The continuous glass/glass interfaces of the dual-phase mixture are thought to enable the tensile plasticity in the nanocomposite. Our results provide an approach to effectively enhance both the strength and tensile ductility of intrinsically brittle oxide glasses.
Nitrogen supply in combination of nitrate and ammonium enhances harnessing of elevated atmospheric CO2 through improved nitrogen and carbon metabolism in wheat (Triticum aestivum)
Authors: Asif Muhammad , Zora Seray , Ceylan Yasemin , Rehman Raheela , Ozturk Levent
Published: February 2020

Elevated carbon dioxide (e-CO2) levels from ambient (a-CO2) enhance plant biomass production and yield. However, this response is highly dependent on the availability and possibly the form of nitrogen (N) supply to plants. This study aimed to investigate changes in C and N metabolism of wheat (Triticum aestivum L.) in response to e-CO2 and N source. e-CO2 enhanced net CO2 assimilation but at highly variable rates depending on the form of N supply. Under e-CO2, net CO2 assimilation rate was in the order NO3– > NH4NO3 > NH4+ > urea. Plants supplied with ammonium and nitrate (i.e. NH4NO3) performed better in terms of biomass production and expressed a higher biomass enhancement ratio by e-CO2 than plants receiving sole applications of NO3–, NH4+ or urea. Supply of NH4NO3 also resulted in lower intercellular CO2, higher photoassimilate translocation to roots and lower accumulation of free amino acids than other N forms, indicating a better exploitation of the e-CO2 environment. Our results conclude that major physiological pathways of photosynthesis and protein and carbohydrate metabolism are differentially influenced by e-CO2 depending on the source of N supply. A balanced supply of NO3– and NH4+ to plant roots is the key to harnessing e-CO2 while minimising its adverse effects on quality of the produce.
HNRNPA1-induced spliceopathy in a transgenic mouse model of myotonic dystrophy
Authors: Li Moyi , Zhuang Yan , Batra Ranjan , Thomas James D. , Li Mao , Nutter Curtis A. , Scotti Marina M. , Carter Helmut A. , Wang Zhan Jun , Huang Xu-Sheng , Pu Chuan Qiang , Swanson Maurice S. , Xie Wei
Published: February 2020

Significance

Myotonic dystrophy type 1 (DM1) is a model for RNA-mediated disease in microsatellite expansion disorders. DM1 is caused by CTG expansions (CTG
exp
) and expression of CUG
exp
RNAs that sequester muscleblind-like (MBNL) proteins, while also triggering hyperphosphorylation of CUGBP1/ETR3-like factor 1 (CELF1). These proteins regulate developmental transitions in RNA processing, so DM1 is characterized by retention of fetal RNA processing patterns in adults. Although current evidence indicates that CELF1 is a specific antagonist of MBNL activity, this study reveals that another protein, HNRNPA1, is also downregulated during normal development but upregulated in DM1, where it also induces fetal splicing shifts. Thus, DM1 disease results from an imbalance in the expression of multiple RNA processing factors important for both proliferation and differentiation.
Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers
Authors: Phillips John W. , Pan Yang , Tsai Brandon L. , Xie Zhijie , Demirdjian Levon , Xiao Wen , Yang Harry T. , Zhang Yida , Lin Chia Ho , Cheng Donghui , Hu Qiang , Liu Song , Black Douglas L. , Witte Owen N. , Xing Yi
Published: February 2020

We sought to define the landscape of alternative pre-mRNA splicing in prostate cancers and the relationship of exon choice to known cancer driver alterations. To do so, we compiled a metadataset composed of 876 RNA-sequencing (RNA-Seq) samples from five publicly available sources representing a range of prostate phenotypes from normal tissue to drug-resistant metastases. We subjected these samples to exon-level analysis with rMATS-turbo, purpose-built software designed for large-scale analyses of splicing, and identified 13,149 high-confidence cassette exon events with variable incorporation across samples. We then developed a computational framework, pathway enrichment-guided activity study of alternative splicing (PEGASAS), to correlate transcriptional signatures of 50 different cancer driver pathways with these alternative splicing events. We discovered that Myc signaling was correlated with incorporation of a set of 1,039 cassette exons enriched in genes encoding RNA binding proteins. Using a human prostate epithelial transformation assay, we confirmed the Myc regulation of 147 of these exons, many of which introduced frameshifts or encoded premature stop codons. Our results connect changes in alternative pre-mRNA splicing to oncogenic alterations common in prostate and many other cancers. We also establish a role for Myc in regulating RNA splicing by controlling the incorporation of nonsense-mediated decay-determinant exons in genes encoding RNA binding proteins.
A layered investigation of Chinese in the linguistic landscape
Authors: Yao Xiaofang , Gruba Paul
Published: February 2020

