bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre-test 68Ga-PSMA-ligand PET/CT positivity in early biochemical recurrent prostate cancer after radical prostatectomy—validation of a prediction model
Authors: Kraft Pia , Maurer Tobias , Gafita Andrei , Krönke Markus , Haller Bernhard , Weber Wolfgang A. , Eiber Matthias , Rauscher Isabel
Published: February 2020

Objectives

The aim of this study was the validation of a recently established comprehensive and compact prediction model for68Ga-PSMA-11-ligand positron-emission tomography (PET) positivity with an independent subsequent patient series.

Methods

A total of 292 consecutive patients with early biochemical recurrence after radical prostatectomy and PSA values between 0.2 and 1 ng/ml who underwent68Ga-PSMA-11-ligand PET/computed tomography (CT) between January 2016 and June 2017 were retrospectively included. The cohort was divided into a very low PSA value (0.2–0.5 ng/ml,n= 151) and a low PSA value (> 0.5–1 ng/ml,n= 141) subgroup. First, pre-test positivity probabilities for each patient were calculated according to the previously published comprehensive prediction model using all clinical variables (PSA value, ISUP grade group, T- and N-stage, patient under androgen deprivation therapy (ADT), previous radiation therapy) and the compact model using just the most predictive factors PSA value, ADT, and grade group. Then, all68Ga-PSMA-11-ligand PET/CTs were analysed by one experienced nuclear medicine physician, and the results were correlated to the calculated pre-test probabilities.

Results

In the very low PSA value subgroup, mean pre-test probability for positive findings in68Ga-PSMA-11-ligand PET/CT was 57% (95% CI 55–60%) according to the compact model and 59% (95% CI 56–61%) according to the comprehensive model. In the low PSA value subgroup, mean pre-test probability was 72% (95% CI 70–74%) in the compact model and 74% (95% CI 72–76%) in the comprehensive model. After image analysis, 59% (89/151) of the patients in the very low PSA value subgroup revealed positive imaging findings. Seventy-nine percent (112/141) of the patients in the low PSA value subgroup presented with positive findings in the68Ga-PSMA-11-ligand PET/CT. The accuracy (AUC) of the prediction models was 0.71 (95% CI 0.65–0.78) for the compact model and 0.74 (95% CI 0.68–0.80) for the comprehensive model.

Conclusion

External validation of the recently proposed prediction models showed a high concordance of the calculated pre-test probabilities and actual68Ga-PSMA-11-ligand PET/CT findings in the validation cohort confirming the prediction models’ ability to determine the presence of a positive lesion at68Ga-PSMA-11-ligand PET. However, the predictive accuracy of the nomogram itself is suboptimal and should be used with caution. Furthermore, the model’s generalizability may be hampered due to the study design (in-house validation). Nevertheless, given the limited health resources and the costs of hybrid imaging techniques, prediction models might be a benefit in patient selection.
MicroRNA gga-miR-200a-3p modulates immune response via MAPK signaling pathway in chicken afflicted with necrotic enteritis
Authors: Pham Thu Thao , Ban Jihye , Hong Yeojin , Lee Jiae , Vu Thi Hao , Truong Anh Duc , Lillehoj Hyun S. , Hong Yeong Ho
Published: February 2020

MicroRNAs (miRNAs) are small non-coding RNAs that contribute to host immune response as post-transcriptional regulation. The current study investigated the biological role of the chicken (Gallus gallus) microRNA-200a-3p (gga-miR-200a-3p), using 2 necrotic enteritis (NE) afflicted genetically disparate chicken lines, 6.3 and 7.2, as well as the mechanisms underlying the fundamental signaling pathways in chicken. The expression of gga-miR-200a-3p in the intestinal mucosal layer of NE-induced chickens, was found to be upregulated during NE infection in the disease-susceptible chicken line 7.2. To validate the target genes, we performed an overexpression analysis of gga-miR-200a-3p using chemically synthesized oligonucleotides identical to gga-miR-200a-3p, reporter gene analysis including luciferase reporter assay, and a dual fluorescence reporter assay in cultured HD11 chicken macrophage cell lines. Gga-miR-200a-3p was observed to be a direct transcriptional repressor of ZAK, MAP2K4, and TGFβ2 that are involved in mitogen-activated protein kinase (MAPK) pathway by targeting the 3′-UTR of their transcripts. Besides, gga-miR-200a-3p may indirectly affect the expression of protein kinases including p38 and ERK1/2 at both transcriptional and translational levels, suggesting that this miRNA may function as an important regulator of the MAPK signaling pathway. Proinflammatory cytokines consisting of IL-1β, IFN-γ, IL-12p40, IL-17A, and LITAF belonging to Th1 and Th17-type cytokines, were upregulated upon gga-miR-200a-3p overexpression. These findings have enhanced our knowledge of the immune function of gga-miR-200a-3p mediating the chicken immune response via regulation of the MAPK signaling pathway and indicate that this miRNA may serve as an important biomarker of diseases in domestic animals.
CRISPR-PCDup: a novel approach for simultaneous segmental chromosomal duplication in Saccharomyces cerevisiae
Authors: Hassan Naim , Sasano Yu , Kimura Shunta , Easmin Farhana , Ekino Keisuke , Taguchi Hisataka , Harashima Satoshi
Published: February 2020

