bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Acid And Hydrolysis Duration on The Characteristics of Arrowroot and Taro Starch Nanoparticles
Authors: Winarti C , Widaningrum  , Surono I S , Uswah M
Published: October 2019

Arrowroot and taro are underutilized tuber. Modification of starch into starch nanoparticles will open to opportunities for further development. The aim of this research was to find out the influence of acid types and hydrolysis length on the characteristics of the resulted starch nanoparticle. There were group of treatments including source of starch: arrowroot and taro beneng starch, and the acid types was HCland H2SO4, and the length of hydrolysis was 3 and 5 hours. The results showed that the yield of arrowroot nanoparticle starch was higher than taro, 21.64 - 34.44% and 33.83 - 51.22%, respectively. Hydrolysis with HCl and H2SO4 produced starch nanoparticles (NP) with different characteristics. Treatment with HCl provides higher yield than that of H2SO4, but particle size was larger. The average size of the taro and arrowroot starch nanoparticles produced by hydrolysis by H2SO4 was 379.2 nm and 464.4 nm, respectively, with high polydispersity index of 0.480 and 0.621. Meanwhile, the crystallinity of taro and arrowroot starch NP increased from 44.1 into 87.3% and 43.5% into 51.3%, respectively. Acid hydrolysis improved solubility of starch nanoparticles but decreased the swelling power and gelatinization temperature. Starch nanoparticles can be implemented as a reinforcing agent for packaging, and carrier material for phytochemicals or agro-chemicals.
Study on Yoghurt Powder Probiotic Quality using Foam-Mat Drying Method
Authors: Miskiyah  , Juniawati  , Ayu K , Mulyati A H
Published: October 2019

Yoghurt powder probiotic has been produced by fermentation of milk using yoghurt cultures, Streptococcus thermophillus ENCC 0040, Lactobacillus bulgaricus ENCC 0041, Lactobacillus casei FNCC 0090 and Bifidobacterium longum ATCC 15707. The aim of this research was to determine the concentration and type of foam material to produce the best quality of yoghurt powder. Two types of foaming agents were used at different concentration as egg albumin 15%, 20%, 25% and tween 80 for 0.75%, 1.25%, 1.75%. The yoghurt foam was dried at 50°C for 3 h in cabinet dryer. The results showed that characteristic of yoghurt powder probiotic using 20% egg albumin meets the standard of the SNI (2981:2009) requirements as it was characterized by physicochemical and microbiologically. Moisture content 6,29%; ash content 4,82%; fat content 15,29%; protein content 26,47%; phosphor (P) content 634,15 ppm; and calcium (Ca) content 5121,71 ppm; acidity (lactic acid) 1,57%; lactic acid bacteria (LAB) count 1.8x1010 CFU/g; and yield 19.05%.
Encapsulation of Yoghurt Starter Using Starch as a Filler Through Emulsification Method
Authors: Abubakar  , Usmiati S , Rahayuningsih M
Published: October 2019

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

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

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

Bioregions 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.
Intrastriatal injection of alpha-synuclein fibrils induces Parkinson-like pathology in macaques
Authors: Dehay Benjamin , Bezard Erwan
Published: October 2019

This scientific commentary refers to ‘Intrastriatal alpha-synuclein fibrils in monkeys: spreading, imaging and neuropathological changes’, by Chu et al. (doi:10.1093/brain/awz296).
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

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

Current 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

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 <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

Systems 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

Marchenko 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

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

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

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

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.
The powers of a social auditor in a global production network: the case of Verité and the exposure of forced labour in the electronics industry
Authors: Raj-Reichert Gale
Published: October 2019