Increased attention to urban diversity as a site of study has fostered the recent development of linguistic
landscape studies. To date, however, much of the research in this area has concerned the use and spread of English to the
exclusion of other global languages. In a case study situated in Box Hill, a large suburb of Melbourne, we adopted a layered
approach to investigate the role of Chinese language in Australia. Our data set consisted of hundreds of photographs of street
signage in one square block area of the shopping district. Results of our analyses show that signage portrays a variety of code
preferences and semiotic choices that in turn reveal insights into the identities, ideologies, and strategies that help to
structure the urban environment. As demonstrated in our study, such complexity requires a renewed and situated understanding of
key principles of linguistic landscape research (Ben-Rafael & Ben-Rafael,
2015).
Falling to one’s death in multiple
landscapes
Authors: Broccias Cristiano
Published: February 2020

This paper discusses whether He fell to
his death is a possible counterexample to Goldberg’s (1995) Unique
Path Constraint, which bans simultaneous motion in multiple
landscapes in caused motion/resultative constructions. On the face
of it, He fell to his death involves the blending
of motion in a physical landscape (as hinted at by
fell) and motion in a metaphorical landscape
(dying is conceptualised as telic motion). A possible solution to
this apparent violation is the claim that He fell to his
death is not an instance of the resultative
construction and/or that to his death is metonymic
for the place where one is presumed to have died. This paper argues
that neither option is feasible: the example at hand instantiates
the resultative construction and metonymy is not relevant. Instead,
our ability for blending intimately connected facets of a complex
event and the satellite-framed nature of English are held to be
decisive factors for the licensing of the example under
discussion.
“They cowardly attack US, so we nobly eliminate them…”
Authors: Mayor-Goicoechea Cristina , Romero-Trillo Jesús
Published: February 2020

The threat of the Islamic State is realised both in its attacks and its discourse. To illustrate the role of
linguistic threats, the present study investigates the ISIS online propaganda magazine Dabiq by combining
Critical Discourse Analysis and Corpus Linguistics (Romero-Trillo 2008; Baker et al. 2008). Following the two groups described by van Dijk (2003), which are represented by the in-group (ISIS) and the out-group (against ISIS), we
propose a third element: the translocal group (i.e., the people in between). The results show the substantial presence of
linguistic strategies enhanced by Dangerous Speech (Benesch 2013) to create a high
segregation between the groups. Also, the analysis shows the inextricable relationship between conflict and dangerous language and
the need to investigate this link further, with special reference to the polarisation of the groups and to the subsequent
escalation of violence in discourse.
Pragmatics lost?
Authors: Baider Fabienne
Published: February 2020

This article argues for a definition of online hate speech as a contextualised speech act that is part of a social process of alienation. It suggests that hate speech comes in degrees, is contextual, involves already existing power dynamics, and ‘others’ its targets by creating in/out groups. I first review the various stances towards understanding the phenomenon of online hate speech, including approaches that focus on online hate speech as an interaction shaped by its medium, while also emphasizing the need to consider the role of implicatures in speech acts when defining hate speech. Second, I argue that the relationality of online speech implies that any message is embedded in idiosyncratic socio-cultural norms, and that therefore a ‘one size fits all’ definition of hate speech is elusive. I conclude by suggesting that contextualized hate speech is embedded in a social process of alienation and should be understood as a continuum.
Linoleic acid, α-linolenic acid, and monolinolenins as antibacterial substances in the heat-processed soybean fermented withRhizopus oligosporus
Authors: Kusumah Dewi , Wakui Misaki , Murakami Mai , Xie Xiaonan , Yukihito Kabuyama , Maeda Isamu
Published: February 2020