In our previous study, a novel genome engineering technology, PCR-mediated chromosome duplication (PCDup), was developed in Saccharomyces cerevisiae that enabled the duplication of any desired chromosomal region, resulting in a segmental aneuploid. From one round of transformation, PCDup can duplicate a single chromosomal region efficiently. However, simultaneous duplication of multiple chromosomal regions is not possible using PCDup technology, which is a serious drawback. Sequential duplication is possible, but this approach requires significantly more time and effort. Because PCDup depends upon homologous recombination, we reasoned that it might be possible to simultaneously create duplications of multiple chromosomal regions if we could increase the frequency of these events. Double-strand breaks have been shown to increase the frequency of homologous recombination around the break point. Thus, we aimed to integrate the genome editing tool CRISPR/Cas9 system, which induces double-strand breaks, with our conventional PCDup. The new method, which we named CRISPR-PCDup increased the efficiency of a single duplication by up to 30 fold. CRISPR-PCDup enabled the simultaneous duplication of long chromosomal segments (160 kb and 200 kb regions). Moreover, we were also able to increase the length of the duplicated chromosome by up to at least 400 kb, whereas conventional PCDup can duplicate up to a maximum of 300 kb. Given the enhanced efficiency of chromosomal segmental duplication and the saving in both labor and time, we propose that CRISPR-PCDup will be an invaluable technology for generating novel yeast strains with desirable traits for specific industrial applications and for investigating genome function in segmental aneuploid.
Effects of some flavonoids on the mycotoxin citrinin reduction by Monascus aurantiacus Li AS3.4384 during liquid-state fermentation
Authors: Wang Yanling , Gao Heng , Xie Jianhua , Li Xiujiang , Huang Zhibing
Published: February 2020

Monascus can produce many beneficial metabolites; however, it can simultaneously also produce citrinin, which seriously limits its application. Therefore, reducing the production of citrinin is of great interest. Herein, Monascus aurantiacus Li AS3.4384 (MAL) was used to optimize the liquid-state fermentation process and investigate the effects of genistein and other flavonoids on citrinin, pigments, and biomass of MAL. Results showed that citrinin decreased by 80%, pigments and biomass increased by approximately 20% in 12 days with addition of 20.0 g/L rice powder as a carbon source and 2.0 g/L genistein during shaking liquid-state fermentation. Further, genistein, daidzein, luteolin, apigenin, quercetin, baicalein, kaempferol myricetin, and genistin exerted different effects on citrinin production by MAL, with genistein causing the highest reduction in citrinin production during liquid-state fermentation, possibly due to the presence of C5-OH, C4′-OH, and C7-OH. Therefore, genistein can be added to the fermentation process of Monascus to reduce citrinin.
Utilization of mechanocatalytic oligosaccharides by ethanologenic Escherichia coli as a model microbial cell factory
Authors: Jin Tao , Käldström Mats , Benavides Adriana , Rechulski Marcelo D. Kaufman , Jarboe Laura R.
Published: February 2020

Mechanocatalysis is a promising method for depolymerization of lignocellulosic biomass. Microbial utilization of the resulting oligosaccharides is one potential route of adding value to the depolymerized biomass. However, it is unclear how readily these oligosaccharides are utilized by standard cell factories. Here, we investigate utilization of cellulose subjected to mechanocatalytic depolymerization, using ethanologenic Escherichia coli as a model fermentation organism. The mechanocatalytic oligosaccharides supported ethanol titers similar to those observed when glucose was provided at comparable concentrations. Tracking of the various oligomers, using maltose (alpha-1,4) and cellobiose (beta-1,4) oligomers as representative standards of the orientation, but not linkage, of the glycosidic bond, suggests that the malto-like-oligomers are more readily utilized than cello-like-oligomers, consistent with poor growth with cellotetraose or cellopentaose as sole carbon source. Thus, mechanocatalytic oligosaccharides are a promising substrate for cell factories, and microbial utilization of these sugars could possibly be improved by addressing utilization of cello-like oligomers.
DNA mismatch repair in the context of chromatin
Authors: Huang Yaping , Li Guo-Min
Published: February 2020

DNA mismatch repair (MMR) maintains replication fidelity by correcting mispaired nucleotides incorporated by DNA polymerases. Defects in MMR lead to cancers characterized by microsatellite instability. Recently, chromatin mechanisms that regulate MMR have been discovered, which sheds new light on MMR deficiency and its role in tumorigenesis. This review summarizes these chromatin-level mechanisms that regulate MMR and their implications for tumor development.
Improved meals service and reduced food waste and costs in medical institutions resulting from employment of a food service dietitian – a case study
Authors: Yona Orit , Goldsmith Rebecca , Endevelt Ronit
Published: February 2020

Background

A recurring problem in medical institutions is patients not always receiving food meeting their nutritional and medical needs. A proposed contributing factor is non- inclusion of dietitians in food service staff. Recently, positions for food service dietitians in hospitals were created. For the newly defined role of “Food Service Dietitian”, comprehensive training courses were developed (70 dietitians participated).

