bluuebunny/crossref_metadata_2025_split huggingface dataset:
Encapsulation of Yoghurt Starter Using Starch as a Filler Through Emulsification Method
Authors: Abubakar  , Usmiati S , Rahayuningsih M 
Published: October 2019

Abstract
The viability of starter culture (Streptococcus thermophilus and Lactobacillus bulgaricus) in yoghurt declined during storage. Therefore, it needs protection to prevent this condition by encapsulation. The encapsulation has been conducted by the emulsification method. This research aimed to determine the best encapsulant which could protect starter culture and to investigate the characteristic of yoghurt produced from the starter using selected encapsulant. The emulsification method was developed by mixing encapsulant materials (maize resistant starch and maltodextrin) with vegetable oil (canola oil containing 0.5% tween 80%), in a ratio by 1:2:2. Subsequently, 0.1% inoculum (cultivated from initial of log phase) was added. The three composition of encapsulant materials were alginate 2%: maize resistant starch 2%; alginate 3%: maltodextrin 1%; and alginate 4%. The best encapsulant was alginate 3%: maltodextrin 1%. This encapsulation increased the viability of the bacteria by 0.27 log CFU/g (on wet beads) and 5.78 log CFU/g (on dry beads) compared to the free cell. Yoghurt produced using a starter with encapsulant 3% alginate: 1% maltodextrin was more acidic than from the free cells, but it was still lower than commercial starter. Based on hedonic test, yoghurt produced from the best encapsulant was not significantly different from the commercial starter.
Characteristics of Snack Bar “Banaris” from Fortified Non Cereal Flour as Emergency Food for Toddler
Authors: Rachmat R , Hastuti W , Darniadi S 
Published: October 2019

Abstract
The objective of the research is the development of banaris bar products using flour-based of local food with FIR technology, that fulfill the economic, social-cultural, nutritional and health eligibility requirements as an alternative food emergency to support diversification national food because this product is needed in accordance with the adequacy of nutrients for the age group of nutrient-prone (infants and toddlers). fortification, testing product characteristics, packaging, shelf life testing, probiotic testing of Bifidobacterium sp and Lactobacillus sp and testing of serum retinol concentrations in children under five year. The effect of giving Banaris bar products gives positive results on increasing subject height. The provision of Banaris bar products containing prebiotics can stimulate the growth of the Lactobacillus sp population in the toddler’s digestive tract in the treatment group compared to the control group toddlers.. The level of crispness, elasticity, stickiness, compactness and fragility of the banaris bar is lower than the regular bar snack. The packaging used is aluminum foil primary packaging and secondary packaging, namely carton. The packaging consists of 3 variants, namely packaging for six pieces with a size of 10.5 x 8 x 3.5 cm, packing for 9 pieces with a size of 15 x 8 x 3.5 cm and packaging for 15 pieces with a size of 15 x 13 x 3.5 cm. Banaris bar products have a shelf life of 10 months.
Exploiting transfer learning for the reconstruction of the human gene regulatory network
Authors: Mignone Paolo , Pio Gianvito , D’Elia Domenica , Ceci Michelangelo 
Published: October 2019

Abstract

Motivation
The reconstruction of gene regulatory networks (GRNs) from gene expression data has received increasing attention in recent years, due to its usefulness in the understanding of regulatory mechanisms involved in human diseases. Most of the existing methods reconstruct the network through machine learning approaches, by analyzing known examples of interactions. However, (i) they often produce poor results when the amount of labeled examples is limited, or when no negative example is available and (ii) they are not able to exploit information extracted from GRNs of other (better studied) related organisms, when this information is available.

Results
In this paper, we propose a novel machine learning method that overcomes these limitations, by exploiting the knowledge about the GRN of a source organism for the reconstruction of the GRN of the target organism, by means of a novel transfer learning technique. Moreover, the proposed method is natively able to work in the positive-unlabeled setting, where no negative example is available, by fruitfully exploiting a (possibly large) set of unlabeled examples. In our experiments, we reconstructed the human GRN, by exploiting the knowledge of the GRN of Mus musculus. Results showed that the proposed method outperforms state-of-the-art approaches and identifies previously unknown functional relationships among the analyzed genes.

