bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rare internalin A premature stop codon on Listeria monocytogenes on Italian PDO cheeses isolates
Authors: Magagna G , Filipello V , Spinelli E , Gori M , Tanzi E , Finazzi G 
Published: October 2021

Abstract

Background
Listeria monocytogenes is a widespread foodborne pathogen that causes listeriosis, a human infection with low morbidity but high mortality. Internalin A (InlA), a L. monocytogenes virulence factor, has a key role in the invasion of human intestinal epithelium through the interaction with E-cadherin receptor. Truncated InlA caused by premature stop-codons (PMSC) have been correlated with attenuated virulence. To date, 29 mutations leading to a PMSC have been reported. In this study, we identified a rare PMSC mutation widespread in isolates from the production chain of the Gorgonzola and Taleggio PDO cheeses.

Methods
Within an ongoing monitoring plan for the characterization of L. monocytogenes, a total of 81 isolates collected in Lombardy (Northern Italy) from food, food processing environments, and clinical cases, between 2013-2021, were characterized using multilocus sequence tying (MLST) and then screened for the presence of PMSC by sequencing the 2400 pb inlA gene.

Results
A mutation leading to PMSC was identified on the position 277 (PMSC mutation type 26). To date, this mutation has been reported only on a CC7 strain from a clinical case. In our study, all isolates harbouring this mutation (n = 21) belong to ST325 (CC31, serotype 1/2a). Among these, 86% (n = 18) belong to the production chain of the Gorgonzola and Taleggio PDO cheeses.

Conclusions
To the best of our knowledge, this is the first report of PMSC mutation type 26 on food and environmental isolates. Although PMSC 26 is rarely found worldwide, our findings suggest that ST325 with this mutation is widespread in the production chain of the two PDO cheeses, and the presence of this PMSC may be correlated with the low incidence of ST325 clinical cases.

Key messages
A rare mutation leading to truncated InlA has been identified in a cluster of isolates correlated to the production chain of two PDO cheeses. Truncated inlA is suggestive of adaptation to the niche to the detriment of virulence.
Italian flu season 2020-2021: reasons for the drop and insights for the future
Authors: Cugudda E , Bert F , Galvagno PF , Lo Moro G , Tatti R , Siliquini R 
Published: October 2021

Abstract

Background
Having seen the trend of 2020 flu season in the Southern hemisphere, the objectives of this study were to describe the trend of 2020-21 flu season in Italy, relating it with containment measures undertaken due to COVID-19, and to provide insights for next flu seasons and prevention of airborne diseases.

Methods
We collected data on Italian influenza virological samples on FluNet. We also collected French, German and Spanish data as a comparison. Data on Italian ILI (influenza-like illness) surveillance system were assessed with InfluNet. We used the Containment and Health Index of the Oxford COVID-19 Government Response Tracker (OxCGRT) to evaluate the impact of containment measures on Italian ILI incidence (Spearman's correlation).

Results
No sample out of 6818 tested positive to influenza virus in Italy in 2020-21 flu season; 21.6% of the samples tested positive to SARS-CoV-2. France, Germany and Spain registered a maximum of 0.10% of positive samples to influenza virus. In Italy the mean of positive samples to influenza virus in seasons from 2015-16 to 2019-20 was 28.8%; the mean number of processed samples in those seasons was 14008. ILI incidence in Italy remained at interseasonal levels during all flu season (mean 1.44/1000; range 0.85-2.04). According to the Containment and Health Index, with increasing containment measures a deflection of ILI incidence in Italy was described (p = 0.015).

Conclusions
Containment measures, along with rise of seasonal flu vaccination, are the most likely factors to explain the drop in cases in Italian 2020-21 flu season. The reduction of cases in neighbouring countries lower the role of the downsizing of Italian surveillance system seen in 2020-21 compared to seasons from 2015-16 to 2019-20. Rules and conducts may perpetrate the benefit on the decreased disease activity seen in 2020-21 flu season.