Research on labour governance actors in global production networks (GPNs) has been limited to civil society organisations, firms and governments. Understanding the influence of actors in GPNs has been dealt with singular and overt modes of relational power. This paper contributes to both debates by examining an intermediary actor—the social auditing organisation Verité—and its exercise of multiple modes of overt and covert powers to illustrate the complex terrain of change in GPNs. Verité, whose exposure of forced labour in Malaysian electronics subsequently changed labour governance practices in the electronics industry, mobilised power resources of credible information to exercise powers of expert authority and acts of dissimulation across various networked relationships in the GPN. This paper puts forth a multi-power framework of analysis to understand the micro-politics of GPNs.
The Trick of the Hedgehog: Case Report and Short Review About Archaeopsylla erinacei (Siphonaptera: Pulicidae) in Human Health
Authors: Greigert Valentin , Brunet Julie , Ouarti Basma , Laroche Maureen , Pfaff Alexander W , Henon Nicolas , Lemoine Jean-Philippe , Mathieu Bruno , Parola Philippe , Candolfi Ermanno , Abou-Bacar Ahmed
Published: October 2019

Fleas are ectoparasites of various animals, including Homo sapiens Linnaeus, 1758 (Primates: Hominidae). Among the species relevant to the human health field, either due to their dermatopathological potential or because of their role as vectors of microorganisms responsible for infectious diseases, such as plague or murine typhus, are the human flea, oriental rat flea, closely related cat and dog fleas, and chigoe flea. However, other species can accidentally infest humans. We have herein reported two unusual cases of humans infested and bitten by Archaeopsylla erinacei, the hedgehog flea. This species has been identified using stereomicroscopy, on the base of key characteristics. Furthermore, a brief literature review has revealed that hedgehog fleas could carry human-infectious agents, such as Rickettsia felis Bouyer et al. 2001 (Rickettsiales: Rickettsiaceae) or Bartonella henselae Regnery et al.1992 (Rhizobiales: Bartonellaceae). Using molecular biology, we thus tested nine A. erinacei specimens taken from these patients, for several bacteria species commonly associated with hematophagous arthropods, implicated in human pathology. However, all our samples were proven negative. The role of A. erinacei in human epidemiology has never been evaluated to date. This report sought to remind us that these fleas can be accidental parasites in humans. In addition, recent findings pertaining to bacteria of medical interest that are present in these insects should be brought to the fore, given that the question of their role as vectors in human infections remains unanswered and deserves further investigation.
The Survival Job Trap: Explaining Refugee Employment Outcomes in Chicago and the Contributing Factors
Authors: Lumley-Sapanski Audrey
Published: October 2019

Refugees resettled through the United States Refugee Admissions Program are expected to become economically self-sufficient by 90 days post arrival. To meet this expectation, refugee resettlement agencies attempt to place refugees in employment as rapidly as possible. Consequently, refugees are placed into pre-identified jobs—termed survival jobs—at partner employers in the secondary labour market largely irrespective of career background. This study examines the long-term employment and socio-economic outcomes of refugees given the agency approach and resulting initial job placement. To do so, I use individual employment records from a refugee resettlement agency in Chicago, semi-structured interviews with refugees and autoethnography conducted over an eight-year period (2008–16). I find that the initial employment placements made by the refugee resettlement agency in the immediate period post-arrival have long-term implications for economic integration. Refugees in general, but in particular those who arrive with less relevant human capital, remain in employment at agency partners five years after arrival. These positions offer limited opportunities for upward economic mobility, leaving many refugees at or near the Federal Poverty Line.
Deblending and classifying astronomical sources with Mask R-CNN deep learning
Authors: Burke Colin J , Aleo Patrick D , Chen Yu-Ching , Liu Xin , Peterson John R , Sembroski Glenn H , Lin Joshua Yao-Yu
Published: October 2019

We apply a new deep learning technique to detect, classify, and deblend sources in multiband astronomical images. We train and evaluate the performance of an artificial neural network built on the Mask Region-based Convolutional Neural Network image processing framework, a general code for efficient object detection, classification, and instance segmentation. After evaluating the performance of our network against simulated ground truth images for star and galaxy classes, we find a precision of 92 per cent at 80 per cent recall for stars and a precision of 98 per cent at 80 per cent recall for galaxies in a typical field with ∼30 galaxies arcmin−2. We investigate the deblending capability of our code, and find that clean deblends are handled robustly during object masking, even for significantly blended sources. This technique, or extensions using similar network architectures, may be applied to current and future deep imaging surveys such as Large Synoptic Survey Telescope and Wide-Field Infrared Survey Telescope. Our code, astro r-cnn, is publicly available at https://github.com/burke86/astro_rcnn.
Characterization and repurposing of the endogenous Type I-F CRISPR–Cas system of Zymomonas mobilis for genome engineering
Authors: Zheng Yanli , Han Jiamei , Wang Baiyang , Hu Xiaoyun , Li Runxia , Shen Wei , Ma Xiangdong , Ma Lixin , Yi Li , Yang Shihui , Peng Wenfang
Published: October 2019