Availability and implementation
http://www.di.uniba.it/∼mignone/systems/biosfer/index.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bioregions in Marine Environments: Combining Biological and Environmental Data for Management and Scientific Understanding
Authors: Woolley Skipton N C , Foster Scott D , Bax Nicholas J , Currie Jock C , Dunn Daniel C , Hansen Cecilie , Hill Nicole , O’Hara Timothy D , Ovaskainen Otso , Sayre Roger , Vanhatalo Jarno P , Dunstan Piers K 
Published: October 2019

AbstractBioregions are important tools for understanding and managing natural resources. Bioregions should describe locations of relatively homogenous assemblages of species occur, enabling managers to better regulate activities that might affect these assemblages. Many existing bioregionalization approaches, which rely on expert-derived, Delphic comparisons or environmental surrogates, do not explicitly include observed biological data in such analyses. We highlight that, for bioregionalizations to be useful and reliable for systems scientists and managers, the bioregionalizations need to be based on biological data; to include an easily understood assessment of uncertainty, preferably in a spatial format matching the bioregions; and to be scientifically transparent and reproducible. Statistical models provide a scientifically robust, transparent, and interpretable approach for ensuring that bioregions are formed on the basis of observed biological and physical data. Using statistically derived bioregions provides a repeatable framework for the spatial representation of biodiversity at multiple spatial scales. This results in better-informed management decisions and biodiversity conservation outcomes.
Pharmacological activation of IKr in models of long QT Type 2 risks overcorrection of repolarization
Authors: Perry Matthew D , Ng Chai-Ann , Mangala Melissa M , Ng Timothy Y M , Hines Adam D , Liang Whitney , Xu Michelle J O , Hill Adam P , Vandenberg Jamie I 
Published: October 2019

Abstract

Aims
Current treatment for congenital long QT syndrome Type 2 (cLQTS2), an electrical disorder that increases the risk of life-threatening cardiac arrhythmias, is aimed at reducing the incidence of arrhythmia triggers (beta-blockers) or terminating the arrhythmia after onset (implantable cardioverter-defibrillator). An alternative strategy is to target the underlying disease mechanism, which is reduced rapid delayed rectifier current (IKr) passed by Kv11.1 channels. Small molecule activators of Kv11.1 have been identified but the extent to which these can restore normal cardiac signalling in cLQTS2 backgrounds remains unclear. Here, we examined the ability of ICA-105574, an activator of Kv11.1 that impairs transition to the inactivated state, to restore function to heterozygous Kv11.1 channels containing either inactivation enhanced (T618S, N633S) or expression deficient (A422T) mutations.

Methods and results
ICA-105574 effectively restored Kv11.1 current from heterozygous inactivation enhanced or expression defective mutant channels in heterologous expression systems. In a human-induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) model of cLQTS2 containing the expression defective Kv11.1 mutant A422T, cardiac repolarization, estimated from the duration of calcium transients in isolated cells and the rate corrected field potential duration (FPDc) in culture monolayers of cells, was significantly prolonged. The Kv11.1 activator ICA-105574 was able to reverse the prolonged repolarization in a concentration-dependent manner. However, at higher doses, ICA-105574 produced a shortening of the FPDc compared to controls. In vitro and in silico analysis suggests that this overcorrection occurs as a result of a temporal redistribution of the peak IKr to much earlier in the plateau phase of the action potential, which results in early repolarization.

Conclusion
Kv11.1 activators, which target the primary disease mechanism, provide a possible treatment option for cLQTS2, with the caveat that there may be a risk of overcorrection that could itself be pro-arrhythmic.
Freshwater microbial community diversity in a rapidly changing High Arctic watershed
Authors: Cavaco Maria Antonia , St. Louis Vincent Lawrence , Engel Katja , St. Pierre Kyra Alexandra , Schiff Sherry Lin , Stibal Marek , Neufeld Josh David 
Published: October 2019

ABSTRACTCurrent models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition (16S rRNA gene sequencing) to physicochemical parameters (e.g. dissolved oxygen and nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: (i) glacial rivers; (ii) active layer thaw-fed streams and waterbodies and (iii) Lake Hazen, into which (i) and (ii) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial communities were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that these communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.
Cationic amphiphiles against Gardnerella vaginalis resistant strains and bacterial vaginosis-associated pathogens
Authors: Weeks Richard M , Moretti Alysha , Song Shuang , Uhrich Kathryn E , Karlyshev Andrey V , Chikindas Michael L 
Published: October 2019