Antibacterial activities against Staphylococcus aureus and Bacillus subtilis were found in an ethanol fraction of tempe, an Indonesian fermented soybean produced using Rhizopus oligosporus. The ethanol fraction contained free fatty acids, monoglycerides, and fatty acid ethyl esters. Among these substances, linoleic acid and α-linolenic acid exhibited antibacterial activities against S. aureus and B. subtilis, whereas 1-monolinolenin and 2-monolinolenin exhibited antibacterial activity against B. subtilis. The other free fatty acids, 1-monoolein, monolinoleins, ethyl linoleate, and ethyl linolenate did not exhibit bactericidal activities. These results revealed that R. oligosporus produced the long-chain polyunsaturated fatty acids and monolinolenins as antibacterial substances against the Gram-positive bacteria during the fungal growth and fermentation of heat-processed soybean.
Invasive aquatic plant (Alternanthera philoxeroides) facilitates the invasion of western Mosquitofish (Gambusia affinis) in Yangtze River, China
Authors: Xiong Wen , Tao Juan , Liu Chunlong , Liang Yangyang , Sun Heying , Chen Kang , Cheng Yu , Chen Yifeng
Published: February 2020

We investigated the seasonal habitat selection of Mosquitofish to increase our understanding of the ecology and invasiveness of this species. Sampling was conducted during the reproductive and non-reproductive season of Mosquitofish in four habitat types: Alternanthera philoxeroides habitat, Typha angustifolia habitat, Paspalum distichum habitat, and no vegetation habitat. Mosquitofish catch per unit effort was significantly lower in Typha habitat than in the other three habitats during the reproductive season. T. angustifolia can exude allelopathic chemicals and have the potential to negatively influence western Mosquitofish abundance. In the non-reproductive season, catch per unit effort of Mosquitofish were significantly higher in Alternanthera habitat than in the other three habitats. These results suggest that mats of A. philoxeroides provided an insulating layer for Mosquitofish overwintering. Therefore, Mosquitofish could expand its range further north in China as A. philoxeroides spreads northward with climate change. We suggest that an effective way of controlling western Mosquitofish is through eradication of the invasive macrophyte (A. philoxeroides) stands while retaining and restoring more native emergent macrophyte (T. angustifolia) stands; this strategy could limit overwintering habitat for western Mosquitofish and may draw them into open water habitats where they can be more easily removed.
Improved functional connectivity network estimation for brain networks using multivariate partial coherence
Authors: Makhtar Siti N , Senik Mohd H , Stevenson Carl W , Mason Rob , Halliday David M
Published: February 2020

Objective. Graphical networks and network metrics are widely used to understand and characterise brain networks and brain function. These methods can be applied to a range of electrophysiological data including electroencephalography, local field potential and single unit recordings. Functional networks are often constructed using pair-wise correlation between variables. The objective of this study is to demonstrate that functional networks can be more accurately estimated using partial correlation than with pair-wise correlation. Approach. We compared network metrics derived from unconditional and conditional graphical networks, obtained using coherence and multivariate partial coherence (MVPC), respectively. Graphical networks were constructed using coherence and MVPC estimates, and binary and weighted network metrics derived from these: node degree, path length, clustering coefficients and small-world index. Main results. Network metrics were applied to simulated and experimental single unit spike train data. Simulated data used a 10x10 grid of simulated cortical neurons with centre-surround connectivity. Conditional network metrics gave a more accurate representation of the known connectivity: Numbers of excitatory connections had range 3–11, unconditional binary node degree had range 6–80, conditional node degree had range 2–13. Experimental data used multi-electrode array recording with 19 single-units from left and right hippocampal brain areas in a rat model for epilepsy. Conditional network analysis showed similar trends to simulated data, with lower binary node degree and longer binary path lengths compared to unconditional networks. Significance. We conclude that conditional networks, where common dependencies are removed through partial coherence analysis, give a more accurate representation of the interactions in a graphical network model. These results have important implications for graphical network analyses of brain networks and suggest that functional networks should be derived using partial correlation, based on MVPC estimates, as opposed to the common approach of pair-wise correlation.
Finding common ground: agreement on increasing wildfire risk crosses political lines
Authors: Hartter Joel , Hamilton Lawrence C , Ducey Mark J , Boag Angela E , Salerno Jonathan D , Christoffersen Nils D , Oester Paul T , Palace Michael W , Stevens Forrest R
Published: February 2020