Key messages
Containment measures and flu vaccinations are the most impacting factors on the drop of influenza cases in 2020-21 in Italy. Though the Italian surveillance system was downsized in 2020-21, the experience of neighbouring countries suggests that the decreased flu activity was factual.
Health care costs for residents diagnosed with diabetes type 2 in Malmö, Sweden between 2011 and 2018
Authors: Zdravkovic S , Jonsson C , Annersten Gershater M , Ericsson Å , Grahn M , Rämgård M , Dozet A 
Published: October 2021

Abstract

Background
During the last decade, type 2 diabetes (T2D) prevalence has increased worldwide, especially among children and young adults. Diabetes is a chronic disease that if not diagnosed in time can lead to serious health complications and put pressure on the societal resources. The aim of this study was to evaluate the economic impact of the increased T2D prevalence in Malmö over time on the regional health care organization.

Methods
A longitudinal population-based study in Malmö, within the Cities Changing Diabetes project. Data was collected from the Patient Administrative System in Region Skåne, classifying T2D by the ICD E11 code. The health care cost (HCC) has been adjusted by the Consumer Price Index (CPI) to 2020 prices.

Results
The prevalence of T2D increased from 2,5% in 2011 to 4,3% in 2018. The increase in T2D prevalence was most noticeable for residents 18 - 64 years. The overall HCC for treating residents with T2D was approximately €47,2 million in 2011 and €90,7 million in 2018. The HCC in 2018 was higher for males than for females (€54,6 million vs €36,2 million). In 2018, the cost was €49,9 million for those 18 - 64 years and €40,5 million for those being 65 years or older. The overall HCC increased during the study period (3,3 times for those 18 - 64 years and 1,4 times for those being 65 years or older). For the age group 18 - 64 the HCC per resident was €5 000 in 2011 and €5 300 in 2018. The HCC per resident for all age groups, has not changed markedly, from €6 200 in 2011 to €6 100 in 2018 as well as the number of health care visits (23 in 2011 and 29 in 2018).

Conclusions
The HCC for T2D has increased markedly since 2011. This increase is most noticeable for people under 65 years. The overall HCC for these patients and its change over time puts an increased strain on the health care provider Region Skåne, mainly due to increased prevalence.

Key messages
The overall HCC during 2011 – 2018 has increased 2 times for residents with T2D and 1.5 times for residents without T2D. This increase is likely to continue if the current trend remains. The main driving force behind the increase in HCC over time is the increase in T2D prevalence and not in HCC per resident.
Use of cancer e-referral data to monitor health-seeking behaviours during the COVID-19 pandemic
Authors: McCarthy T , Dawkins I , Burns H , Nolan E 
Published: October 2021

Abstract

At the outset of the pandemic, concern arose that people with concerning symptoms would not attend their GP and delayed presentations would impact cancer survival. Ireland lacks a national database of GP attendances from which to observe this. Ireland has rapid access clinics in designated cancer centres, providing a streamlined pathway for the diagnosis of certain common cancers. Referral to these clinics can be made electronically from primary care, using a national messaging system Healthlink. Healthlink agreed to report on the volume of referrals at weekly intervals, given the concern regarding non-presentation. Rolling descriptive analytics included the comparison of referral numbers to pre-pandemic weeks in 2020 (Weeks 2-11) and to corresponding time periods in 2019. A marked reduction was observed in wave 1 of the pandemic. Weekly e-referrals dropped by more than 60% in weeks 12-14 (breast 62.5%; lung 57.9%; prostate 61.1%). This was not replicated in subsequent waves. By end-2020, the volume of referrals equated to 112.4% of total referrals in 2019. The objective demonstration of a fall in cancer referrals prompted a media campaign to highlight the importance of early diagnosis and to reassure that cancer diagnostic and treatment services continued to operate. It also prompted national communication in relation to other essential health services. Challenges identified included occasional misinterpretation of referral data as reflective of attendance and investigation at clinics and the potential influence of increased uptake of e-referral systems. While caveats exist in relation to interpretation, e-referral data from primary care to cancer centres is a useful tool to monitor trends in patient presentations with suspected cancer. Automated collection of cancer e-referral data at a national level provides real-time information, compared to manual data collection systems within hospitals which were challenged through redeployment of staff to the Covid response.