Objective

To examine the impact of the addition of the role of a “Food Service Dietitian” in medical institutions on suitability of foods served, food costs and food waste.

Methods

A three years (2014–2017) national case study to examine the new role’s impact was carried out, in 18 hospitals, nine of which employ a food service dietitian (intervention), and 9 without (control). The number of nutritional analyses of menus was checked, as was the extent of kitchen staff training, and how often night meals were served for all patients. Data were gathered regarding food costs and waste with respect to food distributed to staff and patients. Food costs savings and waste reduction were calculated, based on reduction in provision of unnecessary meals, at a cost of 18 NIS per day per meal.

Results

Kitchen staff training was carried out in all intervention institutions, and not in the controls. In most controls, nutritional analyses were not performed, whereas in the intervention hospitals, full analyses were performed and tailoring of menus to specific department requirements improved significantly. In most intervention hospitals, late night snacks were provided, this not being so in the controls. Total food cost savings of $229,569 per annum was seen in the six intervention hospitals, attributable to 4 factors:

Meals not delivered to fasting patients, or those receiving parenteral/enteral nutrition- cost savings of 328,500 NIS ($93,857)

Better tailoring and monitoring of food delivered to the wards and staff (bread, cheese, milk etc)- annual cost savings of 235,000 NIS ($67,142) in the hospitals with a food service dietitian.

Checking expiry dates of medical foods, and improved communication between the wards, the kitchen and the food distribution centers, has lessened food waste with savings of 5% from the medical food budget per annum of 40,000 NIS ($11,428).

As a result of dietitian-performed nutritional analyses, tailoring of food provided according to the patient’s medical and nutrition needs was improved. In one hospital, after re-evaluation of serve sizes in high protein diets, sizes were reduced while retaining adequacy, with immediate cost savings of 200,000 NIS ($57,142) per annum.

Conclusions

Implementation of the new role of Food Service Dietitian led to cost savings and significant improvements in adherence to the nutritional care plan.
A deep learning approach for pressure ulcer prevention using wearable computing
Authors: Cicceri Giovanni , De Vita Fabrizio , Bruneo Dario , Merlino Giovanni , Puliafito Antonio
Published: February 2020

In recent years, statistics have confirmed that the number of elderly people is increasing. Aging always has a strong impact on the health of a human being; from a biological of point view, this process usually leads to several types of diseases mainly due to the impairment of the organism. In such a context, healthcare plays an important role in the healing process, trying to address these problems. One of the consequences of aging is the formation of pressure ulcers (PUs), which have a negative impact on the life quality of patients in the hospital, not only from a healthiness perspective but also psychologically. In this sense, e-health proposes several approaches to deal with this problem, however, these are not always very accurate and capable to prevent issues of this kind efficiently. Moreover, the proposed solutions are usually expensive and invasive. In this paper we were able to collect data coming from inertial sensors with the aim, in line with the Human-centric Computing (HC) paradigm, to design and implement a non-invasive system of wearable sensors for the prevention of PUs through deep learning techniques. In particular, using inertial sensors we are able to estimate the positions of the patients, and send an alert signal when he/she remains in the same position for too long a period of time. To train our system we built a dataset by monitoring the positions of a set of patients during their period of hospitalization, and we show here the results, demonstrating the feasibility of this technique and the level of accuracy we were able to reach, comparing our model with other popular machine learning approaches.
Educational needs assessment among 10–14-year-old girls about puberty adolescent health of Ardebil
Authors: Ziapour Arash , Sharma Manoj , NeJhaddadgar Nazila , Mardi Afrouz , Tavafian Sedigheh Sadat
Published: February 2020

Background

This study aimed to investigate the educational needs of 10–14-year-old girls about adolescent puberty health in Ardabil City in Iran, the matter of adolescent puberty health is one of the most important health priorities, especially for girls.

Methods

This cross-sectional descriptive-correlational study was performed on girl students through stratified-cluster sampling in Ardabil city. The data gathering tool was a self-reported researcher-designed questionnaire consisting of 10 demographic questions and 35 self-care questions in 5 domains of self-care awareness, self-efficacy, enablers, enhancers and behaviors, based on the reviewed articles and resources. Descriptive statistics and chi-square test, correlation coefficient and regression were used to analyze the quantitative data.