Wildfire is a growing threat in the western US, driven by high fuel loads, a warming climate, and rising human activity in the wildland urban interface. Diverse stakeholders must collaborate to mitigate risk and adapt to changing conditions. Communication strategies in collaborative efforts may be most effective if they align with local perspectives on wildfire and climate change. We investigate drivers of residents’ subjective perceptions regarding both issues in eastern Oregon using 2018 survey data, and examine objective evidence regarding local fuel loads, climate, and wildfire to identify trends and contextualize residents’ perceptions. We find that sociopolitical identity strongly predicts climate change beliefs, and that identity and climate beliefs predict both perceptions of recent past climate and likely future trends. Political influences on climate perceptions are strongest among people whose friends mostly belong to the same party. In contrast, perceptions about future wildfire risks are largely independent of climate-change beliefs, and of individual or peer-group politics. Most people accurately perceive the rising frequency of large wildfires, and expect this trend to continue. Decision makers have an opportunity to engage diverse stakeholders in developing policies to mitigate increasing wildfire risk without invoking climate change, which remains politically polarizing in some communities.
How urban densification influences ecosystem services—a comparison between a temperate and a tropical city
Authors: Grêt-Regamey Adrienne , Galleguillos-Torres Marcelo , Dissegna Angela , Weibel Bettina
Published: February 2020

Large scale and rapid urbanization processes call for a better quality of urban planning to support human well-being. While compact cities aim to reduce land consumption, densification puts pressure on the remaining green areas, influencing ecosystem services provision and ultimately the life quality of the growing urban population. Supply of and demand for urban ecosystem services differ however greatly across the globe. In this study, we derive a set of urban typologies and their related ecosystem services bundles in both a temperate and a tropical city. We show that the supply of urban ecosystem services does not increase linearly with green area coverage, but is highly dependent on the urban form. While the surface sealed by infrastructures and the buildings themselves play a key role in influencing ecosystem services provision, we observe that the share of trees is particularly important for supporting regulating ecosystem services in built up neighborhoods. With a similar average surface-to-volume ratio, open midrise neighborhoods in Singapore provide more water flow regulation and air pollution control services than the same urban typology in Zurich. Microclimate regulation, in contrast, does not seem to be dependent on the context, but more on the amount of built up surface. Interestingly, we observe that open midrise neighborhoods synergistically support the supply of many regulating services in both case study areas, including microclimate regulation, water flow regulation and air pollution control. Large water and forest patches are unquestionably essential in both Singapore and Zurich to support bundles of ecosystem services, particularly also for recreational activities. Using open data, the approach can be transferred to other cities and support decision makers in their efforts to plan the sustainable development of cities across the world.
Ectoine production from putrefactive non-volatile amines in the moderate halophile Halomonas elongata
Authors: Nakayama H , Kawamoto R , Miyoshi K
Published: February 2020

The moderate halophile Halomonas elongata can assimilate a variety of sugars and/or amino acids derived from bio-wastes as carbon and/or nitrogen sources. Thus, H. elongata could be a practical cell factory for bioproduction of fine chemicals such as ectoine. In protein-rich bio-wastes, putrefactive non-volatile amines could be formed as biogenic amines by decarboxylation of amino acids during biological rotten processes and be a considerable toxicological risk. Therefore, we investigated whether H. elongata can assimilate major putrefactive non-volatile amines, Histamine and Tyramine, as carbon and/or nitrogen sources or not. Comparative analysis using closely related H. elongata strains, OUT30018 and DSM2581T, revealed that H. elongata OUT30018 can assimilate both Histamine and Tyramine, and produce ectoine under high salinity, while H. elongata DSM2581T cannot. Thus, H. elongata OUT30018 would be a one of the most promising cell factories to produce fine chemicals such as ectoine from the putrefactive non-volatile amines in protein-rich bio-waste.
Effect of storage time and temperatures on growth rate of Eschericia coli BL21 containing JSU construct for Jembrana disease candidate vaccine
Authors: Indriawati  , Volkandari S D , Margawati E T
Published: February 2020