Application of CRISPR-based technologies in non-model microorganisms is currently very limited. Here, we reported efficient genome engineering of an important industrial microorganism, Zymomonas mobilis, by repurposing the endogenous Type I-F CRISPR–Cas system upon its functional characterization. This toolkit included a series of genome engineering plasmids, each carrying an artificial self-targeting CRISPR and a donor DNA for the recovery of recombinants. Through this toolkit, various genome engineering purposes were efficiently achieved, including knockout of ZMO0038 (100% efficiency), cas2/3 (100%), and a genomic fragment of >10 kb (50%), replacement of cas2/3 with mCherry gene (100%), in situ nucleotide substitution (100%) and His-tagging of ZMO0038 (100%), and multiplex gene deletion (18.75%) upon optimal donor size determination. Additionally, the Type I-F system was further applied for CRISPRi upon Cas2/3 depletion, which has been demonstrated to successfully silence the chromosomally integrated mCherry gene with its fluorescence intensity reduced by up to 88%. Moreover, we demonstrated that genome engineering efficiency could be improved under a restriction–modification (R–M) deficient background, suggesting the perturbance of genome editing by other co-existing DNA targeting modules such as the R–M system. This study might shed light on exploiting and improving CRISPR–Cas systems in other microorganisms for genome editing and metabolic engineering practices.
ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology
Authors: Arnaiz Olivier , Meyer Eric , Sperling Linda
Published: October 2019

ParameciumDB (https://paramecium.i2bc.paris-saclay.fr) is a community model organism database for the genome and genetics of the ciliate Paramecium. ParameciumDB development relies on the GMOD (www.gmod.org) toolkit. The ParameciumDB web site has been publicly available since 2006 when the P. tetraurelia somatic genome sequence was released, revealing that a series of whole genome duplications punctuated the evolutionary history of the species. The genome is linked to available genetic data and stocks. ParameciumDB has undergone major changes in its content and website since the last update published in 2011. Genomes from multiple Paramecium species, especially from the P. aurelia complex, are now included in ParameciumDB. A new modern web interface accompanies this transition to a database for the whole Paramecium genus. Gene pages have been enriched with orthology relationships, among the Paramecium species and with a panel of model organisms across the eukaryotic tree. This update also presents expert curation of Paramecium mitochondrial genomes.
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update
Authors: Licata Luana , Lo Surdo Prisca , Iannuccelli Marta , Palma Alessandro , Micarelli Elisa , Perfetto Livia , Peluso Daniele , Calderone Alberto , Castagnoli Luisa , Cesareni Gianni
Published: October 2019

The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regulation) and to the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the up/down-regulation of the target entity. Since its first release, SIGNOR has undergone a significant content increase and the number of annotated causal interactions have almost doubled. SIGNOR 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and other biologically relevant entities: chemicals, phenotypes, complexes, etc. We describe here significant changes in curation policy and a new confidence score, which is assigned to each interaction. We have also improved the compliance to the FAIR data principles by providing (i) SIGNOR stable identifiers, (ii) programmatic access through REST APIs, (iii) bioschemas and (iv) downloadable data in standard-compliant formats, such as PSI-MI CausalTAB and GMT. The data are freely accessible and downloadable at https://signor.uniroma2.it/.
Dietary saturated fat and heart disease: a narrative review
Authors: Heileson Jeffery L
Published: October 2019