Results

The mean age of the girls was 12.98 ± 4.67. There was a significant relationship between the mother’s level of education (p < 0.001) and students ‘knowledge about puberty and between mother’s age (p < 0.002) and students’ awareness of self-care behaviors during adolescence. The results of this study showed that 73.8% of girls were aware of puberty and menstruation problems. About 74.3% of girls had poor self-efficacy. About 77% of female students in the study did not have access to the required educational resources and classes that are one of the most important enablers of behavior formation. Eighty-eight percent of the families did not talk about the hygiene practices related to their children. The most common source of information about maternal health related practices was from mothers (64.8%). Correlation test between adolescents’ health behavior and awareness (r = 0.12p < 0.007) and between self-efficacy and health behaviors (r = 0.14,p < 0.001) revealed significant and positive relationships.

Conclusion

There is a need among adolescent girls for information about adolescent health and related health behaviors. Currently there is lack of adequate and accurate information. The role of mothers is the most important source of information for adolescent girls and educational approaches for mothers and adolescents should be designed.
Outcomes of a novel office-based opioid treatment program in an internal medicine resident continuity practice
Authors: Pytell Jarratt D. , Buresh Megan E. , Graddy Ryan
Published: February 2020

Background

The integration of opioid use disorder (OUD) care and competencies in graduate medical education training is needed. Previous research shows improvements in knowledge, attitudes, and practices after exposure to OUD care. Few studies report outcomes for patients with OUD in resident physician continuity practices.

Methods

A novel internal office-based opioid treatment (OBOT) program was initiated in a resident continuity clinic. Surveys of resident and staff knowledge and attitudes of OBOT were administered at baseline and 4 months. A retrospective chart review of the 15-month OBOT clinic obtained patient characteristics and outcomes.

Results

Twelve patients with OUD were seen in the OBOT clinic. Seven patients (58%) were retained in care at the end of the study period for a range of 9–15 months. Eight patients demonstrated a good clinical response. Surveys of residents and staff at 4 months were unchanged from baseline showing persistent lack of comfort in caring for patients with OUD.

Conclusions

OBOT can be successfully integrated into resident continuity practices with positive patient outcomes. Improvement in resident and staff attitudes toward OBOT were not observed and likely require direct and frequent exposure to OUD care to increase acceptance.
Widespread illegal sales of antibiotics in Chinese pharmacies – a nationwide cross-sectional study
Authors: Chen Jie , Wang Yanmei , Chen Xuejie , Hesketh Therese
Published: February 2020

Background

Access to antibiotics without a prescription from retail pharmacies has been described as a major contributor to anti-microbial resistance (AMR) globally. In the context of high rates of AMR, the Chinese government has recently introduced strict policies regarding hospital antibiotic use, but the existing ban on antibiotic sales without prescription in retail pharmacies has not been strongly enforced. In 2016, a goal of prescription-only antibiotics by 2020 was announced. The objective of the study was to determine progress towards the 2020 goal, through estimating the proportion of retail pharmacies selling antibiotics without prescription across the three regions of mainland China.

Methods

Using the Simulated Patient method, we conducted a cross-sectional survey across purposively-sampled retail pharmacies in urban and rural areas of 13 provinces in eastern, central and western China. Medical students presented a scenario of a mild upper respiratory tract infection, following a strict three-step protocol. They recorded the pharmacy characteristics, and details of their experience, including at which step antibiotics were offered.

Results

Complete data were obtained from 1106 pharmacies. Antibiotics were obtained in 925 (83.6, 95% CI: 81.5, 85.8%) pharmacies without a prescription, 279 (25.2%) at Stage 1 (symptoms only described), 576 (52.1%) at stage 2 (asked for antibiotics), and 70 (6.3%) at Stage 3 (asked for penicillin or cephalosporins). There were significant differences between provinces, with antibiotic access (at any stage) ranging from 57.0% (57/100) in Zhejiang (81/82) to 98.8% in Guizhou. However, there were no significant differences in access to antibiotics by level of city, county, township or village (P = 0.25), whether the pharmacy was part of a chain or independent (P = 0.23), whether a licensed pharmacist was attending (P = 0.82) or whether there was a sign saying that prescriptions were required for antibiotics (P = 0.19).