The viability of Eschericia coli BL21 (DE3) bearing JSU (Jembrana Surface Unit) recombinant protein depend on several factors, such as temperatures and time of storage. JSU act as a vaccine candidate for the Jembrana disease in Bali cattle, therefore, it is important to keep the quality and quantity the yield of JSU recombinant protein, the E. coli need to maintenance. The study was designed to examine the viability of Escherichia coli at different temperatures and time of cultivation. The E. coli BL21 bearing JSU was cultured in LB broth (+Amph 100µg mL−1) overnight and aliquot it in 1.5mL sterile tube (3 tube every temperatures). The tubes were incubated in three storage temperatures (Room Temperatures/RT, 4°C and -20°C. The viabilities of the cells were observed in 24, 48 and 120 hours by measuring the Optical density by spectrophotometer, and then inoculated it in LB plate (+Amp 100µg mL−1). The result showed that statistically, there were significant effect (P<0.05) in temperature -20°C at 24h and 120h observation on viability of E. coli BL21. The viability of E. coli at -20°C and storage time observed at 120h are more stabile, compared the other temperatures (RT and 4°C). There was no significant effect on both temperatures RT and 4°C in OD600 at 24 and 48h and the growth was decreased until 120h observation. The observation at 24h with 4°C cultured has a higher OD600 (1.098) followed by RT (1.070) and -20°C (0.773). The viability of E. coli was decreased at 48h with RT (1.011) and 4°C (1.0611), meanwhile, at -20°C the cells were increased (0.958). Meanwhile, the observation at 120h, the cells was more stabile at -20°C (0.961) compared with cultures from 4°C (0.981) and RT (0.719). Based on the OD600, the viability at the -20°C intended more stabile compared to RT and 4°C, but in the 24h the growth at -20°C are very low because no protectant added in the culture, it will shock the cells and dead. This finding showed that viability of E. coli BL21 bearing JSU recombinant protein better to keep in -20°C for longer period storage time with an addition of protectant agent in the culture media to keep the cells alive and more stabile.
Isolation and Identification of ACC Deaminase Producing Bacteria from Rhizosfer and Plant Roots of Maize, Cowpea, and Groundnut Growing under Saline Stress
Authors: Simarmata R , Dewi D C , Ngadiman
Published: February 2020

ACC deaminase producing bacteria reduces the excess ethylene produced by stressed plant because ACC deaminase catalyzes the cleavage of ACC into ammonium and α-ketobutyrate. ACC deaminase is produced by several rhizospheric and endophytic bacteria. This study was aimed to obtain ACC deaminase producing bacteria isolated from rhizosfer and plant roots of maize, cowpea, and groundnut growing under saline stress. Isolation was conducted by surface plating on NA medium. Qualitative selection was based on the growth of isolate on DF salts medium supplemented with AIB. Quantitative selection based on ACC deaminase activity assay. Identification of the isolates was carried out by morphologycally and sequencing of 16S rRNA gene. Isolation and selection resulted four bacterial isolates (AJG3, RJG6, ATL5, and RTN10). Those bacterial isolates have the ACC deaminase activity between 184.65 to 692.54 nmol α-ketobutyrate. mg−1. h−1. Isolate of AJG3, RJG6, and ATL5 were gram negative bacteria, only one isolate was gram positive bacteria (RTN10). Based on 16S rRNA gene sequence, AJG3, RJG6, ATL5, and RTN10 isolates have a high similarity with Klebsiella variicola, Rhizobium pusense, Agrobacterium tumefaciens, and Bacillus stratosphericus respectively.
Characterization of cassava starch and its potential for fermentable sugar production
Authors: Fathoni A , Hartati NS , Wahyuni H Fitriani , Rahman N , Harmoko R , Perwitasari U
Published: February 2020