Key messages
Monitoring of e-referral rates provided a useful and timely proxy measure of health-seeking behaviour during the Covid pandemic. The significant drop in referrals during the first wave of the pandemic was not repeated, suggesting an improved understanding among the public of the need to investigate symptoms of possible cancer.
The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato
Authors: Selga Catja , Reslow Fredrik , Pérez-Rodríguez Paulino , Ortiz Rodomiro 
Published: October 2021

Abstract
Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T1) which had not undergone any selection, or individuals selected at least once in the field (T2). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T1) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families.
A versatile framework to solve the Helmholtz equation using physics-informed neural networks
Authors: Song Chao , Alkhalifah Tariq , Waheed Umair Bin 
Published: October 2021

SUMMARYSolving the wave equation to obtain wavefield solutions is an essential step in illuminating the subsurface using seismic imaging and waveform inversion methods. Here, we utilize a recently introduced machine-learning based framework called physics-informed neural networks (PINNs) to solve the frequency-domain wave equation, which is also referred to as the Helmholtz equation, for isotropic and anisotropic media. Like functions, PINNs are formed by using a fully connected neural network (NN) to provide the wavefield solution at spatial points in the domain of interest, in which the coordinates of the point form the input to the network. We train such a network by backpropagating the misfit in the wave equation for the output wavefield values and their derivatives for many points in the model space. Generally, a hyperbolic tangent activation is used with PINNs, however, we use an adaptive sinusoidal activation function to optimize the training process. Numerical results show that PINNs with adaptive sinusoidal activation functions are able to generate frequency-domain wavefield solutions that satisfy wave equations. We also show the flexibility and versatility of the proposed method for various media, including anisotropy, and for models with strong irregular topography.
Do laws promoting gender equity and freedom from violence benefit the most vulnerable? A multilevel analysis of women’s and adolescent girls’ experiences in 15 low- and-middle-income countries
Authors: Maxwell Lauren , Khan Zara , Yount Kathryn M 
Published: October 2021

Abstract
In this analysis, we assess whether laws that promote gender equity and freedom from violence are associated with a lower risk of prior-year physical and sexual intimate partner violence (IPV) among adolescent girls and adult women (AGW) and whether these laws protect more and less vulnerable AGW equally. We included all 15 countries that administered the Domestic Violence Module in a Demographic and Health Survey since 2015. The primary exposure was a validated, country-level index of laws on violence against women and girls (LoVI). A multilevel approach was used to model five forms of violence (prior-year partner physical, sexual, physical or sexual violence and prior-year non-partner physical violence or sexual violence) among ever-partnered, non-widowed adolescent girls 13–19 years (n = 6691) and women 20–49 years (n = 119 343). Across countries, partner physical violence ranged from 0% to 33% and sexual violence from 0% to 23%. Laws on marital rape, child marriage and sexual harassment were negatively associated with prior-year physical and sexual IPV for women and girls. Comprehensive domestic violence legislation was unrelated to girls’ experiences of prior-year physical or prior-year sexual IPV. No interaction was observed between LoVI component laws and a score meant to capture adolescent vulnerability. Three of the four LoVI component laws had consistent, negative associations with partner violence for girls and women, but negative associations were stronger for women than girls. Thus, while laws promoting gender equity and freedom from violence are generally protective, they may be more so for women than adolescent girls. Future research should explore the impact of gender equitable laws on women’s and adolescent girls’ experiences of violence, and countries may consider more comprehensive legal protections against violence for adolescent girls.
Combined supplementation of sodium humate and glutamine reduced diarrhea incidence of weaned calves by intestinal microbiota and metabolites changes
Authors: Wang Dong , Du Yuanyi , Huang Siqi , You Zhendong , Zheng Duo , Liu Yun 
Published: October 2021