Conclusions

It is easy to obtain antibiotics without a prescription in retail pharmacies in China, despite the fact it is against the law. This must be addressed as part of the wider anti-microbial stewardship effort which could include intense enforcement of the existing law, supported by a public education campaign.
Mortality associated with carbapenem-susceptible and Verona Integron-encoded Metallo-β-lactamase-positive Pseudomonas aeruginosa bacteremia
Authors: Persoon Marjolein C. , Voor in’t holt Anne F. , Wielders Cornelia C. H. , Gommers Diederik , Vos Margreet C. , Severin Juliëtte A.
Published: February 2020

Background

Studies on various Gram-negative bacteria suggest that resistance to carbapenem antibiotics is responsible for increased mortality in patients; however, results are not conclusive. We first assessed the 28-day in-hospital all-cause mortality in patients with Verona Integron-encoded Metallo-β-lactamase-positive Pseudomonas aeruginosa (VIM-PA) bacteremia compared to patients with VIM-negative, carbapenem-susceptible P. aeruginosa (CS-PA) bacteremia. Second, we identified determinants for mortality and survival.

Methods

All patients with a positive blood culture with VIM-PA or CS-PA between January 2004 and January 2016 were included. Kaplan-Meier survival curves were constructed, and survivors and non-survivors were compared on relevant clinical parameters using univariate analyses, and multivariable analyses using a Cox-proportional hazard model.

Results

In total, 249 patients were included, of which 58 (23.3%) died. Seventeen out of 40 (42.5%) patients with VIM-PA died, compared to 41 out of 209 (19.6%) patients with CS-PA (difference = 22.9%, P-value = 0.001). Assumed acquisition of the bacterium at the intensive care unit was significantly associated with mortality (HR = 3.32, 95%CI = 1.60–6.87), and having had adequate antibiotic therapy in days 1–14 after the positive blood culture was identified as a determinant for survival (HR = 0.03, 95%CI = 0.01–0.06). VIM-PA vs CS-PA was not identified as an independent risk factor for mortality.

Conclusions

The crude mortality rate was significantly higher in patients with a VIM-PA bacteremia compared to patients with a CS-PA bacteremia; however, when analyzing the data in a multivariable model this difference was non-significant. Awareness of the presence of P. aeruginosa in the hospital environment that may be transmitted to patients and rapid microbiological diagnostics are essential for timely administration of appropriate antibiotics. Acquisition of P. aeruginosa should be prevented, independent of resistance profile.
Tax behaviour relating to the review of a revised regional tax policy: a study in Greece
Authors: Varotsis Nikolaos , Katerelos Ioannis
Published: February 2020

The failure over time of the tax system in Greece to harmonize with a sound and efficient fiscal mix raises questions about the possibility of a radical restructuring. The last decade of continuous tax reforms has neither particularly restricted the black economy nor provided the government with fresh fiscal resources, and it has outgrown its arrears. A socially acceptable fiscal policy may lead to a new, sound fiscal policy mix. Tax restructuring that strengthens the tax base at the regional, local or European level—compared to its structuring at the one-sided governmental level to date—may be a key factor in the social acceptance of a new tax system. The degree of tax decentralization of the applied tax policy is likely to improve fiscal order and management on the one hand and, on the other hand, enhance tax revenues by enhancing tax compliance.
Nesting a city input–output table in a multiregional framework: a case example with the city of Bogota
Authors: Monsalve Fabio , Ortiz Mateo , Cadarso María-Ángeles , Gilles Enrique , Zafrilla Jorge , López Luis-Antonio
Published: February 2020

In parallel with the increasing availability of multiregional input–output (MRIO) tables, there has been a growing concern on IO modelling at lower levels of spatial disaggregation, to reflect the particular features of cities better. The urbanization process is one of the salient characteristics of the current stage of globalization, so it is imperative to know more about their global economic, social and environmental impacts. MRIO initiatives are defined at the country level, which means that we are potentially losing some key information about cities and their economic structures. In this paper, we fill this gap by putting together the IOT for the city of Bogota (Colombia) into the well-known OECD’s ICIO database. After describing the structure of both IOTs, we document the harmonization and nesting procedures in a step by step approach, focusing on the main challenges and assumptions that we have to make. Additionally, a case study has been carried out to weight the level of integration of Bogota in global value chains. The analysis proves the low level of global integration: the bulk of the valued-added generated in Bogota due to the city’s exports comes from the economy of the rest of the country and presents a significant deficit in its value-added balance. Apart, we hope it could shed some light to conduct similar adaptations for other cities.
Early inoculation with caecal fermentation broth alters small intestine morphology, gene expression of tight junction proteins in the ileum, and the caecal metabolomic profiling of broilers
Authors: Gong Yujie , Xia Wenrui , Wen Xueting , Lyu Wentao , Xiao Yingping , Yang Hua , Zou Xiaoting
Published: February 2020

Background

The establishment of stable microbiota in early life is beneficial to the individual. Changes in the intestinal environment during early life play a crucial role in modulating the gut microbiota. Therefore, early intervention to change the intestinal environment can be regarded as a new regulation strategy for the growth and health of poultry. However, the effects of intestinal environmental changes on host physiology and metabolism are rarely reported. This study was conducted to investigate the effects of early inoculation with caecal fermentation broth on small intestine morphology, gene expression of tight junction proteins in the ileum, and cecum microbial metabolism of broilers.