This study aimed to characterise starch properties of an improved cassava genotype generated from somaclonal variation, Revita RV1 and investigate its potential for fermentable sugar production. A total of six cassava genotypes including Revita RV1, Manggu, Adira 4, Menti, Kristal Merah and Roti were used for comparison analysis. Morphological properties of starch were observed using light microscope and electron microscope (SEM). Physico-chemical properties such as ratio of amylose and amylopectin, swelling power, syneresis, gelation capacity, and water holding capacity (WHC) and oil holding capacity (OHC) were measured. Glucose from starch fermentation was determined by HPLC. The results showed there was variation in shape (irregular, rounded and truncated) and diameter of starch granule among the six genotypes ranged between 19 and 147 µm. The highest swelling power (SP) was obtained from starch of Menti (7.02 ± 0.30) and the lowest SP was starch of Adira 4 (5.94 ± 0.54). The other properties such as ratio of amylose and amylopectin, syneresis, and gelation capacityalso varied among tested cassava genotypes. HPLC quantification revealed that Roti and Revita RV1 produced fermentable sugar higher than other genotypes with glucose concentration of 110.77 g/L and 102.06 g/L, respectively. The lowest glucose concentration of 89.59 g/L was obtained from Menti. The efficiency of fermentable sugar/glucose production among cassava genotypes is more likely influenced by various properties of starch.
Agronomic Characteristics, Yield Components and Polymorphic Markers between IRBL Kp-K60 and Ciherang for Developing Rice Resistant to Blast
Authors: Nurhasanah A N , Astuti D , Widyajayantie D , Estiati A , Nugroho S , Suwarno
Published: February 2020

Blast is one of the most devastating disesase in rice field in Indonesia which caused by Pyricularia oryzae. Utilising rice resistant variety is one of the most efective, economical dan eco-friendly solution for the disease. To develop rice resistant to blast is required resources of plant with resistance gene and popular variety as the parents. Introgressing gene pik in chromosome 11 from IRBL Kp-K60 into Ciherang was conducted using markers-assisted backcrossing. In this backcrossing program, selection process is a crucial part to gain the goal of the program. The goal of backcrossing program is to obtain plant which has all Ciherang characteristics with additional trait, resistance to blast. Some characteristics of the parents such as agronomic characteristics and yield components must be observed to assist phenotypic selection in the progeny. Moreover, applying DNA markers in backcrossing program will facillitate selection proccess to ensure that resistance gene is already transfered from donor into recepient. Thus, it is important to analyse polymorphic DNA markers between the parents. The aim of the study were to asses parental difference in agronomic characteristics and yields component and analyse polymorphic markers between Ciherang and IRBL Kp-K60 for developing rice resistant to blast disease. The result of study showed that several agronomic characteristics and yield component in Ciherang were more superior than IRBL Kp-K60.Flowering date of Ciherang was more longer than IRBL Kp-K60. Thirty six DNA markers were used in this study from various type of markers, namely CAPs, SSR and SNP. Some DNA markers were dominan and the others were codominan. There were fourthen DNA markers were polymorphics between the parents and can be used in the selection process in the progeny.
High γ Amino Butyric Acid and Low Citrinin Produced by Monascus purpureus Serasi Strain
Authors: Suharna N , Yulinery T , Wulandari N F , Triana E , Nurhidayat N
Published: February 2020

The analysis bioactive production by Monascus purpureus SERASI strain was carried to know its potency for industrial application as herbal medicine. Previously, the fungus was cultured on malt extract agar for 12 days and harvested for inoculum purpose. For Monascus fermented rice (MFR) production, previously sterilized rice strain 24R after soaking treatment of plain water for a night was inoculated by the inoculum. Afterwards, the rice was incubated at 30°C for 6, 8, 10, and 12 days of incubation time period. The MFR was analysed for its GABA, lovastatin and citrinin content by using High Performance Liquid Chromatography. The result showed that the highest amino butyric acid (GABA) content of MFR was at 452 µg/g after 10 days of incubation time period. But it was decreased to 129 µg/g and 316 µg/g after 12 days and 14 days, respectively. While, lovastatin produce was at 315 µg/g after 10 days but decrease dramatically to 16 µg/g and 26 µg/g after 12 days and 14 days. In regard to citrinin, the acceptable content was reached at 0.12 µg/g after 12 days. At day 10 or 14 days, the citrinin content was higher at 13.39 µg/g and 14.18 respectively. Based on high GABA and low citrinin produces, this result showed that M. purpureus Serasi strain might be more potency for industrial purpose as an herbal medicine for anti hypertensive agent. Therefore, further study is needed to confirm MFR with high content of GABA as anti hypertensive agent.
Purification of recombinant human granulocyte colony-stimulating factor from Pichia pastoris using two ninta chromatography methods
Authors: Yuliawati  , Aminah  , Fuad A M
Published: February 2020