ABSTRACT
Antibiotic resistance and infection recurrence are critical issues in treating bacterial vaginosis, the most common vaginal disorder in women of reproductive age. Novel alternatives to traditional antibiotics, such as peptidomimetics, have the potential to address this challenge. Previously, two series of cationic amphiphiles (CAms) were developed with both hydrophilic head groups and non-polar domains, giving them the ability to self-assemble into supramolecular nanostructures with membrane-lytic properties. Those CAms were shown to be effective against biofilms of Gardnerella vaginalis while preserving the commensal microbiota. Two new series of CAms were designed with varying levels of flexibility between the hydrophilic head groups and the hydrophobic domains. Activities against the vaginal pathogen G. vaginalis ranged from 1.3 to 18.5 µM, while the tested vaginal lactobacilli were significantly more tolerant of CAms, with minimal inhibitory concentration values as high as 208 µM. Minimal biofilm bactericidal concentrations of the tested CAms ranged from 21.47 to &lt;388.3 µM, and were lowest against resistant forms of G. vaginalis, while Lactobacillus biofilms were tolerant of concentrations ≥687 µM. Safety aspects of the CAms were also investigated, and they were found to be safe for use against vaginal ectocervical tissue.
Big data in yeast systems biology
Authors: Yu Rosemary , Nielsen Jens 
Published: October 2019

ABSTRACTSystems biology uses computational and mathematical modeling to study complex interactions in a biological system. The yeast Saccharomyces cerevisiae, which has served as both an important model organism and cell factory, has pioneered both the early development of such models and modeling concepts, and the more recent integration of multi-omics big data in these models to elucidate fundamental principles of biology. Here, we review the advancement of big data technologies to gain biological insight in three aspects of yeast systems biology: gene expression dynamics, cellular metabolism and the regulation network between gene expression and metabolism. The role of big data and complementary modeling approaches, including the expansion of genome-scale metabolic models and machine learning methodologies, are discussed as key drivers in the rapid advancement of yeast systems biology.
Marchenko methods in a 3-D world
Authors: Lomas A , Curtis A 
Published: October 2019

SUMMARYMarchenko methods are a suite of geophysical techniques that convert seismograms of energy created by surface sources and measured by surface receivers into seismograms that would have been recorded by a virtual receiver at an arbitrary point inside the subsurface—an operation called redatuming. In principle these redatumed seismograms contain all contributions from direct, primary (singly-reflected) and multiply-reflected waves that would have been recorded by a real subsurface receiver, without requiring prior information about interfaces that generated the reflections. The potential of these methods for seismic imaging and redatuming has been demonstrated extensively in previous literature, but only using 1-D and 2-D Marchenko methods. There remain aspects of the methods that are poorly understood when applied in a 3-D world, so we investigate the application of Marchenko methods to 3-D data, subsurface structures and wavefields. We first show that for waves propagating in three dimensions, Marchenko methods can be applied to seismic data collected using both linear (so-called 2-D seismic) and areal (3-D seismic) acquisition arrays. However, for 2-D acquisition arrays the Marchenko workflow requires additional dimensionality correction factors to obtain accurate solutions, even in a subsurface that only varies with depth. Without these correction factors phase errors occur in redatumed Marchenko estimates; these errors propagate through the Marchenko algorithm and create depth errors in the Marchenko images. Furthermore, applying Marchenko methods to fully 3-D seismic wavefields recorded by linear (2-D seismic) arrays that contain out-of-plane reflections deteriorates surface-to-subsurface Green’s function estimates with spurious energy and resulting images are less accurate than those created using ‘conventional’ imaging methods. The application of fully 3-D Marchenko methods using data recorded on areal arrays solves both of the above problems, creating accurately redatumed wavefields and images with reduced artefact contamination. However, it appears that source–receiver spacing at most of $\lambda _A /4$ is required for accurate results using existing Marchenko methods, where λA is the dominant wavelength and in many real 3-D seismic acquisition scenarios this is impractical.
AKT signaling promotes DNA damage accumulation and proliferation in polycystic kidney disease
Authors: Conduit Sarah E , Davies Elizabeth M , Ooms Lisa M , Gurung Rajendra , McGrath Meagan J , Hakim Sandra , Cottle Denny L , Smyth Ian M , Dyson Jennifer M , Mitchell Christina A 
Published: October 2019