Results

Our data showed that early inoculation with caecal fermentation broth could improve intestine morphology. The small intestine villus height was significantly increased (P < 0.05) in the intervened broilers compared to the control group, especially on day 28. A similar result was observed in the ratio of villus height to crypt depth (P < 0.05). Meanwhile, we found early inoculation significantly increased (P < 0.05) the expression levels of zonula occludens-1 (ZO1) on days 14 and 28, claudin-1 (CLDN1) on day 28, whereas the gene expression of claudin-2 (CLDN2) was significantly decreased (P < 0.05) on days 14 and 28. Gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS) technology was further implemented to systematically evaluate the microbial metabolite profiles. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) displayed a distinct trend towards separation between the fermentation broth group (F group) and the control group (C group). The differentially expressed metabolites were identified, and they were mainly functionally enriched in beta-alanine metabolism and biosynthesis of unsaturated fatty acids. In addition, 1,3-diaminopropane was selected as a key biomarker that responded to early inoculation with caecal fermentation broth.

Conclusions

These results provide insight into intestinal metabolomics and confirm that early inoculation with caecal fermentation broth can be used as a potential strategy to improve intestinal health of broilers.
Black soldier fly and gut health in broiler chickens: insights into the relationship between cecal microbiota and intestinal mucin composition
Authors: Biasato Ilaria , Ferrocino Ilario , Dabbou Sihem , Evangelista Rocchina , Gai Francesco , Gasco Laura , Cocolin Luca , Capucchio Maria Teresa , Schiavone Achille
Published: February 2020

Background

The relationship between diet and intestinal microbiota and mucin composition appears to be fundamental for poultry gut health. The effects of insect meal (whose role as alternative feed ingredient is now well recognized) on gut microbiota and mucin composition have recently been reported in Tenebrio molitor-fed free-range and broiler chickens, but no data are currently available for Hermetia illucens (HI)-fed broilers. The present study evaluated the effects of dietary HI meal inclusion on cecal microbiota and intestinal mucin composition of broiler chickens.

Results

A total of 256 male broiler chickens were allotted to 4 dietary treatments (control diet [C] and 5%, 10% and 15% HI meal inclusion, with 8 replicate pens/treatment and 8 birds/pen) and slaughtered at 35 d of age (2 animals/pen, 16 birds/diet). The cecal microbiota assessment by 16S rRNA amplicon based sequencing showed lower alpha diversity in HI15 chickens (Shannon, P < 0.05) and higher beta diversity (Adonis and ANOSIM, P < 0.001) in birds fed HI diets than C. Furthermore, HI15 birds displayed significant increase of the relative abundance of Proteobacteria phylum (False Discovery Rate [FDR] <  0.05) when compared to HI10. L-Ruminococcus (Ruminococcus from Lachnospiraceae family), Faecalibacterium, Blautia and Clostridium genera were found to be characteristic of HI5 cecal microbiota (FDR < 0.05), while broiler chickens fed HI10 and HI15 diets were characterized (FDR < 0.05) by Lactobacillus and Ruminococcus (HI10) and Bacteroides, Roseburia and Helicobacter genera (HI15). Periodic-acid Schiff, Alcian Blue pH 2.5 and high iron diamine staining on small and large intestine also demonstrated lower mucin staining intensity in the intestinal villi of HI10 and HI15 birds than C (P < 0.05).

Conclusions

Dietary HI meal utilization at low inclusion levels (i.e., 5%) positively influenced either the cecal microbiota or the gut mucin dynamics in terms of selection of potentially beneficial bacteria and increase in villi mucins. However, high inclusion levels (in particular the 15%) may have a negative influence in terms of partial reduction of microbial complexity, reduction of potentially beneficial bacteria, selection of bacteria with mucolytic activity and decrease in villi mucins.
Unveiling ncRNA regulatory axes in atherosclerosis progression
Authors: Navarro Estanislao , Mallén Adrian , Cruzado Josep M. , Torras Joan , Hueso Miguel
Published: February 2020

Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non‐coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non‐coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non‐coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3′UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non‐coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti‐ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.
Assessment and validation of miniaturized technology for the remote tracking of critically endangered Galápagos pink land iguana (Conolophus marthae)
Authors: Loreti Pierpaolo , Bracciale Lorenzo , Colosimo Giuliano , Vera Carlos , Gerber Glenn P. , De Luca Massimiliano , Gentile Gabriele
Published: February 2020

Background

Gathering ecological data for species of conservation concern inhabiting remote regions can be daunting and, sometimes, logistically infeasible. We built a custom-made GPS tracking device that allows to remotely and accurately collect animal position, environmental, and ecological data, including animal temperature and UVB radiation. We designed the device to track the critically endangered Galápagos pink land iguana, Conolophus marthae. Here we illustrate some technical solutions adopted to respond to challenges associated with such task and present some preliminary results from controlled trial experiments and field implementation.