Abstract
This study was conducted to investigate the effects of combined supplementation of sodium humate (HNa) and glutamine (Gln) on growth performance, diarrhea incidence, serum parameters, intestinal microbiome, and metabolites of weaned calves. In Exp. 1, 40 calves were randomly assigned to four treatments: 1) NC (negative control, basal diet), 2) 1% H+1% G (basal diet extra orally gavaged with 1 g of HNa and 1 g of Gln daily), 3) 3% H+1% G (basal diet extra orally gavaged with 3 g of HNa and 1 g of Gln daily), and 4) 5% H+1% G (basal diet extra orally gavaged with 5 g of HNa and 1 g of Gln daily). The HNa and Gln were together mixed with 100 mL of milk replacer (51 to 58 d of age) or water (59 to 72 d of age) and orally administrated to each calf from a bottle before morning feeding. In a 21-d trial, calves on the 5% HNa+1% Gln group had higher (P &lt; 0.05) average daily gain (ADG) and lower (P &lt; 0.05) diarrhea incidence than those in the control group. In Exp. 2, 20 calves were randomly assigned to two treatments fed with a basal diet and a basal diet supplemented with 100 mL of 5% HNa+1% Gln. In a 21-d trial, calves supplemented with HNa and Gln had higher (P &lt; 0.05) ADG, IgG concentration and glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) activities in the serum, but lower (P &lt; 0.05) diarrhea incidence, as well as serum diamine oxidase (DAO), D-isomer of lactic acid (D-lac), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA) concentrations compared with control group. Results of intestinal microbiota indicated that supplementation with HNa and Gln significantly increased (P &lt; 0.05) the abundance of intestinal beneficial microbiota. Moreover, supplementation with HNa and Gln altered 18 metabolites and enriched 6 Kyoto Encyclopedia of Genes and Genomes pathways in weaned calves. In conclusion, combined supplementation with HNa and Gln could decrease diarrhea incidence of weaned calves via altering intestinal microbial ecology and metabolism profile.
Phlebotomus neglectus (Diptera: Psychodidae): New Insights on Its Presence in Iran Based on Three Independent Genetic Loci
Authors: Badakhshan M , Moin-Vaziri V , Sadraei J 
Published: October 2021

Abstract
The idea of the existence of Phlebotomus (Larroussius) neglectus (Diptera: Psychodidae) Tonnoir, 1921 in Iran and the skepticism about the existence of Phlebotomus major s.str. Annandale, 1910 had been grown recently in the country. This study reports a combined analysis of mitochondrial and ribosomal DNA target regions of P. major s.l.Annandale, 1910, specimens collected from different parts of Iran. Two different morphotypes were found among the collected samples based on the shape of the aedeagus, ventrally located hairs of the coxite, and parameral sheets. One morphotype seemed similar to P. neglectus Tonnoir 1921 or P. major krimensis Perfiliv1966 (called here MI.N.K.); the other one was similar to P. neglectus and to some extent to P. notus Artemiev & Neronov 1984 (here called MII.N.NO). Cytochrome B, elongation factor 1-alpha, and internal transcribed spacer II loci were amplified, sequenced, and characterized. High sequence homology (98–100%) was observed between P. neglectus and these morphotypes, and phylogenetic analysis was also concordant. Phlebotomus neglectus sequences available in GenBank are located as the sister group of sequences here, particularly near to morphotype MII.N.NO. Moreover, ITS2 locus provides the maximum resolution for differentiation of two morphotypes. Based on achieving results, although a strong support for the presence of P. neglectus was provided, but it is too early to say that P. major s.str. does/does not exist in Iran. This question could be resolved by studying more samples and, most importantly, by comparing the topotypes of P. neglectus and P. major s. str. if possible in the future.
The formation of massive stellar clusters in converging galactic flows with photoionization
Authors: Dobbs C L , Bending T J R , Pettitt A R , Bate M R 
Published: October 2021