Abstract
Polycystic kidney disease (PKD) results in the formation of renal cysts that can impair function leading to renal failure. DNA damage accumulates in renal epithelial cells in PKD but the molecular mechanisms are unclear and are investigated here. Phosphoinositide 3- kinase (PI3K)/AKT signaling activates mammalian target of rapamycin complex 1 (mTORC1) and hyperactivation of mTORC1 is a common event in PKD, however, mTORC1 inhibitors have yielded disappointing results in clinical trials. Here we demonstrate AKT and mTORC1 hyperactivation in two representative murine PKD models (renal epithelial-specific Inpp5e knockout and collecting duct-specific Pkd1 deletion) and identify a downstream signaling network that contributes to DNA damage accumulation. Inpp5e- and Pkd1-null renal epithelial cells showed DNA damage including double-stranded DNA breaks associated with increased replication fork numbers, multinucleation and centrosome amplification. mTORC1 activated CAD, which promotes de novo pyrimidine synthesis, to sustain cell proliferation. AKT, but not mTORC1, inhibited the DNA repair/replication fork origin firing regulator TOPBP1, which impacts on DNA damage and cell proliferation. Notably, Inpp5e- and Pkd1-null renal epithelial cell spheroid formation defects were rescued by AKT inhibition. These data reveal that AKT hyperactivation contributes to DNA damage accumulation in multiple forms of PKD and cooperates with mTORC1 to promote cell proliferation. Hyperactivation of AKT may play a causal role in PKD by regulating DNA damage and cell proliferation, independent of mTORC1, and AKT inhibition may be a novel therapeutic approach for PKD.
Repurposing auranofin as a Clostridioides difficile therapeutic
Authors: Hutton Melanie L , Pehlivanoglu Havva , Vidor Callum J , James Meagan L , Thomson Melanie J , Lyras Dena 
Published: October 2019

Abstract

Background
Clostridioides difficile (previously Clostridium difficile) is the leading cause of nosocomial, antibiotic-associated diarrhoea worldwide. Currently, the gold standard of treatment for C. difficile infection (CDI) is vancomycin or metronidazole, although these antibiotics also perturb the protective resident microbiota, often resulting in disease relapse. Thus, an urgent need remains for the development of new treatment strategies. Auranofin is an FDA-approved oral antirheumatic drug that was previously shown to inhibit C. difficile vegetative cell growth, toxin production and spore production in vitro.

Objectives
To determine the efficacy of auranofin as a CDI therapeutic by examining the effect of treatment on toxin and spore production in vitro and in vivo, and on disease outcomes in mice.

Methods
C. difficile cultures were treated with auranofin and examined for effects on sporulation and toxin production by sporulation assay and ELISA, respectively. Mice were pretreated with auranofin prior to infection with C. difficile and monitored for physiological conditions, survival and gut damage compared with control animals. Faeces from mice were analysed to determine whether auranofin reduces sporulation and toxin production in vivo.

Results
Auranofin significantly reduces sporulation and toxin production under in vitro conditions and in infected mice in vivo. Mice treated with auranofin lost less weight, displayed a significant increase in survival rates and had significantly less toxin-mediated damage in their colon and caecum compared with control mice.