Results

Our tests show that estimates of temperature and UVB radiation are affected by the design of our device, in particular by its casing. The introduced bias, though, is systematic and can be corrected using linear and quadratic regressions on collected values. Our data show that GPS accuracy loss, although introduced by vegetation and orientation of the devices when attached to the animals, is acceptable, leading to an average error gap of less than 15 m in more than 50% of the cases.

Conclusions

We address some technical challenges related to the design, construction, and operation of a custom-made GPS tracking device to collect data on animals in the wild. Systematic bias introduced by the technological implementation of the device exists. Understanding the nature of the bias is crucial to provide correction models. Although designed to track land iguanas, our device could be used in other circumstances and is particularly useful to track organisms inhabiting locations that are difficult to reach or for which classic telemetry approaches are unattainable.
“It also taught me a lot about myself”: A qualitative exploration of how men understand eating disorder recovery
Authors: Lewke-Bandara Ranidu S. , Thapliyal Priyanka , Conti Janet , Hay Phillipa
Published: February 2020

Background

Eating Disorders (ED) are relatively common in the general population. However, perceived as “female disorders”, EDs in men are often overlooked. Although recovery is often seen as the ideal end goal of ED, there is no single universal definition of recovery. Recovery can be defined in terms of: physical changes, behavioural changes, psychological (cognitive and emotional) and improved quality of life. There is very little research exploring how people with ED define/ understand what recovery is and there is even less research involving men with ED. Therefore, the aim of this study was to explore recovery from men’s perspectives.

Methods

In this qualitative study, eight men from Australia, New Zealand and the United States participated in a semi-structured interview. Data collected on the men’s experiences of recovery were analysed in detail to create a thematic map of their understanding of recovery.

Results

The thematic analysis generated two overarching themes. The first theme focused on psychological recovery in terms of diminished preoccupations with food and disordered eating behaviours, allowing them to eat more freely. They also experienced growth of self-confidence, insight and interpersonal relationships. The second theme viewed recovery as a recursive process without a definite endpoint. The men positioned themselves at different points of the recovery journey and emphasised the importance of support systems and improved resilience to deflect triggers that would otherwise cause relapse.

Conclusions

Recovery was recognised as an improvement in the men’s psychosocial wellbeing from a previous level of functioning. It was a journey which was with no definite endpoint but one that provided benefits such as inner peace, confidence, greater empathy and stronger connections with others around them.
An integrative analysis of genome-wide association study and regulatory SNP annotation datasets identified candidate genes for bipolar disorder
Authors: Qi Xin , Wen Yan , Li Ping , Liang Chujun , Cheng Bolun , Ma Mei , Cheng Shiqiang , Zhang Lu , Liu Li , Kafle Om Prakash , Zhang Feng
Published: February 2020

Background

Bipolar disorder (BD) is a complex mood disorder. The genetic mechanism of BD remains largely unknown.

Methods

We conducted an integrative analysis of genome-wide association study (GWAS) and regulatory SNP (rSNP) annotation datasets, including transcription factor binding regions (TFBRs), chromatin interactive regions (CIRs), mature microRNA regions (miRNAs), long non-coding RNA regions (lncRNAs), topologically associated domains (TADs) and circular RNAs (circRNAs). Firstly, GWAS dataset 1 of BD (including 20,352 cases and 31,358 controls) and GWAS dataset 2 of BD (including 7481 BD patients and 9250 controls) were integrated with rSNP annotation database to obtain BD associated SNP regulatory elements and SNP regulatory element-target gene (E–G) pairs, respectively. Secondly, a comparative analysis of the two datasets results was conducted to identify the common rSNPs and also their target genes. Then, gene sets enrichment analysis (FUMA GWAS) and HumanNet-XC analysis were conducted to explore the functional relevance of identified target genes with BD.

Results

After the integrative analysis, we identified 52 TFBRs target genes, 44 TADs target genes, 55 CIRs target genes and 21 lncRNAs target genes for BD, such asITIH4(Pdataset1 = 6.68 × 10−8,Pdataset2 = 6.64 × 10−7),ITIH3(Pdataset1 = 1.09 × 10−8,Pdataset2 = 2.00 × 10−7),SYNE1(Pdataset1 = 1.80 × 10−6,Pdataset2 = 4.33 × 10−9) andOPRM1(Pdataset1 = 1.80 × 10−6,Pdataset2 = 4.33 × 10−9).