Human granulocyte colony-stimulating factor (hG-CSF) is a glycoprotein that stimulates the production of mature neutrophil and enhances its survival, proliferation, differentiation, and neutrofil precursor function. This study was carried out to determine the purity of recombinant protein employing two purification methods using NiNTA with imidazole and with pH gradient (without imidazole). The synthetic gene (gcsf-cmyc) was cloned into secretive expression vector pPICZαA and methanol utilizing alcohol oxidase (AOX1) promoters before being expressed in Pichia pastoris SMD1168H strain. The recombinant protein was purified using NiNTA chromatography with imidazole and pH gradient. All samples were analyzed using SDS PAGE, followed with detection using coomasie blue. The molecular mass of recombinant hG-CSF expressed in P. pastoris was ∼23kD. The efficiency of hG-CSF purification using NiNTA with imidazole was ∼63%, while with pH gradient was ∼89%. Purification techniques use pH gradients gradients can be applied to avoid used of imidazole, so that it does not contaminate protein samples.
Growth evaluation of taro cv. Bentul (Colocasia esculenta L.) diploid and tetraploid in the greenhouse in response to different soil water content for selection of drought tolerant plants
Authors: Sari L , Susetio M , Efendi D , Wulansari A , Ermayanti T M
Published: February 2020

Taro (Colocasia esculenta L.) is useful as an alternative food. This plant species is popular in Indonesia, especially at Bogor, West Jawa due to many typical foods are made from taro flour having a good market in that area. Taro cv. Bentul is one of the best cultivars having high productivity. Induction of tetraploid plants is aimed to obtain genotypes to have better characteristics in growth, productivity as well as to increase its genetic diversity. Selection of drought tolerant can also be conducted comparing diploid with tetraploid plants. The purpose of this study was to evaluate the growth of taro diploid and tetraploid plants in the greenhouse after treatment with different soil water content. Diploid and tetraploids plants were produced after in vitro micropropagation. Plantlets were acclimatized in a greenhouse then they were subjected for different soil water content treatment in order to select plants tolerant to drought stress. The experiment used factorial randomized complete design. The first factor was Bentul taro genotype which were tetraploid 3.3.6 and diploid clones as control treatment. The second factor was different soil water content which were at 100% of field capacity, 50% of field capacity, and 25% of field capacity. Growth was observed every week by recording length of the petiole, number of leaves, lamina length, and lamina width. Fresh and dry weight, proline content, chlorophyll concentration, roots and stomata morphology were also recorded at 12 weeks after planting. The results showed that taro tetraploid 3.3.6 had higher growth significantly difference compared to diploid (control) plant. Diploid taro has greater number of stomata densities than that of tetraploid 3.3.6 at 100% of the field capacity. Taro tetraploid 3.3.6 grown with 50% of the field capacity had higher biomass production compared to diploid taro. Therefore, tetraploid clone 3.3.6 plant could be assumed to be a drought tolerant plant.
Screening and activity of yeast-associated with cocoa-bean fermentation against phytopathogenic yeast and fungi
Authors: Putri R E , Lisdiyanti P , Fahrurrozi
Published: February 2020

Cocoa-bean fermentation has been associated with the involvement of diverse microbial assemblages which consist of a wide array of bacteria and yeast. We attempted to screen and to identify the potential antifungal yeast from this assemblage against phytopathogenic fungi. We employed in-vitro antagonism assay using agar plug methods to performpreliminary screening from 35 yeast isolates followed by total protein production and measurement with Bradford methods. We found three yeast strains that were effective against Trichoderma sp. T009, and two moulds associated with cocoa (Penicilliumsp. Cocoa2 and Fusariumsp.Cocoa 1). The three bioactive yeast strains were identified as Saccharomyces cerevisiae IDI-002, Hanseniasporauvarum IDE-056 and Hanseniasporauvarum IDE-271 based on molecular identification and phylogenetic analysis. The production of antifungal protein from pure cultures on YEPG media resulted intotal protein concentration between 6.20 - 8.17 mg/L. Cell suspension showed higherinhibitory activity compared to thecell-free supernatant gave indication that antifungal proteins in the bulk fermentation was below the minimal inhibitory concentration to cause the inhibitory effect. Further characterization, purification, and optimization are still needed before the up-scale production of antifungal metabolites and its biological control application.
Characterization of α-Amylase and Protease from Indigenous Lactobacillus fermentum EN17-2 and Its Use in Tuber Paste Flour
Authors: Khusniati Tatik , Gresi Hatmaya Priskila , Amir Mellova , Rachmach Junia , Safriana Vilya , Sulistiani
Published: February 2020