The American Heart Association (AHA) recently published a meta-analysis that confirmed their 60-year-old recommendation to limit saturated fat (SFA, saturated fatty acid) and replace it with polyunsaturated fat to reduce the risk of heart disease based on the strength of 4 Core Trials. To assess the evidence for this recommendation, meta-analyses on the effect of SFA consumption on heart disease outcomes were reviewed. Nineteen meta-analyses addressing this topic were identified: 9 observational studies and 10 randomized controlled trials. Meta-analyses of observational studies found no association between SFA intake and heart disease, while meta-analyses of randomized controlled trials were inconsistent but tended to show a lack of an association. The inconsistency seems to have been mediated by the differing clinical trials included. For example, the AHA meta-analysis only included 4 trials (the Core Trials), and those trials contained design and methodological flaws and did not meet all the predefined inclusion criteria. The AHA stance regarding the strength of the evidence for the recommendation to limit SFAs for heart disease prevention may be overstated and in need of reevaluation.
Migration of endothelial cells into photo-responsive hydrogels with tunable modulus under the presence of pro-inflammatory macrophages
Authors: Cao Wangbei , Li Xuguang , Zuo Xingang , Gao Changyou
Published: October 2019

Cell migration in three-dimensional environment is extremely important for tissue regeneration and other biological processes. In this work, a model system was developed to study how endothelial cells (ECs) migrate into photo-responsive hydrogels under the presence of pro-inflammatory macrophages. The hydrogel was synthesized from hyaluronic acid grafted with coumarin and methacrylate moieties by both carbon–carbon covalent linking and coumarin dimerization under UV irradiation at 365 nm. The structure of the hydrogel was conveniently modulated by UV irradiation at 254 nm to decompose the coumarin dimers, leading to the significant decrease of modulus and increase of swelling ratio and mesh size. Under the presence of M1 macrophages, ECs were induced to migrate into the hydrogels with a different degree. A significant larger net displacement of ECs was found in the softer hydrogel obtained by irradiation with UV at 254 nm than in the stiffer original one at day 7.
Implementation of a Meaning-Centered Psychotherapy training (MCPT) program for oncology clinicians: a qualitative analysis of facilitators and barriers
Authors: Polacek Laura C , Reisch Sally , Saracino Rebecca M , Pessin Hayley , Breitbart William
Published: October 2019

The Meaning-Centered Psychotherapy training program (MCPT) is a multimodal, intensive, in-person program that trains cancer care providers in the evidence-based psychosocial treatment Meaning-Centered Psychotherapy (MCP). This analysis aimed to identify barriers and facilitators to clinical implementation (CI) at 1 year post-training. Trainee feedback regarding CI was collected via a mixed-methods questionnaire, including rating the ease of CI and free-text response identifying facilitators and barriers to CI. Descriptive statistics and thematic content analysis of follow-up data from the first five MCPT training cohorts (n = 55) were performed to assess CI and its facilitators and barriers. One third of participants indicated that it was at least somewhat difficult to implement MCP in clinical practice. Trainee-identified facilitators and barriers to CI were characterized within four main categories: program, patient, treatment, and institution. Within each of these factors, clinicians reported a variety of components that contributed to or hindered their ability to implement MCP. MCPT itself was reported as a facilitator. Patient access and interest were simultaneously identified as facilitators for some and barriers for others. Some trainees found the MCP treatment structure helpful in addressing important patient psychosocial needs, while others felt it was too restrictive. Institutional support played an important role in whether trainees felt hindered or helped to implement MCP. These initial results provide important insight into the program’s strengths and have fostered improvements to the MCPT program to better facilitate CI. Further study of MCPT CI is warranted, and theme refinement will be possible with a larger sample.
Analysis of Changes in Oil Palm Canopy Architecture From Basal Stem Rot Using Terrestrial Laser Scanner
Authors: Azuan N. H. , Khairunniza-Bejo S. , Abdullah A. F. , Kassim M. S. M. , Ahmad D.
Published: October 2019