Conclusion

We conducted a large-scale integrative analysis of GWAS and 6 common rSNP information datasets to explore the potential roles of rSNPs in the genetic mechanism of BD. We identified multiple candidate genes for BD, supporting the importance of rSNP in the development of BD.
Genetic and histologic spatiotemporal evolution of recurrent, multifocal, multicentric and metastatic glioblastoma
Authors: Georgescu Maria-Magdalena , Olar Adriana
Published: February 2020

Glioblastoma is the most frequent and aggressive primary brain tumor, characterized by extensive brain invasion and rarely, systemic metastases. The pathogenesis of metastatic glioblastoma is largely unknown. We present the first integrated clinical/histologic/genetic analysis of 5 distinct brain and lung foci from a unique case of recurrent, multifocal, multicentric and metastatic glioblastoma. The initial right frontotemporal gliosarcoma received standard surgical/chemoradiation therapy and recurred 1.5 years later, co-occurring with three additional masses localized to the ipsilateral temporal lobe, cerebellum and lung. Synchronous metastatic lung carcinoma was suspected in this long-term smoker patient with family history of cancer. However, glioblastoma was confirmed in all tumors, although with different morphologic patterns, including ependymomatous and epithelioid. Genomic profiling revealed a germline FANCD2 variant of unknown significance, and a 4-gene somatic mutation signature shared by all tumors, consisting of TERT promoter and PTEN, RB1 and TP53 tumor suppressor mutations. Additional GRIN2A and ATM heterozygous mutations were selected in the cerebellar and lung foci, but were variably present in the supratentorial foci, indicating reduced post-therapeutic genetic evolution in brain foci despite morphologic variability. Significant genetic drift characterized the lung metastasis, likely explaining the known resistance of circulating glioblastoma cells to systemic seeding. MET overexpression was detected in the initial gliosarcoma and lung metastasis, possibly contributing to invasiveness. This comprehensive analysis sheds light on the temporospatial evolution of glioblastoma and underscores the importance of genetic testing for diagnosis and personalized therapy.
RETRACTED ARTICLE: Criminal tendency detection from facial images and the gender bias effect
Authors: Hashemi Mahdi , Hall Margeret
Published: February 2020

Explosive performance and memory space growth in computing machines, along with recent specialization of deep learning models have radically boosted the role of images in semantic pattern recognition. In the same way that a textual post on social media reveals individual characteristics of its author, facial images may manifest some personality traits. This work is the first milestone in our attempt to infer personality traits from facial images. With this ultimate goal in mind, here we explore a new level of image understanding, inferring criminal tendency from facial images via deep learning. In particular, two deep learning models, including a standard feedforward neural network (SNN) and a convolutional neural network (CNN) are applied to discriminate criminal and non-criminal facial images. Confusion matrix and training and test accuracies are reported for both models, using tenfold cross-validation on a set of 10,000 facial images. The CNN was more consistent than the SNN in learning to reach its best test accuracy, which was 8% higher than the SNN’s test accuracy. Next, to explore the classifier’s hypothetical bias due to gender, we controlled for gender by applying only male facial images. No meaningful discrepancies in classification accuracies or learning consistencies were observed, suggesting little to no gender bias in the classifier. Finally, dissecting and visualizing convolutional layers in CNN showed that the shape of the face, eyebrows, top of the eye, pupils, nostrils, and lips are taken advantage of by CNN in order to classify the two sets of images.
Smart devices employment in teaching and learning: reality and challenges in Jordan universities
Authors: Al-Hamad Nouwar Q. , AlHamad Asma Q. , Al-Omari Faruq A.
Published: February 2020

The aim of this study was to investigate the reality of smart devices’ employment in teaching and learning in Jordanian universities from the perspective of instructors. A random sample of (364) instructors were targeted. A structured interview was used to collect data and qualitative analysis was performed to reveal results. Obtained results showed that (68.1%) of respondents were against technology use specially inside the class, whereas (31.9%) were in-favor. Although a high percentage were against technology use, yet most of them use the technology by some means. Distraction, misuse, and lack of skills were the most commonly reported drawbacks. On the other hand, enriched interaction and excitement were the main aspects encouraging instructors to employ the technology in the teaching process.
Problematizing teaching and learning mathematics as “given” in STEM education
Authors: Li Yeping , Schoenfeld Alan H.
Published: February 2020

Mathematics is fundamental for many professions, especially science, technology, and engineering. Yet, mathematics is often perceived as difficult and many students leave disciplines in science, technology, engineering, and mathematics (STEM) as a result, closing doors to scientific, engineering, and technological careers. In this editorial, we argue that how mathematics is traditionally viewed as “given” or “fixed” for students’ expected acquisition alienates many students and needs to be problematized. We propose an alternative approach to changes in mathematics education and show how the alternative also applies to STEM education.
Unravelling the effects of tropical land use conversion on the soil microbiome
Authors: Berkelmann Dirk , Schneider Dominik , Meryandini Anja , Daniel Rolf
Published: February 2020

Background

The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry (“jungle rubber”) and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia.

Results

The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility- and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils.

Conclusions

Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility- and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.