α-Amylase and protease are biocatalyst which can be used in paste flour to produce natural sweet paste flour. Production of these enzyme in Indonesia are limited, so, to increase those enzyme production, α-amylase and protease from indigenous bacteria are needed. This research focused in characterization of α-amylase and protease from indigenousLactobacillus fermentumEN17-2 and its use in tuber paste flour. Crude enzymes of α-amylase and protease were characterized. Tuber sources were cassava (Manihot esculenta) and sweet potato (Ipomoea batatas) with wheat (Triticum) as comparison. α-Amylase activity and reduction sugar were detected by DNS methods, while protease was detected by tyrosin method and protein degradation was detected by titration. The results show that optimum activity of αamylase fromL. fermentumEN17-2 was reached at pH 5.5, 45°C, while that optimum activity of protease was at pH 6.5, 35°C. Stability of α-amylase fromL.fermentumEN17-2 was at pH 5.0-6.5, 30-60°C; while that protease was at pH 4.5-8.0, 20-50°C. The reduction sugar content of cassava and sweet potato paste flour were 13.50% and 23.70%, respectively, while that the reduction sugar content of those flour added α-amylase fromL. fermentumEN17-2 were 32.54% and 24.30%. The protein degradation of those paste flour were 0.49% and 1.17%, respectively, while that the protein degradation of those flour added protease were 1.90 % and 1.68%. The increase of reduction sugar in those paste flour were 58.51% and 2.47%, while that protein degradation were 1.40% and 0.50%, respectively. Based on the increase of reduction sugar and protein degradation in those treated paste flour, it concluded that the characterized α-amylase and protease fromL. fermentumEN17-2 was better to be used as biocatalyst in cassava pasta flour to produce natural sweet paste flour than that sweet potato.
Histology-Independent Signature Distinguishes Kikuchi-Fujimoto Disease/Systemic Lupus Erythematosus–Associated Lymphadenitis From Benign and Malignant Lymphadenopathies
Authors: Scott Gregory D , Kumar Jyoti , Oak Jean S , Boyd Scott D , Raess Philipp W , Gratzinger Dita A
Published: February 2020

Objectives

Kikuchi-Fujimoto disease (KFD) and systemic lupus erythematosus (SLE) are benign entities with histologic features that raise concern about malignancy and infection. We searched for a histology-independent KFD/SLE signature relying on only immunophenotype and basic clinical characteristics.

Methods

A histology-independent KFD/SLE signature was generated using 975 excised lymph nodes with flow immunophenotyping, including 16 cases of KFD/SLE. This signature was then evaluated in 1,198 fine-needle aspiration (FNA) specimens.

Results

The top flow cytometry discriminant for KFD/SLE was uniform CD38+ expression on CD19+ events. Immunohistochemistry demonstrated nodules of IgD+, IgM− B cells surrounding necrotizing and activated T-cell areas. A signature combining 6 flow cytometry criteria with age and sample site had a positive predictive value of 88% for KFD/SLE, which had a prevalence of 1.6%. All 4 signature-positive FNA cases with follow-up excision were KFD/SLE. At a second institution, 4 of 5 KFD/SLE cases passed the top discriminant.

Conclusions

A flow cytometry signature combined with age and biopsy site identifies KFD/SLE independent of histology, suggesting a shared immune composition and independently confirming that KFD/SLE represents a distinct entity. Unexpectedly, an IgD+CD38+ small B-cell population is a distinctive feature of KFD/SLE, suggesting a possible pathologic role for anergic/autoreactive B cells.