Conclusions
Auranofin shows promise as a prospective therapeutic option for C. difficile infections.
Evolution of hypervirulence in carbapenem-resistant Klebsiella pneumoniae in China: a multicentre, molecular epidemiological analysis
Authors: Zhang Yawei , Jin Longyang , Ouyang Pengwen , Wang Qi , Wang Ruobing , Wang Juan , Gao Hua , Wang Xiaojuan , Wang Hui ,   China Carbapenem-Resistant Enterobacteriaceae (CRE) Network, Kang Haiquan , Gu Bing , Wang Chunlei , Cao Bin , Yang Chunxia , Jin Liang , Liao Kang , Zhang Xiaoqian , Ma Xiaobo , Xie Liangyi , Zheng Rui , Zou Hong , Wang Shifu , Pei Fengyan , Man Sijin , Li Wei , Zhang Yumei , Cui Qiaozhen , Jia Xianghong , Guo Dawen , Fu Quan , Zhang Zhijie , Guo Zhusheng , Li Zhenpeng , Xu Yuanyuan , Ma Xiaoling , Li Yang , Jin Yan , Liu Zhiwu , Zeng Ji , Li Xiaoying , Zou Cuimei , Ji Ping , Jin Chunmei , Huang Jiaming , Tian Jinjing , Wu Weiqing , Xu Xichi , Wen Hainan , Yuan Jing 
Published: October 2019

Abstract

Objectives
Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) have been increasingly reported in China. Here, a multicentre, longitudinal surveillance study on CR-hvKP is described.

Methods
We retrospectively investigated carbapenem-resistant K. pneumoniae (CRKP) in 56 centres across China during 2015–17 and screened the virulence genes (iucA, iroN, rmpA and rmpA2) for the presence of virulence plasmids. Hypermucoviscosity, serum killing and Galleria mellonella lethality experiments were conducted to identify CR-hvKP among strains with all four virulence genes. Capsule typing, fitness and plasmid features of CR-hvKP were also investigated.

Results
A total of 1052 CRKP were collected. Among these, 34.2% (360/1052) carried virulence genes and 72 of them had all four of the virulence genes tested. Fifty-five (76.4%) were considered to be CR-hvKP using the G. mellonella infection model, with KPC-2-producing K64-ST11 being the most common type (80%, 44/55). Prevalence of CR-hvKP differed greatly between regions, with the highest in Henan (25.4%, 17/67) and Shandong (25.8%, 25/97). A significant increase in CR-hvKP among KPC-2-producing ST11 strains was observed, from 2.1% (3/141) in 2015 to 7.0% (23/329) in 2017 (P=0.045). Alarmingly, compared with classic CRKP, no difference in growth was found among CR-hvKP (P=0.7028), suggesting a potential risk for dissemination. The hybrid virulence and resistance-encoding plasmid evolved from pLVPK and the resistance plasmid harbouring blaKPC-2, indicating evolution existed between the hypervirulence and hyper-resistance plasmid.

Conclusions
CR-hvKP were more frequently detected than previously assumed, especially among KPC-2-producing ST11. Dissemination of hypervirulence could be extremely rapid due to limited fitness cost. Also, the evolution of resistance genes into hypervirulence plasmids was identified, presenting significant challenges for public health and infection control.
Effects of Aggregation Lure and Tree Species on Halyomorpha halys (Hemiptera: Pentatomidae) Seasonal Oviposition
Authors: Formella Adam , Dorman Seth J , Taylor Sally V , Kuhar Thomas P 
Published: October 2019

Abstract
The brown marmorated stink bug, Halyomorpha halys (Stål), is a polyphagous pest that feeds on a wide variety of agricultural commodities including tree fruits, berries, vegetables, field crops, and ornamental trees and shrubs. Accurate knowledge of where H. halys lays eggs is critical to optimize the potential release of Trissolcus japonicus (Ashmead), a scelionid egg parasitoid native to the same host region as H. halys. Ideally, parasitoids should be released in and around areas with high host density. In southwestern Virginia in 2017 and 2018, we searched trees for egg masses in an urban environment and nonmanaged wooded border environment. We also evaluated the effects of a commercial aggregation lure on the number of eggs being deposited. This aggregation lure, when combined with methyl (E,E,Z)-2,4,6-decatrienoate (MDT), has been shown to attract both adult and nymph H. halys and its effects on egg laying were not known. Results of this study showed no difference between the number of eggs laid on trees with and without lures. Catalpa trees, Catalpa bignonioides Walter, had the most egg masses throughout the course of the study; however, the redbud, Cercis canadensis L., had similar numbers in the late July and August. There was an overall trend with more eggs masses found on trees with fruiting structures present. This information can provide insight on where and when to make augmentative releases of egg parasitoids for H. halys.