ABSTRACT
We have performed simulations of cluster formation along two regions of a spiral arm taken from a global Milky Way simulation, including photoionizing feedback. One region is characterized by strongly converging flows, the other represents a more typical spiral arm region. We find that more massive clusters are able to form on shorter time-scales for the region with strongly converging flows. Mergers between clusters are frequent in the case of the strongly converging flows and enable the formation of massive clusters. We compare equivalent clusters formed in simulations with and without ionization. Photoionization does not prevent massive cluster formation, but can be seen to limit the masses of the clusters. On average, the mass is reduced by around 20 per cent, but we see a large spread from ionization having minimal difference to leading to a 50 per cent reduction in mass. Photoionization is also able to clear out the gas in the vicinity of the clusters on Myr time-scales, which can produce clusters with larger radii that are surrounded by more massive stellar haloes. We find that the ionizing feedback has more impact in our second region that is less dense and has less strongly converging flows.
The impact of precession on the observed population of ULXs
Authors: Khan Norman , Middleton Matthew J , Wiktorowicz Grzegorz , Dauser Thomas , Roberts Timothy P , Wilms Joern 
Published: October 2021

Abstract
The discovery of neutron stars powering several ultraluminous X-ray sources (ULXs) raises important questions about the nature of the underlying population. In this paper we build on previous work studying simulated populations by incorporating a model where the emission originates from a precessing, geometrically beamed wind-cone, created by a super-critical inflow. We obtain estimates – independent of the prescription for the precession period of the wind – for the relative number of ULXs that are potentially visible (persistent or transient) for a range of underlying factors such as the relative abundance of black holes or neutron stars within the population, maximum precessional angle, and LMXB duty cycle. We make initial comparisons to existing data using a catalogue compiled from XMM-Newton. Finally, based on estimates for the precession period, we determine how the eROSITA all-sky survey (eRASS) will be able to constrain the underlying demographic.
Orion Bar as a window to the evolution of PAHs
Authors: Murga Maria S , Kirsanova Maria S , Wiebe Dmitry S , Boley Paul A 
Published: October 2021

ABSTRACT
We investigate the mid-infrared (IR) emission in the Orion Bar photodissociation region (PDR), using archival photometric and spectroscopic observations from the United Kingdom Infrared Telescope (UKIRT), Spitzer, Infrared Space Observatory(ISO), and Stratospheric Observatory for Infrared Astronomy (SOFIA) telescopes. Specifically, we consider flux densities of the emission bands at 3.3, 3.4, 3.6, 6.6, 7.7, and 11.2 $\mu$m in several locations and a spectrum from 3 to 45 $\mu$m in one location. We study the behaviour of band flux ratios, which are sensitive to external conditions, as revealed by their variations with the distance from an ionizing source. Assuming that the mid-IR emission arises mostly from polycyclic aromatic hydrocarbons (PAHs), and that a weak emission feature at 3.4 $\mu$m is related to PAHs with extra hydrogen atoms (H-PAHs), we trace variations of the ratios using a model for PAH evolution. Namely, we estimate how populations of PAHs of different sizes, hydrogenation and ionization states change across the Orion Bar over a time interval approximately equal to its lifetime. The obtained ensembles of PAHs are further used to calculate the corresponding synthetic spectra and band flux densities. The model satisfactorily describes the main features of the ratios I3.6/I11.2, I7.7/I11.2, I7.7/I3.6, and I3.3/I3.4. We conclude that the best coincidence between modelling and observations is achieved if C loss of PAHs is limited by the number of carbon atoms NC = 60, and the band at 3.4 $\mu$m may indeed be attributed to H-PAHs. We confirm that large cations dominate at the surface of the PDR but small neutral PAHs and anions are abundant deeper in the molecular cloud.