Basal stem rot (BSR), caused by the Ganoderma fungus, is an infectious disease that affects oil palm (Elaeis guineensis) plantations. BSR leads to a significant economic loss and reductions in yields of up to Malaysian Ringgit (RM) 1.5 billion (US$400 million) yearly. By 2020, the disease may affect ∼1.7 million tonnes of fresh fruit bunches. The plants appear symptomless in the early stages of infection, although most plants die after they are infected. Thus, early, accurate, and nondestructive disease detection is crucial to control the impact of the disease on yields. Terrestrial laser scanning (TLS) is an active remote-sensing, noncontact, cost-effective, precise, and user-friendly method. Through high-resolution scanning of a tree’s dimension and morphology, TLS offers an accurate indicator for health and development. This study proposes an efficient image processing technique using point clouds obtained from TLS ground input data. A total of 40 samples (10 samples for each severity level) of oil palm trees were collected from 9-year-old trees using a ground-based laser scanner. Each tree was scanned four times at a distance of 1.5 m. The recorded laser scans were synched and merged to create a cluster of point clouds. An overhead two-dimensional image of the oil palm tree canopy was used to analyze three canopy architectures in terms of the number of pixels inside the crown (crown pixel), the degree of angle between fronds (frond angle), and the number of fronds (frond number). The results show that the crown pixel, frond angle, and frond number are significantly related and that the BSR severity levels are highly correlated (R2 = 0.76, P < 0.0001; R2 = 0.96, P < 0.0001; and R2 = 0.97, P < 0.0001, respectively). Analysis of variance followed post hoc tests by Student–Newman–Keuls (Newman–Keuls) and Dunnett for frond number presented the best results and showed that all levels were significantly different at a 5% significance level. Therefore, the earliest stage that a Ganoderma infection could be detected was mildly infected (T1). For frond angle, all post hoc tests showed consistent results, and all levels were significantly separated except for T0 and T1. By using the crown pixel parameter, healthy trees (T0) were separated from unhealthy trees (moderate infection [T2] and severe infection [T3]), although there was still some overlap with T1. Thus, Ganoderma infection could be detected as early as the T2 level by using the crown pixel and the frond angle parameters. It is hard to differentiate between T0 and T1, because during mild infection, the symptoms are highly similar. Meanwhile, T2 and T3 were placed in the same group, because they showed the same trend. This study demonstrates that the TLS is useful for detecting low-level infection as early as T1 (mild severity). TLS proved beneficial in managing oil palm plantation disease.
Patient-Level Value Analysis: An Innovative Approach to Optimize Care Delivery
Authors: McCreary Dylan L. , Dugarte Anthony J. , Vang Sandy , Plowman Brad , Williams Benjamin R. , Parikh Harsh R. , Cunningham Brian P.
Published: October 2019

Background:

An increasing emphasis has been placed on developing value-based care delivery systems in orthopaedics to combat rising health care costs. The goal of these systems is to both measure and improve the provisional value of care. Patient-level value analysis creates a mechanism to quantify and optimize value within a procedure, in contrast to traditional methods, which only measures value. The purpose of this study was to develop a patient-level value analysis model and determine the efficacy of this model to improve value in orthopaedic care.

Methods:

Patients treated operatively for isolated closed ankle fractures at a single level 1 trauma center were prospectively identified. Short musculoskeletal function assessment was collected at the time of the initial clinical presentation and 6 months postoperatively. The cost of care was determined using time-driven activity-based costing, which included personnel, supplies, length of stay, implants, pharmacy, and radiology. Value was defined as each patient's change in the outcome score divided by their cost as determined by time-driven activity-based costing. A multiple linear regression was performed to determine which aspects of care significantly predicted value.

Results:

Forty-nine patients met inclusion/exclusion criteria. The multiple linear regression indicated treatment by physician D (β = −0.135, P = 0.04) and inpatient stay (β = −0.468, P < 0.01) were predictors of lesser value and represent areas for potential care pathway and value improvement.

Conclusions:

Patient-level value analysis represents a paradigm shift in the quantification of value. We recommend surgeons, practices, and health care systems begin implementing a system to quantify and optimize the value of care provided.

Level of Evidence:

Level III. See Instructions for Authors for a complete description of levels of evidence.